Author Report for: Lindquist ENo contact information in database for Lindquist E
Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E and Gladden JM <3 more author(s)> Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM (- 3) Ref: Applied Microbiology & Biotechnology, 101:2603, 2017 : PubMed ESTHER: Wu_2017_Appl.Microbiol.Biotechnol_101_2603 PubMedSearch: Wu 2017 Appl.Microbiol.Biotechnol 101 2603 PubMedID: 28078400 Gene_locus related to this paper: 9pezi-a0a1y2u1s8, 9pezi-a0a1y2x077, 9pezi-a0a1y2vv92, 9pezi-a0a1y2txs8, 9pezi-a0a1y2wzb7, 9pezi-a0a1y2ufj7, 9pezi-a0a1y2vvc9, 9pezi-a0a1y2w3w4 Abstract Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and beta-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms. Title: Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M and Grigoriev IV <107 more author(s)> de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram O, Benocci T, Braus-Stromeyer SA, Caldana C, Canovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damasio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hilden KS, Hope R, Hossain A, Karabika E, Karaffa L, Karanyi Z, Krasevec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, Maccabe A, Makela MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnar AP, Mule G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramon A, Rauscher S, Record E, Riano-Pachon DM, Robert V, Rohrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sandor E, Sanguinetti M, Schutze T, Sepcic K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pocsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV (- 107) Ref: Genome Biol, 18:28, 2017 : PubMed ESTHER: de Vries_2017_Genome.Biol_18_28 PubMedSearch: de Vries 2017 Genome.Biol 18 28 PubMedID: 28196534 Gene_locus related to this paper: asptu-a0a1l9nhd0, aspve-a0a1l9pxx8, aspve-a0a1l9q4m3, aspwe-a0a1l9s133, 9euro-a0a1l9t3v9, aspwe-a0a1l9rcx6, aspna-g3y5a6, aspgl-a0a1l9v4d3, 9euro-a0a1l9sa36, aspsb-a0a319eji6, aspve-a0a1l9px96, 9euro-a0a1l9tay1, aspgl-a0a1l9vbc0, aspc5-a0a1r3rh65, 9euro-a0a2v5i956, aspwe-a0a1l9rpp6, aspna-g3xpw9, aspve-a0a1l9plv1, 9euro-a0a1l9tk47, aspve-a0a1l9pde9, aspve-a0a1l9pz72, aspwe-a0a1l9rde6, 9euro-a0a1l9tdb5, aspkw-g7xq95, aspbc-a0a1l9u6h4, aspbc-a0a1l9u2l4, asptc-a0a1l9mx83, aspgl-a0a1l9ve90, aspve-a0a1l9pvz9, 9euro-a0a1l9tdh3, aspc5-a0a1r3rmn9, aspwe-a0a1l9rlq2, asptc-a0a1l9nby7, aspng-a0a100i8t9, aspc5-a0a1r3rem6, aspbc-a0a1l9uy89, aspa1-anee, aspa1-aneh, aspa1-acrc, aspbc-alba, aspa1-acui Abstract BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi. Title: Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1 Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL Ref: Front Microbiol, 6:978, 2015 : PubMed ESTHER: Firrincieli_2015_Front.Microbiol_6_978 PubMedSearch: Firrincieli 2015 Front.Microbiol 6 978 PubMedID: 26441909 Gene_locus related to this paper: rhogw-a0a0p9evi9 Title: Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Duenas FJ, Held B and Cullen D <31 more author(s)> Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Duenas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutierrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kues U, Berka RM, Martinez AT, Covert SF, Blanchette RA, Cullen D (- 31) Ref: PLoS Genet, 10:e1004759, 2014 : PubMed ESTHER: Hori_2014_PLoS.Genet_10_E1004759 PubMedSearch: Hori 2014 PLoS.Genet 10 E1004759 PubMedID: 25474575 Gene_locus related to this paper: phlgi-a0a0c3nds0, phlgi-a0a0c3niq6, phlgi-a0a0c3pc91, phlgi-a0a0c3pv58, phlgi-a0a0c3rra0, phlgi-a0a0c3rvc4, phlgi-a0a0c3rvu0, phlgi-a0a0c3s394, phlgi-a0a0c3s606, phlgi-a0a0c3s673, phlgi-a0a0c3s8d3, phlgi-a0a0c3sce4, phlgi-a0a0c3sdt8 Abstract Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes. Title: The genome of Eucalyptus grandis Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H and Schmutz J <70 more author(s)> Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Kulheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J (- 70) Ref: Nature, 510:356, 2014 : PubMed ESTHER: Myburg_2014_Nature_510_356 PubMedSearch: Myburg 2014 Nature 510 356 PubMedID: 24919147 Gene_locus related to this paper: eucgr-a0a059d0n8, eucgr-a0a059cm68, eucgr-a0a059d783, eucgr-a0a059af93, eucgr-a0a059awi0, eucgr-a0a059awt4, eucgr-a0a059ar83, eucgr-a0a059ayw5, eucgr-a0a059az75, eucgr-a0a059azj1, eucgr-a0a059azq5, eucgr-a0a059bkm2, eucgr-a0a059bl38, eucgr-a0a059a7m2, eucgr-a0a059a6p6, eucgr-a0a059a6p1, eucgr-a0a059a5e9 Abstract Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology. Title: Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J and Turgeon BG <20 more author(s)> Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG (- 20) Ref: PLoS Genet, 9:e1003233, 2013 : PubMed ESTHER: Condon_2013_PLoS.Genet_9_E1003233 PubMedSearch: Condon 2013 PLoS.Genet 9 E1003233 PubMedID: 23357949 Gene_locus related to this paper: cocsn-m2rnc6, coch5-m2tnl8, coch4-n4xap8, sett2-r0j560, cocsn-m2thl9, coch5-m2v1s2, coch4-n4xzy1, cocsn-m2sqr3, cocsn-m2rnk8, coch4-n4xdv7, coch5-m2uds0, coch5-m2um94, sett2-r0i8c5, coch4-n4wlc8, coch4-n4x9p3, cocsn-m2rh47, cocsn-m2qz08, sett2-r0jqq6, sett2-r0imb6, coch4-n4x7u3, cocsn-m2rv02, cocsn-m2sy95, coch5-m2ubd5, cocsn-m2t3d2, sett2-r0kl84, sett2-r0jts7, coch4-n4x2h3, sett2-r0jxt9, coch4-n4x7r9, cocsn-m2sh75, cocsn-m2t5z2, coch5-m2ucf6, sett2-r0k664, cocsn-m2t3q1, sett2-r0k4b4, cocsn-m2t4i1, coch5-m2th93, cocsn-m2svm8, cocsn-m2s6q4, cocsn-m2s5h5, coch4-n4xf94, sett2-r0kdl8, cocsn-m2qvi9, sett2-r0kfg6, cocsn-m2szq4, sett2-r0j437, coch4-n4x7j4, coch5-m2twk3, coch5-m2usf2, sett2-r0kjt7, sett2-r0k7y2, cocsn-m2th03, sett2-r0iy92, sett2-r0kbr9, sett2-r0k997, coch5-m2sik6, sett2-r0jzj5, cocsn-m2r0j6, coch4-n4x6a4, cocsn-m2s7a5, cocsn-m2sv79, sett2-r0knx4, sett2-r0ksh8, sett2-r0ip86, cocmi-w6yyy3, cocsn-m2sqe4, coch4-n4xzc8, cocvi-w7eyp1, cocmi-w6zf65, cocvi-w7er28, cocca-w6yw25, cocvi-w7e2g6, cocmi-w6z7k5, cocca-w6ys73, cocca-w6ydq2, cocca-w6y7i5, cocmi-w6yyr0, cocca-w6yh47, cocmi-w6zju4, cocca-w6ynq5, cocmi-w6zm44, cocca-w6xx85, cocmi-w6z011, cocca-w6yre4, cocmi-w6z9l3, cocca-w6yfp7, cocmi-w6zlc2, cocca-w6yar2, cocmi-w6yjr7, cocca-w6yhs1, cocca-w6xux8, cocmi-w6z9s8, cocca-w6yq27, cocmi-w6zqk9, cocca-w6xq19, cocca-w6y1r6, cocca-w6ygj2, cocmi-w6zgn4, cocca-w6ybh2, cocmi-w6z710, cocca-w6yk86, cocmi-w6zjz2, cocmi-w6z7f2, cocca-w6xn57, cocca-w6ybq4, cocmi-w6yxn5, cocmi-w6zf08, cocsn-m2rtg8, cocmi-w6zuj7, cocca-w6xtb2, cocca-w6yk97, coch5-m2t2x3, cocmi-w6z646, cocsn-m2sze4, sett2-r0kjg6, cocmi-w6yrn5, sett2-r0k5q0, cocvi-w7ezb7, sett2-r0jtm1, cocmi-w6ywa1, cocsn-m2t3e8, coch5-m2ulw5, coch5-m2urw9, sett2-r0knn5, cocmi-w6ysb2, cocvi-w7eag7, cocca-w6y1v2, sett2-r0i9k2, coch5-m2uul8, cocsn-m2sl21 Abstract The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25x higher than those between inbred lines and 50x lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. Title: Reference genome sequence of the model plant Setaria Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN and Devos KM <24 more author(s)> Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (- 24) Ref: Nat Biotechnol, 30:555, 2012 : PubMed ESTHER: Bennetzen_2012_Nat.Biotechnol_30_555 PubMedSearch: Bennetzen 2012 Nat.Biotechnol 30 555 PubMedID: 22580951 Gene_locus related to this paper: setit-k3xwe0, setit-k3xfs7, setit-k3yh36, setit-k3zes3, setit-k3zlj8, setvi-a0a4u6wd58, setit-a0a368qif6, setit-a0a368sru6, setit-a0a368q9x4, setit-k3zri0 Abstract We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The approximately 400-Mb assembly covers approximately 80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum). Title: The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E and Van Etten JL <11 more author(s)> Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Proschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL (- 11) Ref: Genome Biol, 13:R39, 2012 : PubMed ESTHER: Blanc_2012_Genome.Biol_13_R39 PubMedSearch: Blanc 2012 Genome.Biol 13 R39 PubMedID: 22630137 Gene_locus related to this paper: 9chlo-i0z4k0, 9chlo-i0ylt0, cocsc-i0ytb9, cocsc-i0yin5 Abstract BACKGROUND: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Title: Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH and Archibald JM <63 more author(s)> Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Obornik M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Hoppner MP, Ishida K, Kim E, Koreny L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM (- 63) Ref: Nature, 492:59, 2012 : PubMed ESTHER: Curtis_2012_Nature_492_59 PubMedSearch: Curtis 2012 Nature 492 59 PubMedID: 23201678 Gene_locus related to this paper: guith-l1i9i5, guith-l1k167, guitc-l1jmn9 Abstract Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. Title: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW and Hibbett DS <61 more author(s)> Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Gorecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kues U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Duenas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS (- 61) Ref: Science, 336:1715, 2012 : PubMed ESTHER: Floudas_2012_Science_336_1715 PubMedSearch: Floudas 2012 Science 336 1715 PubMedID: 22745431 Gene_locus related to this paper: aurde-j0d098, aurde-j0dc31, glota-s7rlc1, fompi-s8f7s4, dacsp-m5fpg2, dicsq-r7sm16, dacsp-m5g7q5, dacsp-m5fr12, glota-s7q5w3, fompi-s8f826.1, fompi-s8f826.2, dicsq-r7sy09, glota-s7rt87, dicsq-r7t032, glota-s7rym7, fompi-s8fiv2, dacsp-m5gda3.2, dicsq-r7swi6, dacsp-m5frf2, fompi-s8ebb6, dicsq-r7sln3, dicsq-r7sya6, dacsp-m5g7g1, dicsq-r7syx7, dicsq-r7sx57, dacsp-m5fps7, glota-s7pwi7, dicsq-r7swj6, fompi-s8ejq6, dicsq-r7spc3, glota-s7q258, dacsp-m5ft65, glota-s7q3m7, fompi-s8dkc7, glota-s7q1z1, fompi-s8eqi2, glota-s7q1z8, fompi-s8du50, dacsp-m5gg33, dacsp-m5g3a7, fompi-s8ecd7, fompi-s8dps1, dacsp-m5fwr0, dicsq-r7sub7, glota-s7q8k9, fompi-s8ffc3, dacsp-m5g2f9, fompi-s8ecc2, dacsp-m5g868, fompi-s8f890, dicsq-r7t1a8, fompi-s8ebx4, fompi-s8eb97, glota-s7q222, glota-s7puf0, fompi-s8f6v9, dacsp-m5g0z2, dacsp-m5gdh9, fompi-s8fb37, dacsp-m5fy91, glota-s7q5v6, fompi-s8fl44, dicsq-r7stv9, dicsq-r7szk3, fompi-s8epq9, glota-s7rh56, dacsp-m5gbt1, punst-r7s3x9, punst-r7s0t5, glota-s7q312, glota-s7rhh6, dicsq-r7t117, dicsq-r7slz3 Abstract Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period. Title: Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen Olson A, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canback B, Coutinho PM, Cullen D and Stenlid J <43 more author(s)> Olson A, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canback B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LT, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Hogberg N, James TY, Karlsson M, Kohler A, Kues U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lunden K, Morin E, Murat C, Park J, Raffaello T, Rouze P, Salamov A, Schmutz J, Solheim H, Stahlberg J, Velez H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J (- 43) Ref: New Phytol, 194:1001, 2012 : PubMed ESTHER: Olson_2012_New.Phytol_194_1001 PubMedSearch: Olson 2012 New.Phytol 194 1001 PubMedID: 22463738 Gene_locus related to this paper: 9homo-w4jrb9, 9homo-w4jsg4, 9homo-w4kds7, 9homo-w4jwl9, 9homo-w4kjy2, 9homo-w4jw43, 9homo-w4ka20, 9homo-w4k8t3, 9homo-w4jz43, 9homo-w4k8q2, 9homo-w4k910, 9homo-w4k6f5, 9homo-w4k6j3, 9homo-w4k8n2, 9homo-w4jrf3, 9homo-w4ke07, 9homo-w4k3i8, 9homo-w4jqh1, 9agam-w4k203, 9agam-w4jpy3, 9agam-w4jn81, 9agam-w4jmz2 Abstract Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes. Title: The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S and Aime MC <11 more author(s)> Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC (- 11) Ref: Fungal Genet Biol, 49:217, 2012 : PubMed ESTHER: Padamsee_2012_Fungal.Genet.Biol_49_217 PubMedSearch: Padamsee 2012 Fungal.Genet.Biol 49 217 PubMedID: 22326418 Gene_locus related to this paper: walsc-i4y6w1, walmc-i4y5m3 Abstract Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic. Title: Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, vanKuyk PA and Master ER <14 more author(s)> Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, vanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER (- 14) Ref: BMC Genomics, 13:444, 2012 : PubMed ESTHER: Suzuki_2012_BMC.Genomics_13_444 PubMedSearch: Suzuki 2012 BMC.Genomics 13 444 PubMedID: 22937793 Gene_locus related to this paper: phacs-k5whx2, phacs-k5v2s8, phacs-k5v5r2, phacs-k5vyk5, phacs-k5vzf8, phacs-k5wbu9, phacs-k5wc10, phacs-k5wpw0, phacs-k5wzn6, phacs-k5x1t8, phacs-k5x5g6, phacs-k5x5p4 Abstract BACKGROUND: Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome. Title: The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P and Bradshaw RE <29 more author(s)> de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE (- 29) Ref: PLoS Genet, 8:e1003088, 2012 : PubMed ESTHER: de Wit_2012_PLoS.Genet_8_E1003088 PubMedSearch: de Wit 2012 PLoS.Genet 8 E1003088 PubMedID: 23209441 Gene_locus related to this paper: mycpj-q30dw8, mycp1-n1pnd6, mycp1-n1per0, mycp1-n1pg49, mycp1-n1pwj1, mycp1-n1pcl8, mycp1-m2y2b1, mycp1-n1pwu7, mycp1-n1ppa8, mycp1-m2yk59, mycp1-n1pps5, mycp1-n1pw13, mycp1-n1pe19, mycp1-m2xhl1, mycp1-n1pnh6, mycp1-n1psn5, mycp1-n1puh9, mycp1-n1phf7, mycp1-m2y2h4, mycp1-n1q523, dotsn-n1q1b1, dotsn-n1q415, dotsn-est1 Abstract We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an alpha-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation. Title: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R and Baker SE <37 more author(s)> Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE (- 37) Ref: Genome Res, 21:885, 2011 : PubMed ESTHER: Andersen_2011_Genome.Res_21_885 PubMedSearch: Andersen 2011 Genome.Res 21 885 PubMedID: 21543515 Gene_locus related to this paper: aspna-g3y4g9, aspna-g3yal2, aspna-g3ycq2, aspnc-a2qbh3, aspnc-a2qe77, aspnc-a2qf54, aspnc-a2qfe9, aspnc-a2qg33, aspnc-a2qh76, aspnc-a2qhe2, aspnc-a2qi32, aspnc-a2ql89, aspnc-a2ql90, aspnc-a2qla0, aspnc-a2qmk5, aspnc-a2qn56, aspnc-a2qs22, aspnc-a2qti9, aspnc-a2qtz0, aspnc-a2quc1, aspnc-a2qx92, aspnc-a2qyf0, aspnc-a2qys7, aspnc-a2qz72, aspnc-a2qzn6, aspnc-a2qzr0, aspnc-a2qzx0, aspnc-a2qzx4, aspnc-a2r0p4, aspnc-a2r1r5, aspnc-a2r2i5, aspnc-a2r5r4, aspnc-a2r6h5, aspnc-a2r8r3, aspnc-a2r8z3, aspnc-a2r273, aspnc-a2r496, aspnc-a2r502, aspnc-a5abe5, aspnc-a5abe8, aspnc-a5abh9, aspnc-a5abk1, aspnc-axe1, aspnc-cuti1, aspnc-cuti2, aspng-a2qs46, aspng-a2qv27, aspni-EstA, aspkw-g7y0v7, aspnc-a2qt47, aspnc-a2qt66, aspna-g3xpq9, aspnc-a2qqa1, aspna-g3xsl3, aspna-g3y5a6, aspna-g3xpw9, aspaw-a0a401kpx5, aspnc-a2qw57, aspaw-a0a401kcz4, aspna-alba, aspna-azac Abstract The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi. Title: The Selaginella genome identifies genetic changes associated with the evolution of vascular plants Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T and Grigoriev IV <93 more author(s)> Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riano-Pachon DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sorensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loque D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV (- 93) Ref: Science, 332:960, 2011 : PubMed ESTHER: Banks_2011_Science_332_960 PubMedSearch: Banks 2011 Science 332 960 PubMedID: 21551031 Gene_locus related to this paper: selml-d8qua5, selml-d8qva1, selml-d8qyh7, selml-d8qza0, selml-d8r5d4, selml-d8r6d4, selml-d8r504, selml-d8r506, selml-d8rbi1, selml-d8rbs1, selml-d8rck8, selml-d8rf38, selml-d8rkl6, selml-d8rpr1, selml-d8rpy0, selml-d8ru47, selml-d8ry54, selml-d8rzp6, selml-d8rzy7, selml-d8s0c9, selml-d8s0u3, selml-d8s2t1, selml-d8s3z8, selml-d8s401, selml-d8sba6, selml-d8sch9, selml-d8spq2, selml-d8sq37, selml-d8ssx7, selml-d8swp2, selml-d8t7a3, selml-d8t8v4, selml-d8taz4, selml-d8tdq6, selml-d8rai8, selml-d8qt54, selml-d8r2d8, selml-d8rmd3, selml-d8rra9, selml-d8slg4, selml-d8swp0, selml-d8s7i0, selml-d8qz37, selml-d8sz00, selml-d8s776, selml-d8qw15, selml-d8ska7, selml-d8t0c4, selml-d8r194, selml-d8s5m8, selml-d8s7r2, selml-d8ta80 Abstract Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes. Title: Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C and Tsang A <29 more author(s)> Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LD, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A (- 29) Ref: Nat Biotechnol, 29:922, 2011 : PubMed ESTHER: Berka_2011_Nat.Biotechnol_29_922 PubMedSearch: Berka 2011 Nat.Biotechnol 29 922 PubMedID: 21964414 Gene_locus related to this paper: thiha-cip2, thite-g2r8b5, thite-g2rcm8, thite-g2r192, thiha-g2qdy2, thiha-g2qh51, thite-g2rae6, thite-g2r5h0, thiha-g2qj94, thiha-g2qnb2, thite-g2rg14, myctt-g2q973, thite-g2qtu3, myctt-g2qpr0, thite-g2rhm0, 9pezi-a0a3s4b069, myctt-g2qmb4, thett-g2qur2 Abstract Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics. Title: The ecoresponsive genome of Daphnia pulex Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ and Boore JL <59 more author(s)> Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (- 59) Ref: Science, 331:555, 2011 : PubMed ESTHER: Colbourne_2011_Science_331_555 PubMedSearch: Colbourne 2011 Science 331 555 PubMedID: 21292972 Gene_locus related to this paper: dappu-e9fut0, dappu-e9fut9, dappu-e9fvw6, dappu-e9fxt4, dappu-e9fyr6, dappu-e9fzg6, dappu-e9g1e2, dappu-e9g1e6, dappu-e9g1e7, dappu-e9g1e8, dappu-e9g1v3, dappu-e9g1z2, dappu-e9gb99, dappu-e9gba0, dappu-e9gcb4, dappu-e9gdv5, dappu-e9gdv7, dappu-e9gi24, dappu-e9gj77, dappu-e9gja7, dappu-e9gmp5, dappu-e9gmr0, dappu-e9gn32, dappu-e9gp76, dappu-e9gp82, dappu-e9gp98, dappu-e9gp99, dappu-e9gvl2, dappu-e9gzn7, dappu-e9h1p4, dappu-e9h2c8, dappu-e9h2c9, dappu-e9h6x9, dappu-e9h6y4, dappu-e9h7w9, dappu-e9h8r4, dappu-e9hd06, dappu-e9hh56, dappu-e9hh57, dappu-e9hh59, dappu-e9hmp4, dappu-e9hp64, dappu-e9hp65, dappu-e9hpy8, dappu-e9htg8, dapul-ACHE1, dapul-ACHE2, dappu-e9gnj1, dappu-e9gu36, dappu-e9hpc4, dappu-e9gb07, dappu-e9glp6, dappu-e9glp5, dappu-e9gjv2, dappu-e9h0c7, dappu-e9g4g2, dappu-e9gw69, dappu-e9h3h9, dappu-e9g545, dappu-e9gw71, dappu-e9gw68, dappu-e9h3e7, dappu-e9gfg9, dappu-e9fvy6, dappu-e9hgt2 Abstract We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges. Title: The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K and Watkinson SC <38 more author(s)> Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kues U, Hibbett DS, Hoffmeister D, Hogberg N, Martin F, Grigoriev IV, Watkinson SC (- 38) Ref: Science, 333:762, 2011 : PubMed ESTHER: Eastwood_2011_Science_333_762 PubMedSearch: Eastwood 2011 Science 333 762 PubMedID: 21764756 Gene_locus related to this paper: serl3-f8prj2, serl3-f8qcc4, serl9-f8ngp6, serl9-f8nhd7, serl9-f8nhq9, serl9-f8nq77, serl9-f8nr67, serl9-f8nrt5, serl9-f8nvy7.1, serl9-f8nvy7.2, serl9-f8nvy8, serl9-f8nxt0.1, serl9-f8nxt0.2, serl9-f8nzr3, serl9-f8p0f0, serl9-f8p6v0, serl9-f8p015, serl9-f8p018, serl9-f8p386, serl9-f8paz8, serl9-f8pbv1, serl9-f8pby1, serl9-f8pc25, serl9-f8pc39, serl9-f8nia7, serl3-f8pju2, serl9-f8peh1, serl9-nps3 Abstract Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota. Title: Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J and Kema GH <47 more author(s)> Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canche B, Churchill AC, Conde-Ferraez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH (- 47) Ref: PLoS Genet, 7:e1002070, 2011 : PubMed ESTHER: Goodwin_2011_PLoS.Genet_7_E1002070 PubMedSearch: Goodwin 2011 PLoS.Genet 7 E1002070 PubMedID: 21695235 Gene_locus related to this paper: zymti-f9wzw8, zymti-f9x2y6, zymti-f9x423, zymti-f9x813, zymti-f9xa54, zymti-f9xb42, zymti-f9xbu5, zymti-f9xcr9, zymti-f9xdr7, zymti-f9xer1, zymti-f9xez8, zymti-f9xfz9, zymti-f9xh29, zymti-f9xhe7, zymti-f9xhr4, zymti-f9xk09, zymti-f9xns5, zymti-f9xiu1, zymti-f9xng3, zymti-f9x4f2, zymti-f9x4s7, zymti-f9xdm8, zymti-f9wwy9, zymti-f9xkf2, zymti-f9xlt3, zymti-f9x0i3, zymti-f9wwa6, zymti-f9wyk7, zymti-f9x3z1, zymti-f9xf16, zymtr-a0a1x7rhi5, zymti-f9xfj3, zymti-pks1 Abstract The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors. Title: The genome of Tetranychus urticae reveals herbivorous pest adaptations Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, Osborne EJ, Dermauw W, Ngoc PC and Van de Peer Y <45 more author(s)> Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernandez-Crespo P, Diaz I, Martinez M, Navajas M, Sucena E, Magalhaes S, Nagy L, Pace RM, Djuranovic S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y (- 45) Ref: Nature, 479:487, 2011 : PubMed ESTHER: Grbic_2011_Nature_479_487 PubMedSearch: Grbic 2011 Nature 479 487 PubMedID: 22113690 Gene_locus related to this paper: tetur-ACHE Abstract The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies. Title: Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA and Grigoriev IV <54 more author(s)> Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Dohren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (- 54) Ref: Genome Biol, 12:R40, 2011 : PubMed ESTHER: Kubicek_2011_Genome.Biol_12_R40 PubMedSearch: Kubicek 2011 Genome.Biol 12 R40 PubMedID: 21501500 Gene_locus related to this paper: hypai-g9nem6, hypai-g9ng36, hypai-g9ngu2, hypai-g9nks5, hypai-g9nks6, hypai-g9nqe5, hypai-g9nqk5, hypai-g9nrx6, hypai-g9nsx1, hypai-g9ntn3, hypai-g9nzc9, hypai-g9nzd7, hypai-g9p1t1, hypai-g9p1v2, hypai-g9p2n8, hypai-g9p4z2, hypai-g9p878, hypai-g9pa17, hypai-g9pbz9, hypvg-g9mem8, hypvg-g9mg52, hypvg-g9mga2, hypvg-g9mhi3, hypvg-g9mjc7, hypvg-g9mk44, hypvg-g9mms1, hypvg-g9mnf0, hypvg-g9mng3, hypvg-g9mpt0, hypvg-g9mrp9, hypvg-g9ms16, hypvg-g9ms32, hypvg-g9msv5, hypvg-g9muh6, hypvg-g9muk0, hypvg-g9mwe2, hypvg-g9my79, hypvg-g9n0p7, hypvg-g9n2g3, hypvg-g9n2g4, hypvg-g9n4k5, hypvg-g9n9n0, hypvg-g9n561, hypvg-g9n988, hypvg-g9nb12, hypvg-g9nb54, hypvg-g9nbh8, hypai-g9npz7, hypai-g9njw6, hypvg-g9mx08, hypvg-g9mlt2, hypai-g9p4j3, hypvg-g9nbd3, hypai-g9nxf6, hypvg-g9n3y9, hypvg-g9mgs4, hypai-g9p6m2, hypvg-g9my62, hypvg-g9nbv2, hypvg-g9my22, hypai-g9p2e2, hypai-g9p596, hypai-g9nf87, hypvg-g9me87, hypvg-g9ndn9, hypai-g9niy5, hypai-g9ntx6, hypvg-g9n3e7, hypai-g9nu29, hypvg-g9n2z0, hypvg-g9ndf4, 9hypo-a0a2p4zt82, hypvg-g9n0g0, hypvg-g9muj2, hypvg-g9mud0 Abstract BACKGROUND: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Title: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E and Grigoriev IV <31 more author(s)> Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV (- 31) Ref: Genome Biol, 12:R20, 2011 : PubMed ESTHER: Sucgang_2011_Genome.Biol_12_R20.1 PubMedSearch: Sucgang 2011 Genome.Biol 12 R20.1 PubMedID: 21356102 Gene_locus related to this paper: dicpu-f0z7q0, dicpu-f0z822, dicpu-f0zfi0, dicpu-f0zjs1, dicpu-f0zks4, dicpu-f0zmm3, dicpu-f0zmm8, dicpu-f0zmm9, dicpu-f0zni7, dicpu-f0znl3, dicpu-f0zq90, dicpu-f0zvn5, dicpu-f0zxa4, dicpu-f0zyf9, dicpu-f1a3n5, dicpu-f1a5b4, dicpu-f1a269, dicpu-f1a615, dicpu-f0ztw9, dicpu-f0zri3 Abstract BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Title: The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J and Van Etten JL <7 more author(s)> Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL (- 7) Ref: Plant Cell, 22:2943, 2010 : PubMed ESTHER: Blanc_2010_Plant.Cell_22_2943 PubMedSearch: Blanc 2010 Plant.Cell 22 2943 PubMedID: 20852019 Gene_locus related to this paper: chlva-e1z3j3, chlva-e1z3n9, chlva-e1z620, chlva-e1z882, chlva-e1zd56, chlva-e1zdd9, chlva-e1zde0, chlva-e1ze02, chlva-e1zeh7, chlva-e1zhu4, chlva-e1zie3, chlva-e1zii9, chlva-e1zmj6, chlva-e1ztt0, chlva-e1z5k1, chlva-e1ztf4 Abstract Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes. Title: The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J and Dawson SC <14 more author(s)> Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC (- 14) Ref: Cell, 140:631, 2010 : PubMed ESTHER: Fritz-Laylin_2010_Cell_140_631 PubMedSearch: Fritz-Laylin 2010 Cell 140 631 PubMedID: 20211133 Gene_locus related to this paper: naegr-d2ux86, naegr-d2uyl7, naegr-d2uyn1, naegr-d2uzk6, naegr-d2uzp4, naegr-d2v1m1, naegr-d2v3p5, naegr-d2v5p1, naegr-d2v6f6, naegr-d2v6y9, naegr-d2v8x8, naegr-d2v186, naegr-d2v339, naegr-d2v556, naegr-d2vbq7, naegr-d2vdq6, naegr-d2ve51, naegr-d2vga2, naegr-d2vgm9, naegr-d2vh14, naegr-d2vha2, naegr-d2vj80, naegr-d2vjj7, naegr-d2vl41, naegr-d2vmj5, naegr-d2vms7, naegr-d2vqi5, naegr-d2vr44, naegr-d2vrq2, naegr-d2vs01, naegr-d2vs58, naegr-d2vts5, naegr-d2vu69, naegr-d2vvg8, naegr-d2vxp2, naegr-d2vyl1, naegr-d2vzy5, naegr-d2w0l5, naegr-d2w0v9, naegr-d2w3g8, naegr-d2w3v7, naegr-d2w3v8, naegr-d2vct1 Abstract Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules. Title: The genome of the Western clawed frog Xenopus tropicalis Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S and Rokhsar DS <38 more author(s)> Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS (- 38) Ref: Science, 328:633, 2010 : PubMed ESTHER: Hellsten_2010_Science_328_633 PubMedSearch: Hellsten 2010 Science 328 633 PubMedID: 20431018 Gene_locus related to this paper: xenla-q6pcj9, xentr-a9umk0, xentr-abhdb, xentr-ACHE, xentr-b0bm77, xentr-b1h0y7, xentr-b2guc4, xentr-b7zt03, xentr-b7ztj4, xentr-BCHE1, xentr-BCHE2, xentr-cxest2, xentr-d2x2k4, xentr-d2x2k6, xentr-f6rff6, xentr-f6v0g3, xentr-f6v2j6, xentr-f6v3z1, xentr-f6y4c8, xentr-f6yve5, xentr-f7a4y9, xentr-f7acc5, xentr-f7e2e2, xentr-LOC394897, xentr-ndrg1, xentr-q0vfb6, xentr-f7cpl7, xentr-f6yj44, xentr-f7ejk4, xentr-f6q8j8, xentr-f6z8f0, xentr-f7d709, xentr-b0bmb8, xentr-f7af63, xentr-a0a1b8y2w9, xentr-f7d4k9, xentr-f6r032, xentr-f6yvq3, xentr-a0a1b8y2z3, xentr-f7afg4, xentr-f6xb15, xentr-f7e1r2, xentr-a4ihf1, xentr-f7eue5, xentr-f6u7u3, xentr-f172a, xentr-f7equ8, xentr-f7dd89, xentr-a9jtx5 Abstract The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage. Title: Genome sequence of the model mushroom Schizophyllum commune Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A and Wosten HA <22 more author(s)> Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kues U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wosten HA (- 22) Ref: Nat Biotechnol, 28:957, 2010 : PubMed ESTHER: Ohm_2010_Nat.Biotechnol_28_957 PubMedSearch: Ohm 2010 Nat.Biotechnol 28 957 PubMedID: 20622885 Gene_locus related to this paper: schcm-d8pqz6, schcm-d8prj2, schcm-d8pug6, schcm-d8pxe8, schcm-d8pxe9, schcm-d8pxz1, schcm-d8q1c7, schcm-d8q2b4, schcm-d8q3j1, schcm-d8q5m5, schcm-d8q7x7.1, schcm-d8q7x7.2, schcm-d8q8y8, schcm-d8q9n6, schcm-d8q697, schcm-d8qip8, schcm-d8q5s5, schcm-d8ppb3, schcm-d8ppb6, schcm-d8pv73, schcm-d8pzm1, schcm-d8q5a7, schcm-d8qif0 Abstract Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals. Title: Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T and Rokhsar DS <18 more author(s)> Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS (- 18) Ref: Science, 329:223, 2010 : PubMed ESTHER: Prochnik_2010_Science_329_223 PubMedSearch: Prochnik 2010 Science 329 223 PubMedID: 20616280 Gene_locus related to this paper: volca-d8tmz1, volca-d8tne9, volca-d8tnn6, volca-d8tns6, volca-d8tr92, volca-d8u2d3, volca-d8u5r0, volca-d8u7s7, volca-d8u7s8, volca-d8u9w4, volca-d8u460, volca-d8uab7, volca-d8uai0, volca-d8uev0, volca-d8uhi9, volca-d8uiw9, volca-d8ujv0, volca-d8uf23, volca-d8tmz9, volca-d8u6e0 Abstract The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity. Title: Genome sequence of the palaeopolyploid soybean Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ and Jackson SA <35 more author(s)> Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (- 35) Ref: Nature, 463:178, 2010 : PubMed ESTHER: Schmutz_2010_Nature_463_178 PubMedSearch: Schmutz 2010 Nature 463 178 PubMedID: 20075913 Gene_locus related to this paper: soybn-c6t4m5, soybn-c6t4p4, soybn-c6tav4, soybn-c6tdf9, soybn-c6tiz7, soybn-c6tmg3, soybn-i1jgq5, soybn-i1kpj2, soybn-i1kwe7, soybn-i1l7e3, soybn-i1l497, soybn-i1ll09, soybn-i1lpi4, soybn-i1jcw2, soybn-i1jcw3, soybn-i1jcw4, soybn-i1jcw7, soybn-i1k217, soybn-i1kfz3, soybn-i1lhi0, soybn-k7k6s4, soybn-i1jtw1, soybn-c6tas4, soybn-i1m910, soybn-c6t7k8, soybn-i1k636, soybn-i1kju7, soybn-i1j4c6, soybn-i1lbk2, soybn-i1jqy5, soybn-i1nbj8, soybn-i1j855, soybn-i1l5a3, soybn-k7mt28, soybn-i1lau7, soybn-i1lay0, soybn-i1net3, soybn-i1jr09, soybn-i1ms08, soybn-i1mmh5, soybn-i1mly5, soybn-i1mmh3, soybn-i1mmh4, soybn-i1ngu7, soybn-k7ll20, soybn-i1mly4, soybn-a0a0r0i9y7, soybn-a0a0r0j241, soybn-i1les8, soybn-k7n313, soybn-i1kfj1, soybn-a0a0r0k7x4, soybn-i1ly30, soybn-i1mwr8, soybn-i1kfg5, soybn-i1kly2, soybn-a0a0r0ixi2, soybn-i1jew0, glyso-a0a445l5n1, soybn-i1kfz9, soybn-i1jqs1, soybn-i1nbc7, soybn-k7mm57, soybn-a0a0r0fec7, soybn-a0a0r0hcn9, soybn-i1jx17, soybn-k7kvv2, soybn-i1kcl6, soybn-i1kcl7 Abstract Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties. Title: Genome sequencing and analysis of the model grass Brachypodium distachyon. Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M and Baxter I <127 more author(s)> Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, McKenzie N, Huo N, Gu YQ, Lazo GR, Anderson OD, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Idziak D, Hasterok R, Lindquist E, Wang M, Fox SE, Priest HD, Filichkin SA, Givan SA, Bryant DW, Chang JH, Wu H, Wu W, Hsia AP, Schnable PS, Kalyanaraman A, Barbazuk B, Michael TP, Hazen SP, Bragg JN, Laudencia-Chingcuanco D, Weng Y, Haberer G, Spannagl M, Mayer K, Rattei T, Mitros T, Lee SJ, Rose JK, Mueller LA, York TL, Wicker T, Buchmann JP, Tanskanen J, Schulman AH, Gundlach H, Bevan M, de Oliveira AC, Maia Lda C, Belknap W, Jiang N, Lai J, Zhu L, Ma J, Sun C, Pritham E, Salse J, Murat F, Abrouk M, Bruggmann R, Messing J, Fahlgren N, Sullivan CM, Carrington JC, Chapman EJ, May GD, Zhai J, Ganssmann M, Gurazada SG, German M, Meyers BC, Green PJ, Tyler L, Wu J, Thomson J, Chen S, Scheller HV, Harholt J, Ulvskov P, Kimbrel JA, Bartley LE, Cao P, Jung KH, Sharma MK, Vega-Sanchez M, Ronald P, Dardick CD, De Bodt S, Verelst W, Inz D, Heese M, Schnittger A, Yang X, Kalluri UC, Tuskan GA, Hua Z, Vierstra RD, Cui Y, Ouyang S, Sun Q, Liu Z, Yilmaz A, Grotewold E, Sibout R, Hematy K, Mouille G, Hofte H, Michael T, Pelloux J, O'Connor D, Schnable J, Rowe S, Harmon F, Cass CL, Sedbrook JC, Byrne ME, Walsh S, Higgins J, Li P, Brutnell T, Unver T, Budak H, Belcram H, Charles M, Chalhoub B, Baxter I (- 127) Ref: Nature, 463:763, 2010 : PubMed ESTHER: Vogel_2010_Nature_463_763 PubMedSearch: Vogel 2010 Nature 463 763 PubMedID: 20148030 Gene_locus related to this paper: bradi-i1grm0, bradi-i1gx82, bradi-i1hb80, bradi-i1hkv6, bradi-i1hpu6, bradi-i1i3e4, bradi-i1i9i0, bradi-i1i435, bradi-i1ix93, bradi-i1gsk6, bradi-i1hk44, bradi-i1hk45, bradi-i1hnk7, bradi-i1hsd5, bradi-i1huy4, bradi-i1huy9, bradi-i1huz0, bradi-i1gxx9, bradi-i1hl25, bradi-i1hcw7, bradi-i1hyv6, bradi-i1hyb5, bradi-i1hvr8, bradi-i1hmu2, bradi-i1hf05, bradi-i1gry7, bradi-i1hf06, bradi-i1i5z8, bradi-i1icy3, bradi-i1j1h3, bradi-i1h1e3, bradi-i1hvr9, bradi-a0a0q3r7i7, bradi-i1i377, bradi-i1hjg5, bradi-i1h3i9, bradi-i1gsg5, bradi-a0a0q3mph9, bradi-i1h682, bradi-a0a0q3lc91 Title: The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ and Vanetten HD <29 more author(s)> Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EG, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnar I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, Vanetten HD (- 29) Ref: PLoS Genet, 5:e1000618, 2009 : PubMed ESTHER: Coleman_2009_PLoS.Genet_5_E1000618 PubMedSearch: Coleman 2009 PLoS.Genet 5 E1000618 PubMedID: 19714214 Gene_locus related to this paper: fusso-cutas, nech7-c7yh18, nech7-c7yir8, nech7-c7yiz6, nech7-c7yjl4, nech7-c7yjp7, nech7-c7yjq0, nech7-c7ymg9, nech7-c7ymv6, nech7-c7yna5, nech7-c7ynt6, nech7-c7yq59, nech7-c7yq86, nech7-c7yqb0, nech7-c7yqx3, nech7-c7ysz7, nech7-c7ysz8, nech7-c7ytb2, nech7-c7yum7, nech7-c7yvb1, nech7-c7yvb8, nech7-c7yvf1, nech7-c7yvq8, nech7-c7yw21, nech7-c7yx47, nech7-c7yx92, nech7-c7yxe7, nech7-c7yxq5, nech7-c7yxz4, nech7-c7yy47, nech7-c7yyj7, nech7-c7yym7, nech7-c7z0d7, nech7-c7z0s1, nech7-c7z1g9, nech7-c7z1k9, nech7-c7z2k4, nech7-c7z2m9, nech7-c7z2z2, nech7-c7z3z3, nech7-c7z4a4, nech7-c7z5n1, nech7-c7z5y2, nech7-c7z6g5, nech7-c7z7d0, nech7-c7z7w8, nech7-c7z8q7, nech7-c7z9e7, nech7-c7z073, nech7-c7z354, nech7-c7z389, nech7-c7z688, nech7-c7z855, nech7-c7z987, nech7-c7za94, nech7-c7zah0, nech7-c7zb79, nech7-c7zbr8, nech7-c7zcd1, nech7-c7zdx8, nech7-c7ze42, nech7-c7ze84, nech7-c7zed8, nech7-c7zeh0, nech7-c7zes2, nech7-c7zgw2, nech7-c7zha0, nech7-c7zhy2, nech7-c7zi55, nech7-c7zig4, nech7-c7zjg0, nech7-c7zjv2, nech7-c7zk96, nech7-c7zkb5, nech7-c7zkh4, nech7-c7zla9, nech7-c7zld2, nech7-c7zlz1, nech7-c7zm00, nech7-c7zmn4, nech7-c7zmu6, nech7-c7zp06, nech7-c7zp78, nech7-c7zq58, nech7-c7zq86, nech7-c7zqb5, nech7-c7zqk4, nech7-c7zqp9, nech7-c7zr59, nech7-c7zrh2, nech7-c7zrh3, nech7-dapb, nech7-kex1, nech7-c7zgl9, nech7-c7z935, nech7-c7znc0, nech7-c7yiq8, nech7-c7yiq7, nech7-c7zhu0, nech7-c7yw61, nech7-c7yqd3, nech7-c7zkb6, nech7-c7z3b4, nech7-c7ytr4, nech7-c7zgf7, 9hypo-a0a3m2s2j6, nech7-c7yq54, fusv7-cbpya Abstract The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches. Title: Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT and Cullen D <43 more author(s)> Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (- 43) Ref: Proc Natl Acad Sci U S A, 106:1954, 2009 : PubMed ESTHER: Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954 PubMedSearch: Martinez 2009 Proc.Natl.Acad.Sci.U.S.A 106 1954 PubMedID: 19193860 Gene_locus related to this paper: pospm-b8p1f3, pospm-b8p2q7, pospm-b8p4n0, pospm-b8p4n9, pospm-b8p5g9, pospm-b8p5r9, pospm-b8p6h2, pospm-b8p7b1, pospm-b8p7c4, pospm-b8p8w7, pospm-b8p9j1, pospm-b8p164, pospm-b8p280, pospm-b8p423.1, pospm-b8p423.2, pospm-b8p858, pospm-b8pam2, pospm-b8pam5, pospm-b8pb68, pospm-b8pbm3, pospm-b8pc54, pospm-b8pc56, pospm-b8pce4, pospm-b8pd91, pospm-b8pdk6, pospm-b8ph32, pospm-b8ph43, pospm-b8phc9, pospm-b8php7, pospm-b8phy5, pospm-b8pjg8, pospm-b8pji9, pospm-b8plr5, pospm-b8pmk3, pospm-b8pfg0, pospm-b8pg35, pospm-b8pa20.1, pospm-b8pa20.2, pospm-b8p4g8, pospm-b8phn6 Abstract Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. Title: The Phaeodactylum genome reveals the evolutionary history of diatom genomes Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F and Grigoriev IV <67 more author(s)> Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV (- 67) Ref: Nature, 456:239, 2008 : PubMed ESTHER: Bowler_2008_Nature_456_239 PubMedSearch: Bowler 2008 Nature 456 239 PubMedID: 18923393 Gene_locus related to this paper: phatc-b7fp91, phatc-b7fqd3, phatc-b7frf9, phatc-b7fry8, phatc-b7ftw8, phatc-b7fv70, phatc-b7fw66, phatc-b7g2b2, phatc-b7g5z5, phatc-b7g6f1, phatc-b7g6r8, phatc-b7g957, phatc-b7ga73, phatc-b7gb22, phatc-b7gc60, phatc-b7gdm3, phatc-b7gdq6, phatc-b7ge82, phatc-b7gee0, phatr-b7frs5, phatr-b7g1k3, phatr-b7s4a4, thaps-b8bsy4, thaps-b8cfn8, phatc-b7g635, phatc-b7gaj3, thaps-b8c079 Abstract Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans. Title: The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E and Grigoriev IV <58 more author(s)> Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buee M, Brokstein P, Canback B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, Difazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbe J, Lin YC, Legue V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kues U, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouze P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV (- 58) Ref: Nature, 452:88, 2008 : PubMed ESTHER: Martin_2008_Nature_452_88 PubMedSearch: Martin 2008 Nature 452 88 PubMedID: 18322534 Gene_locus related to this paper: lacbs-b0cns1, lacbs-b0cpl4, lacbs-b0cr62, lacbs-b0cr66, lacbs-b0csq9, lacbs-b0ct56, lacbs-b0ctt5, lacbs-b0cuw1, lacbs-b0cv23, lacbs-b0cxm7, lacbs-b0cz37, lacbs-b0czx3, lacbs-b0d0z5, lacbs-b0d4i0, lacbs-b0d4j3, lacbs-b0d5n6, lacbs-b0d8k0, lacbs-b0d263, lacbs-b0dhh1, lacbs-b0dkp6, lacbs-b0dmr2, lacbs-b0dmt4, lacbs-b0dsx5, lacbs-b0dt05, lacbs-b0dtw4, lacbs-b0du88, lacbs-b0dsl6 Abstract Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity. Title: The amphioxus genome and the evolution of the chordate karyotype Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A and Rokhsar DS <27 more author(s)> Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (- 27) Ref: Nature, 453:1064, 2008 : PubMed ESTHER: Putnam_2008_Nature_453_1064 PubMedSearch: Putnam 2008 Nature 453 1064 PubMedID: 18563158 Gene_locus related to this paper: brafl-ACHE1, brafl-ACHE2, brafl-ACHEA, brafl-ACHEB, brafl-c3xqm2, brafl-c3xqm5, brafl-c3xtl0, brafl-c3xtl1, brafl-c3xut6, brafl-c3xut7, brafl-c3xvw5, brafl-c3xx27, brafl-c3xx28, brafl-c3xx30, brafl-c3xx32, brafl-c3xx36, brafl-c3xx38, brafl-c3xx39, brafl-c3xx40, brafl-c3xx41, brafl-c3xxt9, brafl-c3xyd7, brafl-c3xyd8, brafl-c3xyd9, brafl-c3xye0, brafl-c3xyt7, brafl-c3xzy1, brafl-c3xzy2, brafl-c3y1p9, brafl-c3y1t3, brafl-c3y2u3, brafl-c3y4l1, brafl-c3y6v9, brafl-c3y6y4, brafl-c3y7d7, brafl-c3y7s1, brafl-c3y8k5, brafl-c3y8t3, brafl-c3y8t4, brafl-c3y8t5, brafl-c3y8v8, brafl-c3y8w1.1, brafl-c3y8w2, brafl-c3y9i7, brafl-c3y9i8, brafl-c3y9l9, brafl-c3y9y3, brafl-c3y087, brafl-c3yan2, brafl-c3yaw4, brafl-c3ybw7, brafl-c3yc67, brafl-c3ydm8, brafl-c3yfm5, brafl-c3yfz8, brafl-c3ygc7, brafl-c3ygc9.1, brafl-c3ygd0, brafl-c3ygd1, brafl-c3ygd2.1, brafl-c3ygd4, brafl-c3ygg6, brafl-c3ygr1, brafl-c3yi63, brafl-c3yi64, brafl-c3yi67, brafl-c3yi68, brafl-c3yi69, brafl-c3yk61, brafl-c3ykb2, brafl-c3yla7, brafl-c3ylp9, brafl-c3ylq0, brafl-c3ylq1, brafl-c3ymu0, brafl-c3yne9, brafl-c3ypm6, brafl-c3yr72, brafl-c3yra8, brafl-c3ys59, brafl-c3yv27, brafl-c3ywf1, brafl-c3ywh9, brafl-c3yx17, brafl-c3yx19, brafl-c3yxb9, brafl-c3yxi7, brafl-c3yyq5, brafl-c3yz04, brafl-c3z1c7, brafl-c3z1u9, brafl-c3z1v0, brafl-c3z3n7, brafl-c3z5c8, brafl-c3z9f4, brafl-c3z066, brafl-c3z139, brafl-c3z975, brafl-c3zab8, brafl-c3zab9, brafl-c3zbr4, brafl-c3zci7, brafl-c3zcy8, brafl-c3zd14, brafl-c3zer1, brafl-c3zf44, brafl-c3zf47, brafl-c3zf48, brafl-c3zfs6, brafl-c3zhm6, brafl-c3ziv7.1, brafl-c3ziv7.2, brafl-c3zlg0, brafl-c3zlg2, brafl-c3zlg3, brafl-c3zli5, brafl-c3zme7, brafl-c3zme8, brafl-c3zmp8, brafl-c3zmv1, brafl-c3zmv2, brafl-c3znd6, brafl-c3znl2, brafl-c3zqg7, brafl-c3zqz2, brafl-c3zs46, brafl-c3zs49, brafl-c3zs56, brafl-c3zv54, brafl-c3zvv1, brafl-c3zwz6, brafl-c3zxg2, brafl-c3zxq3, brafl-c3yim2, brafl-c3zfs5, brafl-c3zfs3, brafl-c3xr79, brafl-c3y7r2, brafl-c3yj62, brafl-c3zg22, brafl-c3y2t9, brafl-c3y2u0, brafl-c3ycg1, brafl-c3ycg2, brafl-c3ycg4, brafl-c3z1l3, brafl-c3zn71, brafl-c3zj72, brafl-c3yf35, brafl-c3z474, brafl-c3zqr8, brafl-c3yde6 Abstract Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution. Title: Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P and Richardson PM <3 more author(s)> Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM (- 3) Ref: Nat Biotechnol, 25:319, 2007 : PubMed ESTHER: Jeffries_2007_Nat.Biotechnol_25_319 PubMedSearch: Jeffries 2007 Nat.Biotechnol 25 319 PubMedID: 17334359 Gene_locus related to this paper: picst-a3geu9, picst-a3gfu2, picst-a3ggh9, picst-a3gha8, picst-a3ghe3, picst-a3gi73, picst-a3lmu3, picst-a3ln06, picst-a3ln59, picst-a3lnv8, picst-a3lp77, picst-a3lqt4, picst-a3lrt0, picst-a3ls15, picst-a3lsj8, picst-a3lu11, picst-a3luu0, picst-a3lv87, picst-a3lvi5, picst-a3lvu9, picst-a3lvv2, picst-a3lwa4, picst-a3lxl2, picst-a3lxs8, picst-a3lyi3, picst-atg15, picst-bna7, picst-a3lyh1, picst-a3lnc5, picst-a3lr32 Abstract Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions. Title: The Chlamydomonas genome reveals the evolution of key animal and plant functions Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK and Grossman AR <107 more author(s)> Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (- 107) Ref: Science, 318:245, 2007 : PubMed ESTHER: Merchant_2007_Science_318_245 PubMedSearch: Merchant 2007 Science 318 245 PubMedID: 17932292 Gene_locus related to this paper: chlre-a0a2k3e2k6, chlre-a8hmd4, chlre-a8hqa9, chlre-a8htq0, chlre-a8hus6.1, chlre-a8hus6.2, chlre-a8icg4, chlre-a8iwm0, chlre-a8ize5, chlre-a8j2s9, chlre-a8j5w6, chlre-a8j7f8, chlre-a8j8u9, chlre-a8j8v0, chlre-a8j9u6, chlre-a8j143, chlre-a8j248, chlre-a8jd32, chlre-a8jd42, chlre-a8jgj2, chlre-a8jhc8, chlre-a8jhe5, chlre-a8iwj1, chlre-a8j7d5, chlre-a0a2k3dii0 Abstract Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella. Title: Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E and Rokhsar DS <9 more author(s)> Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS (- 9) Ref: Science, 317:86, 2007 : PubMed ESTHER: Putnam_2007_Science_317_86 PubMedSearch: Putnam 2007 Science 317 86 PubMedID: 17615350 Gene_locus related to this paper: nemve-a7rfc6, nemve-a7rhs0, nemve-a7rhw2, nemve-a7ric9, nemve-a7riu9, nemve-a7rk54, nemve-a7rlg8, nemve-a7rlv4, nemve-a7rn07, nemve-a7rn08, nemve-a7rn68, nemve-a7rnv3, nemve-a7rpb3, nemve-a7rpq4, nemve-a7rqa8, nemve-a7rqw3, nemve-a7rwv1, nemve-a7rxl6, nemve-a7s1d5, nemve-a7s3l3, nemve-a7s3q1, nemve-a7s5u3, nemve-a7s6g4, nemve-a7s6s7, nemve-a7sa46, nemve-a7sbd9, nemve-a7sbe0, nemve-a7sbm6, nemve-a7scy7, nemve-a7sex0, nemve-a7sfa0, nemve-a7sff3, nemve-a7sgb1, nemve-a7shf2, nemve-a7siv4, nemve-a7sj77, nemve-a7sjw1, nemve-a7skr3, nemve-a7slm1, nemve-a7slm2, nemve-a7sp35, nemve-a7sq47, nemve-a7sq73, nemve-a7sqk0, nemve-a7su21, nemve-a7su25, nemve-a7svn0, nemve-a7svu2, nemve-a7sx21, nemve-a7syk4, nemve-a7t3e6, nemve-a7suy2, nemve-a7s803, nemve-a7t3m9, nemve-a0a1t4jh34, nemve-a7rvd5, nemve-a7rhu9, nemve-a7si15 Abstract Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor. | |||||||
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