Author Report for: Hellsten UNo contact information in database for Hellsten U
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A and Rokhsar DS <64 more author(s)> Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS (- 64) Ref: Nature, 538:336, 2016 : PubMed ESTHER: Session_2016_Nature_538_336 PubMedSearch: Session 2016 Nature 538 336 PubMedID: 27762356 Gene_locus related to this paper: xenla-a0a1l8f4t7, xenla-a0a1l8fbc6, xenla-a0a1l8fct2, xenla-q2tap9, xenla-q4klb6, xenla-q5xh09, xenla-q6ax59, xenla-q6dcw6, xenla-q6irp4, xenla-q6pad5, xenla-q7sz70, xenla-Q7ZXQ6, xenla-q66kx1, xenla-q640y7, xenla-q642r3, xenla-Q860X9, xenla-BCHE2, xenla-a0a1l8g7v4, xenla-a0a1l8g1u7, xenla-a0a1l8fmc5, xenla-a0a1l8g467, xenla-a0a1l8g4e4, xenla-a0a1l8ga66, xenla-a0a1l8gaw4, xenla-a0a1l8gt68, xenla-a0a1l8h0b2, xenla-a0a1l8fdr1, xenla-a0a1l8fdt7, xenla-a0a1l8fi72, xenla-a0a1l8fi73, xenla-a0a1l8fi77, xenla-a0a1l8fi96, xenla-a0a1l8hc38, xenla-a0a1l8hn27, xenla-a0a1l8hry6, xenla-a0a1l8hw96, xenla-a0a1l8i2x6, xenla-a0a1l8hei7, xenla-a0a1l8gnd1, xenla-a0a1l8i2g3, xenla-a0a1l8hdn0, xenla-a0a1l8h622 Abstract To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. 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: A reference genome for common bean and genome-wide analysis of dual domestications Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q and Jackson SA <31 more author(s)> Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA (- 31) Ref: Nat Genet, 46:707, 2014 : PubMed ESTHER: Schmutz_2014_Nat.Genet_46_707 PubMedSearch: Schmutz 2014 Nat.Genet 46 707 PubMedID: 24908249 Gene_locus related to this paper: phavu-v7azs2, phavu-v7awu7 Abstract Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement. Title: Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing Hellsten U, Wright KM, Jenkins J, Shu S, Yuan Y, Wessler SR, Schmutz J, Willis JH, Rokhsar DS Ref: Proc Natl Acad Sci U S A, 110:19478, 2013 : PubMed ESTHER: Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478 PubMedSearch: Hellsten 2013 Proc.Natl.Acad.Sci.U.S.A 110 19478 PubMedID: 24225854 Gene_locus related to this paper: erygu-a0a022qsc9, erygu-a0a022qjb4, erygu-a0a022px28, erygu-a0a022rcn8, erygu-a0a022r7z4, erygu-a0a022rcp2, erygu-a0a022r9s7, erygu-a0a022put8, erygu-a0a022r922, erygu-a0a022qmg0, erygu-a0a022rf01, erygu-a0a022qnf5, erygu-a0a022qs63, erygu-a0a022rvn4, erygu-a0a022rnw2, erygu-a0a022s0h3, erygu-a0a022qr26, erygu-a0a022qi72, erygu-a0a022qi30, erygu-a0a022q165, erygu-a0a022r728, erygu-a0a022r7n8, erygu-a0a022rm64, erygu-a0a022s4c6, erygu-a0a022rbl0, erygu-a0a022rwi3, erygu-a0a022rzg9 Abstract Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms. Title: Insights into bilaterian evolution from three spiralian genomes Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J and Rokhsar DS <16 more author(s)> Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS (- 16) Ref: Nature, 493:526, 2013 : PubMed ESTHER: Simakov_2013_Nature_493_526 PubMedSearch: Simakov 2013 Nature 493 526 PubMedID: 23254933 Gene_locus related to this paper: capte-r7t7t5, capte-r7tx98, capte-r7ua57, capte-r7ua73, capte-ACHE1, capte-ACHE2, capte-ACHE3, capte-ACHE4, helro-ACHE1, helro-ACHE1b, lotgi-ACHE1, lotgi-ACHE2, lotgi-v4aaa2, lotgi-v3zx52, lotgi-v4b4v9, capte-r7tuq9, capte-r7v997, capte-r7vgb9, lotgi-v3zwe9, capte-r7tu45, lotgi-v4bvy3, lotgi-v3zh31, capte-r7uie6, lotgi-v4b898, capte-r7u3w8, capte-r7uxb2, lotgi-v3za62, capte-r7ux79, capte-r7uq81, capte-r7vcc3, capte-r7ts12, capte-r7u1x0, capte-r7uhi1, capte-r7vei7, capte-r7v0v3, lotgi-v4bvi8, lotgi-v3zyd8, capte-r7tzy6, lotgi-v3z9i1, helro-t1fsg3, capte-x1yv75, capte-x2b306, lotgi-v3zcw8, capte-r7thp6, helro-t1fy80, lotgi-v4bky5, capte-r7tsq9, lotgi-v4ali9, lotgi-v4a9f2, lotgi-v3zjj3, helro-t1eej5, helro-t1g9b7, capte-r7tiy1, capte-r7tbl5, helro-t1exa6, lotgi-v4a5l7, helro-t1fm33, capte-r7ud05, capte-r7tql8, capte-r7u5g6, capte-r7u5z3, capte-r7ue07, lotgi-v3zk54, lotgi-v4a4r1, lotgi-v4aw76, lotgi-v4b250, lotgi-v4bbk1, lotgi-v3zq85, lotgi-v4a6s5, lotgi-v4amq2, lotgi-v4aqm2, lotgi-v4crq0, capte-r7tad7, capte-r7vgm6, lotgi-v4agl2, lotgi-v3zur2, lotgi-v4aui4, capte-r7tlv8, lotgi-v3zu07, helro-t1g0w9 Abstract Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome. 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 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: The dynamic genome of Hydra Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J and Steele RE <64 more author(s)> Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Bottger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE (- 64) Ref: Nature, 464:592, 2010 : PubMed ESTHER: Chapman_2010_Nature_464_592 PubMedSearch: Chapman 2010 Nature 464 592 PubMedID: 20228792 Gene_locus related to this paper: 9burk-c9y6c0, 9burk-c9y8q9, 9burk-c9y9d4, 9burk-c9ya28, 9burk-c9yb37, 9burk-c9ycr9, 9burk-c9ydq0, 9burk-c9ydr2, 9burk-c9yew1, 9burk-c9yf78, 9burk-c9ygh2, 9burk-c9y7j2 Abstract The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction. 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: 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: The Sorghum bicolor genome and the diversification of grasses Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T and Rokhsar DS <35 more author(s)> Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (- 35) Ref: Nature, 457:551, 2009 : PubMed ESTHER: Paterson_2009_Nature_457_551 PubMedSearch: Paterson 2009 Nature 457 551 PubMedID: 19189423 Gene_locus related to this paper: sorbi-b3vtb2, sorbi-c5wp75, sorbi-c5wts6, sorbi-c5wu07, sorbi-c5wvl7, sorbi-c5ww85, sorbi-c5ww86, sorbi-c5wxa4, sorbi-c5x1f6, sorbi-c5x2x9, sorbi-c5x5z9, sorbi-c5x6q0, sorbi-c5x230, sorbi-c5x290, sorbi-c5x345, sorbi-c5x399, sorbi-c5x610, sorbi-c5xbm4, sorbi-c5xct0, sorbi-c5xdv0, sorbi-c5xe87, sorbi-c5xf40, sorbi-c5xfu9, sorbi-c5xh40, sorbi-c5xh41, sorbi-c5xh42, sorbi-c5xh43, sorbi-c5xh44, sorbi-c5xh46, sorbi-c5xhr2, sorbi-c5xiw7, sorbi-c5xjf0, sorbi-c5xky2, sorbi-c5xm54, sorbi-c5xmb9, sorbi-c5xmz5, sorbi-c5xp10, sorbi-c5xpm6, sorbi-c5xr91, sorbi-c5xr92, sorbi-c5xs33, sorbi-c5xtz0, sorbi-c5xwd3, sorbi-c5y0d2, sorbi-c5y0h4, sorbi-c5y3i5, sorbi-c5y7x0, sorbi-c5y517, sorbi-c5y545, sorbi-c5ydr3, sorbi-c5yec0, sorbi-c5yf71, sorbi-c5yi32, sorbi-c5yih2, sorbi-c5ylw6, sorbi-c5yn66, sorbi-c5ynp8, sorbi-c5yt11, sorbi-c5yur5, sorbi-c5ywz3, sorbi-c5ywz4, sorbi-c5yx73, sorbi-c5yyn0, sorbi-c5z2m6, sorbi-c5z6a9, sorbi-c5z6j1, sorbi-c5z6s5, sorbi-c5z177, sorbi-Q9XE80, sorbi-c5xyg4, sorbi-c5z4q0, sorbi-c5xly4, sorbi-c5z4u8, sorbi-c5xxg5, sorbi-c5z9b9, sorbi-a0a1z5r970, sorbi-c5xhf9, sorbi-c5yxt7, sorbi-c5yxt6, sorbi-c5y1m2, sorbi-c5xdy6, sorbi-a0a194ysf6, sorbi-a0a1b6pnr2, sorbi-a0a1b6qcb9 Abstract Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance. Title: The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y and Rokhsar D <26 more author(s)> King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D (- 26) Ref: Nature, 451:783, 2008 : PubMed ESTHER: King_2008_Nature_451_783 PubMedSearch: King 2008 Nature 451 783 PubMedID: 18273011 Gene_locus related to this paper: monbe-a9up87, monbe-a9uq69, monbe-a9uq70, monbe-a9uqa7, monbe-a9urz6, monbe-a9usu1, monbe-a9usy8, monbe-a9uta2, monbe-a9uu09, monbe-a9uxl2, monbe-a9uy23, monbe-a9uy95, monbe-a9uym3, monbe-a9uyw1, monbe-a9uzc1, monbe-a9v0e1, monbe-a9v2b0, monbe-a9v3a5, monbe-a9v3t2, monbe-a9v4h5, monbe-a9v6i1, monbe-a9v7b2, monbe-a9v7c1, monbe-a9v8k9, monbe-a9v8u8, monbe-a9v9i9, monbe-a9v9k6, monbe-a9v028, monbe-a9v108, monbe-a9v315, monbe-a9v345, monbe-a9v368, monbe-a9v719, monbe-a9v871, monbe-a9vac5, monbe-a9vah5, monbe-a9van7, monbe-a9vbp2, monbe-a9vcn6, monbe-a9vd99, monbe-a9vdj5, monbe-a9vag0 Abstract Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans. 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: The Trichoplax genome and the nature of placozoans Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A and Rokhsar DS <11 more author(s)> Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS (- 11) Ref: Nature, 454:955, 2008 : PubMed ESTHER: Srivastava_2008_Nature_454_955 PubMedSearch: Srivastava 2008 Nature 454 955 PubMedID: 18719581 Gene_locus related to this paper: triad-b3rka6, triad-b3rkc3, triad-b3rkc4, triad-b3rkc5, triad-b3rkr2, triad-b3rks9, triad-b3rkt0, triad-b3rl14, triad-b3rls2, triad-b3rnj7, triad-b3rnw5, triad-b3rrr2, triad-b3rsh1, triad-b3rsh3, triad-b3rty7, triad-b3ru11, triad-b3rur2, triad-b3rut0, triad-b3rvc1, triad-b3rw12, triad-b3rwp0, triad-b3rwr4, triad-b3rxn2, triad-b3ry59, triad-b3s1y9, triad-b3s3d8, triad-b3s3e9, triad-b3s8a0, triad-b3s9x4, triad-b3s445, triad-b3s449, triad-b3s478, triad-b3s705, triad-b3s706, triad-b3s898, triad-b3s899, triad-b3s949, triad-b3s950, triad-b3sa20, triad-b3sa22, triad-b3sa23, triad-b3sa24, triad-b3sa25, triad-b3sa26, triad-b3sa27, triad-b3sa28, triad-b3sa29, triad-b3sa31, triad-b3sa33, triad-b3sa34, triad-b3sa36, triad-b3sb39, triad-b3scd3, triad-b3scg3, triad-b3scg4, triad-b3scr3, triad-b3seb0, triad-b3seb1, triad-b3seu9, triad-b3sf12, triad-b3rt61, triad-b3rt62, triad-b3rj15, triad-b3sdi1 Abstract As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages. 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. Title: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S and Rokhsar D <100 more author(s)> Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (- 100) Ref: Science, 313:1596, 2006 : PubMed ESTHER: Tuskan_2006_Science_313_1596 PubMedSearch: Tuskan 2006 Science 313 1596 PubMedID: 16973872 Gene_locus related to this paper: burvg-a4jw31, delas-a9c1v9, poptr-a9pfp5, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9giq0, poptr-b9gjs0, poptr-b9gl72, poptr-b9gmx8, poptr-b9gnp9, poptr-b9gny4, poptr-b9grg2, poptr-b9gsc2, poptr-b9gvp3, poptr-b9gvs3, poptr-b9gwn9, poptr-b9gy32, poptr-b9gyq1, poptr-b9gys8, poptr-b9h0h0, poptr-b9h4j2, poptr-b9h6c2, poptr-b9h6c5, poptr-b9h6l8, poptr-b9h8c9, poptr-b9h301, poptr-b9h579, poptr-b9hbl2, poptr-b9hbw5, poptr-b9hcn9, poptr-b9hee0, poptr-b9hee2, poptr-b9hee5, poptr-b9hee6, poptr-b9hef3, poptr-b9hfa7, poptr-b9hfd3, poptr-b9hfi6, poptr-b9hft8, poptr-b9hg83, poptr-b9hif5, poptr-b9hll5, poptr-b9hmd0, poptr-b9hnv3, poptr-b9hqr6, poptr-b9hqr7, poptr-b9hrv7, poptr-b9hs66, poptr-b9huf0, poptr-b9hur3, poptr-b9hux1, poptr-b9hwp2, poptr-b9hxr7, poptr-b9hyk8, poptr-b9hyx2, poptr-b9i2q8, poptr-b9i5b8, poptr-b9i5j8, poptr-b9i5j9, poptr-b9i5k0, poptr-b9i6b6, poptr-b9i7b7, poptr-b9i9p8, poptr-b9i484, poptr-b9i994, poptr-b9ial3, poptr-b9ial4, poptr-b9ib28, poptr-b9ibr8, poptr-b9id97, poptr-b9idr4, poptr-b9iid9, poptr-b9iip0, poptr-b9ik80, poptr-b9ik90, poptr-b9il63, poptr-b9ink7, poptr-b9iqa0, poptr-b9iqd5, poptr-b9mwf1, poptr-b9mwi8, poptr-b9n0c6, poptr-b9n0n1, poptr-b9n0n4, poptr-b9n0z5, poptr-b9n1t8, poptr-b9n1z3, poptr-b9n3m7, poptr-b9n233, poptr-b9n236, poptr-b9n395, poptr-b9nd33, poptr-b9nd34, poptr-b9ndi6, poptr-b9ndj5, poptr-b9p9i8, poptr-a9pfa7, poptr-b9hdp2, poptr-b9inj0, poptr-b9n5g7, poptr-b9i8q4, poptr-u5g0r4, poptr-u5gf59, poptr-u7e1l9, poptr-b9hj61, poptr-b9hwd0, poptr-u5fz17, poptr-a0a2k2brq1, poptr-a0a2k2b9i6, poptr-a0a2k1x9y8, poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2a850, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, poptr-a0a2k2blg2, poptr-a0a2k1xpi3, poptr-a0a2k1xpj0, poptr-a0a2k2b331, poptr-a0a2k2byl7, poptr-b9iek5, poptr-a9pfg4 Abstract We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport. Title: The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE and Rokhsar DS <35 more author(s)> Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (- 35) Ref: Science, 306:79, 2004 : PubMed ESTHER: Armbrust_2004_Science_306_79 PubMedSearch: Armbrust 2004 Science 306 79 PubMedID: 15459382 Gene_locus related to this paper: thaps-b5ymy7, thaps-b5yn04, thaps-b5ynz7, thaps-b8bq57, thaps-b8bsn5, thaps-b8bsy4, thaps-b8bv00, thaps-b8bxb3, thaps-b8byx0, thaps-b8bzg5, thaps-b8c0a3, thaps-b8c2d8, thaps-b8c2k9, thaps-b8c2s5, thaps-b8c3p0, thaps-b8c5l7, thaps-b8c6y7, thaps-b8c9k8, thaps-b8c9t6, thaps-b8c345, thaps-b8c584, thaps-b8c885, thaps-b8c954, thaps-b8cdd7, thaps-b8cdt3, thaps-b8cf07, thaps-b8cfn8, thaps-b8c079 Abstract Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments. Title: The DNA sequence and biology of human chromosome 19 Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O and Lucas SM <88 more author(s)> Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM (- 88) Ref: Nature, 428:529, 2004 : PubMed ESTHER: Grimwood_2004_Nature_428_529 PubMedSearch: Grimwood 2004 Nature 428 529 PubMedID: 15057824 Abstract Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu. Title: The sequence and analysis of duplication-rich human chromosome 16 Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM and Pennacchio LA <112 more author(s)> Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, DeJong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA (- 112) Ref: Nature, 432:988, 2004 : PubMed ESTHER: Martin_2004_Nature_432_988 PubMedSearch: Martin 2004 Nature 432 988 PubMedID: 15616553 Gene_locus related to this paper: human-CES1, human-CES2, human-CES3, human-CES4A, human-CES5A Abstract Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility. | |||||||
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