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Author Report for: Coutinho PM

Title: Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain
Ji B, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB and Wu LF <17 more author(s)> Ji B, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian J, Yang J, Zhang L, Zhang W, Pan H, Henrissat B, Coutinho PM, Li Y, Xiao T, Medigue C, Barbe V, Pignol D, Talla E, Wu LF (- 17)
Ref: Environ Microbiol, 16:525, 2014 : PubMed
Abstract


ESTHER: Ji_2014_Environ.Microbiol_16_525
PubMedSearch: Ji 2014 Environ.Microbiol 16 525
PubMedID: 23841906
Gene_locus related to this paper: 9prot-w6k5m7, 9prot-w6khf2, 9prot-w6kbu9

Abstract

Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.



        

Title: Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis
Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D and Cullen D <55 more author(s)> Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavin JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kues U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D (- 55)
Ref: Proc Natl Acad Sci U S A, 109:5458, 2012 : PubMed
Abstract


ESTHER: Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedSearch: Fernandez-Fueyo 2012 Proc.Natl.Acad.Sci.U.S.A 109 5458
PubMedID: 22434909
Gene_locus related to this paper: cers8-m2r3x2, cers8-m2qf37, cers8-m2pcy7, cers8-m2pcz3, cers8-m2qn26, cers8-m2r654, cers8-m2r8g9, cers8-m2ps90, cers8-m2qn44, cers8-m2q837, cers8-m2pjy6, cers8-m2r609, cers8-m2qy35, cers8-m2r1n1, cers8-m2rl22, cers8-m2qkx5, cers8-m2qib7, cers8-m2rgs8, cers8-m2rlx6, cers8-m2r4p3, cers8-m2rf62, cers8-m2qyx5, cers8-m2pcz2, cers8-m2rm22, cers8-m2qwb7, cers8-m2r9u3, cers8-m2pp23, cers8-m2r613, cers8-m2rup8, cers8-m2piv7, cers8-m2rch3, cers8-m2qvf7, cers8-m2qvb7, cers8-m2qvb2, cers8-m2pip7, cers8-m2rb73, cers8-m2qgd3, cers8-m2rcg8, cers8-m2rb68

Abstract

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.



        

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
Abstract


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: Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A and Martin F <33 more author(s)> Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hilden K, Kues U, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wosten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F (- 33)
Ref: Proc Natl Acad Sci U S A, 109:17501, 2012 : PubMed
Abstract


ESTHER: Morin_2012_Proc.Natl.Acad.Sci.U.S.A_109_17501
PubMedSearch: Morin 2012 Proc.Natl.Acad.Sci.U.S.A 109 17501
PubMedID: 23045686
Gene_locus related to this paper: agabu-k5x1b4, agabu-k5x521, agabu-k5w389, agabu-k5wbk9, agabu-k5wrh0, agabu-k5ws85, agabu-k5wsf9, agabu-k5wxv1, agabu-k5x0d9, agabu-k5x588, agabu-k5x5x2, agabu-k5xd51, agabu-k5xh54, agabu-k5xsm1, agabu-k5xsp8, agabu-k5xtc1, agabu-k5y2v2, agabb-k9i3g9, agabb-k9hnv7, agabb-k9hr46, agabu-k5wys0

Abstract

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and beta-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.



        

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
Abstract


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: Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS and Dickman M <62 more author(s)> Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Guldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuveglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Segurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M (- 62)
Ref: PLoS Genet, 7:e1002230, 2011 : PubMed
Abstract


ESTHER: Amselem_2011_PLoS.Genet_7_E1002230
PubMedSearch: Amselem 2011 PLoS.Genet 7 E1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas, botci-q6rki2, botf4-g2y7k8, botfb-dapb, botfu-g2xyd8, botfu-g2ynh8, scls1-a7e814, scls1-a7edc9, scls1-a7edh1, scls1-a7emm0, scls1-a7eti8, scls1-a7eu48, scls1-a7f208, scls1-dapb, botf4-g2xqp7, scls1-a7eqq8, botf4-g2xqc6, scls1-a7ebs4, botf4-g2xn51, scls1-a7f5m9, botf4-g2xti4, botf4-g2xtu7, botf4-g2yfp1, scls1-a7f534, botf4-g2yys3, scls1-a7erz9, botf4-g2y037, botf4-g2y0e1, scls1-a7f706, scls1-a7ewt6, botf4-g2yuj6, botf1-m7u3d1, botf1-m7u430, botf1-m7tei8, botf1-m7u0w9, botf1-m7tij6, botf1-m7u819, botf1-m7u6d8, botf1-m7tzd4, botf1-m7tqd7, botf1-m7tyz9, botf1-m7unl9, botf1-m7u429, botf1-m7u4s5, botf1-m7ul92, botf1-m7tx42, botf1-m7u9h4, botf1-m7u187, botf1-m7uz64, botf1-m7u4q4, botf1-m7u2f6, botf1-m7tt59, botf1-m7v3h2, botf1-m7u6c9, botf1-m7tud9, botf1-m7u309, scls1-a7et87, botf4-g2ylt4, scls1-a7f5a0, scls1-a7f900, botf4-g2yib9, scls1-a7f3m9, scls1-a7er46, botf4-g2y3y4, botf4-g2xyy5, botf1-m7uct5, scls1-a7ea78, scls1-kex1, scls1-cbpya, botfb-cbpya, scls1-a7ecx1

Abstract

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.



        

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
Abstract


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: Obligate biotrophy features unraveled by the genomic analysis of rust fungi
Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J and Martin F <40 more author(s)> Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kues U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouze P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F (- 40)
Ref: Proc Natl Acad Sci U S A, 108:9166, 2011 : PubMed
Abstract


ESTHER: Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedSearch: Duplessis 2011 Proc.Natl.Acad.Sci.U.S.A 108 9166
PubMedID: 21536894
Gene_locus related to this paper: pucgt-e3k840, pucgt-e3kaq6, pucgt-e3kw59, pucgt-e3kz16, pucgt-e3l9v6, pucgt-e3l279, pucgt-h6qt25, mellp-f4reh4, mellp-f4rhc8, mellp-f4reh2, mellp-f4r3y0, mellp-f4rz15, mellp-f4rz64, mellp-f4rl14, mellp-f4rz66, mellp-f4s751, mellp-f4s2g6, pucgt-e3l1z7, pucgt-e3l803, pucgt-e3kst2, pucgt-e3kst5, mellp-f4ru03, pucgt-e3l1z8, pucgt-e3ktz7, pucgt-e3jun4, mellp-f4rl65, mellp-f4rz16, mellp-f4ru02, mellp-f4sav4, mellp-f4sav3, mellp-f4s1j0, mellp-f4rkp0, mellp-f4s483, pucgt-e3kzu5, pucgt-h6qtq8, mellp-f4r5l5, pucgt-e3krw7, pucgt-e3l7w5, pucgt-e3k2w6, pucgt-e3kfg2, pucgt-kex1

Abstract

Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.



        

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
Abstract


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
Abstract


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: 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
Abstract


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, hypai-g9nkx5

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.
RESULTS: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.
CONCLUSIONS: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.



        

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
Abstract


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, dicpu-f0zys7

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.
RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.
CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.



        

Title: Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M and Rep M <53 more author(s)> Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M (- 53)
Ref: Nature, 464:367, 2010 : PubMed
Abstract


ESTHER: Ma_2010_Nature_464_367
PubMedSearch: Ma 2010 Nature 464 367
PubMedID: 20237561
Gene_locus related to this paper: fusox-a0a1d3s5h0, gibf5-fus2, fusof-f9f2k2, fusof-f9f3l6, fusof-f9f6t8, fusof-f9f6v2, fusof-f9f132, fusof-f9f781, fusof-f9fd72, fusof-f9fd90, fusof-f9fem0, fusof-f9fhk2, fusof-f9fj19, fusof-f9fj20, fusof-f9fki8, fusof-f9fmx2, fusof-f9fnt4, fusof-f9fpy4, fusof-f9fvs6, fusof-f9fwu0, fusof-f9fxz4, fusof-f9fzy5, fusof-f9g2a2, fusof-f9g3b1, fusof-f9g5h7, fusof-f9g6e6, fusof-f9g6y7, fusof-f9g7b0, fusof-f9g797, fusof-f9g972, fusof-f9ga50, fusof-f9gck4, fusof-f9gd15, gibze-a8w610, gibze-b1pdn0, gibze-i1r9e6, gibze-i1rda9, gibze-i1rdk7, gibze-i1rec8, gibze-i1rgs0, gibze-i1rgy0, gibze-i1rh52, gibze-i1rhi8, gibze-i1rig9, gibze-i1rip5, gibze-i1rpg6, gibze-i1rsg2, gibze-i1rv36, gibze-i1rxm5, gibze-i1rxp8, gibze-i1rxv5, gibze-i1s1u3, gibze-i1s3j9, gibze-i1s6l7, gibze-i1s8i8, gibze-i1s9x4, gibze-q4huy1, gibze-i1rg17, fuso4-j9mvr9, fuso4-j9ngs6, fuso4-j9niq8, fuso4-j9nqm2, gibze-i1rb76, gibze-i1s1m7, gibze-i1s3z6, gibze-i1rd78, gibze-i1rgl9, gibze-i1rjp7, gibze-i1s1q6, gibze-i1ri35, gibze-i1rf76, gibze-i1rhp3, fusc1-n4uj11, fusc4-n1s9p6, gibf5-s0dqr2, gibm7-w7n1b5, fusof-f9g6q0, gibm7-w7n497, fusox-x0bme4, gibm7-w7mcf8, gibm7-w7mak5, fusox-x0a2c5, gibm7-w7mum7, fusox-w9iyc7, gibm7-w7maw6, gibm7-w7msi0, gibm7-w7luf0, gibm7-w7msa3, gibm7-w7mna8, gibm7-w7n8b7, gibm7-w7n564, fusox-w9jpi0, gibm7-w7ngc3, gibm7-w7m4v6, gibm7-w7m4v2, gibm7-w7lt61, gibm7-w7mly6, gibm7-w7ncn3, fusox-w9ibd7, fusof-f9fnm6, gibm7-w7n526, gibza-a0a016pda4, gibza-a0a016pl96, gibm7-w7muq1, fusof-f9gfd3, gibm7-w7mt52, gibze-i1rjb5, gibf5-s0ehu3, fusox-w9hvf0, gibze-i1rkc4, gibm7-w7mv30, gibze-a0a1c3ylb1, fuso4-a0a0c4diy4, gibm7-w7n4n0, gibze-gra11, gibze-fsl2, gibf5-fub4, gibf5-fub5, gibf5-fus5, gibm7-dlh1

Abstract

Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.



        

Title: Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B and Wincker P <41 more author(s)> Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buee M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marcais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, Wincker P (- 41)
Ref: Nature, 464:1033, 2010 : PubMed
Abstract


ESTHER: Martin_2010_Nature_464_1033
PubMedSearch: Martin 2010 Nature 464 1033
PubMedID: 20348908
Gene_locus related to this paper: 9pezi-d5g8f4, 9pezi-d5gi84, 9pezi-d5gph4, tubmm-d5g4w2, tubmm-d5g4w3, tubmm-d5g4w6, tubmm-d5g5r5, tubmm-d5g8z4, tubmm-d5g938, tubmm-d5ga65, tubmm-d5gcz1, tubmm-d5giz0, tubmm-d5gkr8, tubmm-d5glm4, tubmm-d5gnw0, tubmm-dapb, tubmm-d5gfj1, tubmm-d5gpf4, tubmm-TmEst2, tubmm-TmEst1, tubmm-TmEst3, 9pezi-a0a292py12, tubmm-kex1

Abstract

The Perigord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.



        

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
Abstract


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: Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche
Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, Coutinho PM, Henrissat B, Nelson KE
Ref: Microb Ecol, 60:721, 2010 : PubMed
Abstract


ESTHER: Purushe_2010_Microb.Ecol_60_721
PubMedSearch: Purushe 2010 Microb.Ecol 60 721
PubMedID: 20585943
Gene_locus related to this paper: prebr-d8dt96, prebr-d8du06, prebr-d8dv28, prebr-d8dwg8, prebr-d8dy06, prer2-d5esm6, prebr-d8dul5, prebr-d8dxa2, prebr-d8dw03, prer2-d5erq4, prer2-d5ewz1, prebr-d8dv01, prer2-axea1, prer2-axfa

Abstract

The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.



        

Title: Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B and Potocki-Veronese G <4 more author(s)> Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Dore J, Monsan P, Remaud-Simeon M, Potocki-Veronese G (- 4)
Ref: Genome Res, 20:1605, 2010 : PubMed
Abstract


ESTHER: Tasse_2010_Genome.Res_20_1605
PubMedSearch: Tasse 2010 Genome.Res 20 1605
PubMedID: 20841432
Gene_locus related to this paper: bactn-BT2525, bacun-a7uyk8

Abstract

The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 10(9) bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.



        

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
Abstract


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: Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V and Gordon JI <8 more author(s)> Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, VerBerkmoes NC, Hettich RL, Gordon JI (- 8)
Ref: Proc Natl Acad Sci U S A, 106:5859, 2009 : PubMed
Abstract


ESTHER: Mahowald_2009_Proc.Natl.Acad.Sci.U.S.A_106_5859
PubMedSearch: Mahowald 2009 Proc.Natl.Acad.Sci.U.S.A 106 5859
PubMedID: 19321416
Gene_locus related to this paper: eube2-c4z2j4, eube2-c4z5d5, eube2-c4z6k4, eube2-c4z179, eube2-c4z180, eubr3-c4z8a6, eubr3-c4zfm2, eubr3-c4zhp3, eubr3-c4zf28

Abstract

The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.



        

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
Abstract


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: Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M and Kuske CR <36 more author(s)> Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR (- 36)
Ref: Applied Environmental Microbiology, 75:2046, 2009 : PubMed
Abstract


ESTHER: Ward_2009_Appl.Environ.Microbiol_75_2046
PubMedSearch: Ward 2009 Appl.Environ.Microbiol 75 2046
PubMedID: 19201974
Gene_locus related to this paper: korve-q1ihr9, korve-q1ii02, korve-q1iit0, korve-q1ilk4, korve-q1imj9, korve-q1ims4, korve-q1iqj0, korve-q1isy7, korve-q1itj5, korve-q1itz6, korve-q1ivc8, acic5-c1f1u6, acic5-c1f2i7, acic5-c1f4m6, acic5-c1f4y4, acic5-c1f5a7, acic5-c1f5u2, acic5-c1f7a9, acic5-c1f7x6, acic5-c1f8y9, acic5-c1f9m2, acic5-c1f594, acic5-c1f609, acic5-c1f692, acic5-c1f970, acic5-c1fa52, korve-q1iiw2, korve-q1ivn9, solue-q01nb0, solue-q01qj6, solue-q01r37, solue-q01rq8, solue-q01rz0, solue-q01t44, solue-q01t57, solue-q01ts5, solue-q01tv4, solue-q01vd8, solue-q01vr3, solue-q01vw5, solue-q01w12, solue-q01wt9, solue-q01y40, solue-q01ym8, solue-q01z24, solue-q01z97, solue-q01zl4, solue-q01zm0, solue-q01zm5, solue-q01zm7, solue-q02aa4, solue-q02ab9, solue-q02b72, solue-q02bs8, solue-q02bt7, solue-q02cp0, solue-q02d61, solue-q020h3, solue-q020i8, solue-q021i6, solue-q022b1, solue-q022p8, solue-q022q2, solue-q022q3, solue-q022x2, solue-q022x5, solue-q022x6, solue-q022x8, solue-q023e7, solue-q024d9, solue-q025c1, solue-q026j1, solue-q026k6, solue-q026r6, solue-q027p2, solue-q027r8, solue-q01zt5, korve-q1itw6, solue-q01yh7, solue-q02ad6, korve-q1imj6, korve-q1iuf6, acic5-c1f891, solue-q026h7

Abstract

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.



        

Title: Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E and Grigoriev IV <41 more author(s)> Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV (- 41)
Ref: Science, 324:268, 2009 : PubMed
Abstract


ESTHER: Worden_2009_Science_324_268
PubMedSearch: Worden 2009 Science 324 268
PubMedID: 19359590
Gene_locus related to this paper: 9chlo-c1e363, 9chlo-c1ehp8, 9chlo-c1fhv2, 9chlo-c1mis3, 9chlo-c1na62, micpc-c1mh04, micpc-c1mhj0, micpc-c1mie7, micpc-c1mj20, micpc-c1mjh0, micpc-c1mny7, micpc-c1mpb2, micpc-c1mrl2, micpc-c1msr1, micpc-c1mvk4, micpc-c1mvx4, micpc-c1n5d2, micpc-c1n6i2, micpc-c1n842, micsr-c1dzu1, micsr-c1e0v8, micsr-c1e2u5, micsr-c1e4q6, micsr-c1e6z5, micsr-c1e046, micsr-c1e286, micsr-c1eap0, micsr-c1ec00, micsr-c1edy4, micsr-c1efl2, micsr-c1eh15, micsr-c1ei44, micsr-c1eii9, micsr-c1eiz1, micsr-c1fft1, micsr-c1fi89, micsr-c1fj57, micsr-c1e9f6, micsr-c1e9u2, micsr-c1fgg8, micpc-c1mie3, micpc-c1ms20, micpc-c1n640, miccc-c1e278, micpc-c1mpa6

Abstract

Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.



        

Title: The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms)
Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B and Distel DL <28 more author(s)> Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL (- 28)
Ref: PLoS ONE, 4:e6085, 2009 : PubMed
Abstract


ESTHER: Yang_2009_PLoS.ONE_4_E6085
PubMedSearch: Yang 2009 PLoS.ONE 4 E6085
PubMedID: 19568419
Gene_locus related to this paper: tertt-c5bif5, tertt-c5bkb0, tertt-c5bkv2, tertt-c5bmq4, tertt-c5bmw5, tertt-c5bmx1, tertt-c5bmz8, tertt-c5bn23, tertt-c5bn62, tertt-c5bpb2, tertt-c5bpu2, tertt-c5bru8, tertt-c5btp6, tertt-c5buc2, tertt-metx, tertt-c5br42, tertt-c5bpt0, tertt-c5btk3

Abstract

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2-40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.



        

Title: The genome sequence of the model ascomycete fungus Podospora anserina
Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Segurens B and Silar P <25 more author(s)> Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Segurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Dequard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarre B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P (- 25)
Ref: Genome Biol, 9:R77, 2008 : PubMed
Abstract


ESTHER: Espagne_2008_Genome.Biol_9_R77
PubMedSearch: Espagne 2008 Genome.Biol 9 R77
PubMedID: 18460219
Gene_locus related to this paper: podan-b2a8u1, podan-b2a9c4, podan-b2a9k6, podan-b2aa90, podan-b2ab33, podan-b2abs0, podan-b2ac17, podan-b2ack2, podan-b2ad07, podan-b2adj6, podan-b2adk0, podan-b2ae59, podan-b2aee7, podan-b2af51, podan-b2afn5, podan-b2afu6, podan-b2akq7, podan-b2aly0, podan-b2am11, podan-b2an24, podan-b2ank1, podan-b2apa8, podan-b2api8, podan-b2apj6, podan-b2arl9, podan-b2arz7, podan-b2ase4, podan-b2atn0, podan-b2au46, podan-b2aun9, podan-b2av47, podan-b2ava6, podan-b2avm3, podan-b2avu5, podan-b2avx3, podan-b2awk8, podan-b2axk2, podan-b2axz2, podan-b2b1p7, podan-b2b5e4, podan-b2b6n7, podan-b2b069, podan-b2b073, podan-b2b395, podan-dapb, podan-b2afr0, podan-b2a9k8, podan-b2atb3, podan-b2aca3, podan-b2arv3, podan-b2ank5, podan-b2ax54, podan-b2ad56, podan-b2anm1, podan-b2aya1, podan-b2b164, podan-a0a090d4h4, podan-a0a090ccl8, podan-b2b5p4, podan-b2azp1, podan-b2af75, podan-b2alm5, podan-b2ass5, podan-b2aez8, podan-kex1, podan-cbpya

Abstract

BACKGROUND: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. CONCLUSION: The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.



        

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
Abstract


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: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM and Brettin TS <35 more author(s)> Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (- 35)
Ref: Nat Biotechnol, 26:553, 2008 : PubMed
Abstract


ESTHER: Martinez_2008_Nat.Biotechnol_26_553
PubMedSearch: Martinez 2008 Nat.Biotechnol 26 553
PubMedID: 18454138
Gene_locus related to this paper: hypjq-g0rh85, hypjq-cip2, hypjq-g0r9d1, hypjq-g0r810, hypjq-g0rbm4, hypjq-g0rez4, hypjq-g0rfr3, hypjq-g0rg60, hypjq-g0rij9, hypjq-g0riu1, hypjq-g0rl87, hypjq-g0rlh4, hypjq-g0rme5, hypjq-g0rwy5, hypje-axylest, hypje-q7z9m3, hypjq-g0r6x2, hypje-a0a024s1b8, hypjr-a0a024s1s9, hypjq-g0rxi5

Abstract

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.



        

Title: Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T
Weiner RM, Taylor LE, 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG and Hutcheson S <9 more author(s)> Weiner RM, Taylor LE, 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S (- 9)
Ref: PLoS Genet, 4:e1000087, 2008 : PubMed
Abstract


ESTHER: Weiner_2008_PLoS.Genet_4_E1000087
PubMedSearch: Weiner 2008 PLoS.Genet 4 E1000087
PubMedID: 18516288
Gene_locus related to this paper: sacd2-q21f03, sacd2-q21l72, sacd2-q21ms2, sacd2-q21ll5

Abstract

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.



        

Title: Gene overexpression and biochemical characterization of the biotechnologically relevant chlorogenic acid hydrolase from Aspergillus niger
Benoit I, Asther M, Bourne Y, Navarro D, Canaan S, Lesage-Meessen L, Herweijer M, Coutinho PM, Record E
Ref: Applied Environmental Microbiology, 73:5624, 2007 : PubMed
Abstract


ESTHER: Benoit_2007_Appl.Environ.Microbiol_73_5624
PubMedSearch: Benoit 2007 Appl.Environ.Microbiol 73 5624
PubMedID: 17630312
Gene_locus related to this paper: aspnc-a2qn56

Abstract

The full-length gene that encodes the chlorogenic acid hydrolase from Aspergillus niger CIRM BRFM 131 was cloned by PCR based on the genome of the strain A. niger CBS 513.88. The complete gene consists of 1,715 bp and codes for a deduced protein of 512 amino acids with a molecular mass of 55,264 Da and an acidic pI of 4.6. The gene was successfully cloned and overexpressed in A. niger to yield 1.25 g liter(-1), i.e., 330-fold higher than the production of wild-type strain A. niger CIRM BRFM131. The histidine-tagged recombinant ChlE protein was purified to homogeneity via a single chromatography step, and its main biochemical properties were characterized. The molecular size of the protein checked by mass spectroscopy was 74,553 Da, suggesting the presence of glycosylation. ChlE is assembled in a tetrameric form with several acidic isoforms with pIs of around 4.55 and 5.2. Other characteristics, such as optimal pH and temperature, were found to be similar to those determined for the previously characterized chlorogenic acid hydrolase of A. niger CIRM BRFM 131. However, there was a significant temperature stability difference in favor of the recombinant protein. ChlE exhibits a catalytic efficiency of 12.5 x 10(6) M(-1) s(-1) toward chlorogenic acid (CGA), and its ability to release caffeic acid from CGA present in agricultural by-products such as apple marc and coffee pulp was clearly demonstrated, confirming the high potential of this enzyme.



        

Title: Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R and Stam H <59 more author(s)> Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H (- 59)
Ref: Nat Biotechnol, 25:221, 2007 : PubMed
Abstract


ESTHER: Pel_2007_Nat.Biotechnol_25_221
PubMedSearch: Pel 2007 Nat.Biotechnol 25 221
PubMedID: 17259976
Gene_locus related to this paper: aspna-g3yal2, aspnc-a2q8r7, aspnc-a2q814, aspnc-a2qb93, aspnc-a2qbd3, aspnc-a2qbh3, aspnc-a2qbx7, aspnc-a2qdj6, aspnc-a2qe77, aspnc-a2qf54, aspnc-a2qfe9, aspnc-a2qg33, aspnc-a2qgj6, aspnc-a2qgm6, aspnc-a2qh52, aspnc-a2qh76, aspnc-a2qh85, aspnc-a2qhe2, aspnc-a2qi32, aspnc-a2qib2, aspnc-a2qk14, aspnc-a2ql23, aspnc-a2ql89, aspnc-a2ql90, aspnc-a2qla0, aspnc-a2qlz0, aspnc-a2qm14, aspnc-a2qmk5, aspnc-a2qms0, aspnc-a2qn29, aspnc-a2qn56, aspnc-a2qn70, aspnc-a2qnw9, aspnc-a2qr21, aspnc-a2qs22, aspnc-a2qt50, aspnc-a2qti9, aspnc-a2qtz0, aspnc-a2quc1, aspnc-a2qw06, aspnc-a2qwz6, aspnc-a2qx92, aspnc-a2qyf0, aspnc-a2qys7, aspnc-a2qz72, aspnc-a2qzn6, aspnc-a2qzr0, aspnc-a2qzs1, aspnc-a2qzx0, aspnc-a2qzx4, aspnc-a2r0p4, aspnc-a2r0u0, aspnc-a2r1p3, aspnc-a2r1r5, aspnc-a2r2i5, aspnc-a2r2l0, aspnc-a2r3s8, aspnc-a2r4c0, aspnc-a2r4j8, aspnc-a2r5r4, aspnc-a2r6g3, aspnc-a2r6h5, aspnc-a2r6h8, aspnc-a2r7q1, aspnc-a2r8r3, aspnc-a2r8z3, aspnc-a2r9y8, aspnc-a2r032, aspnc-a2r040, aspnc-a2r273, aspnc-a2r496, aspnc-a2r502, aspnc-a2ra07, aspnc-a2rap4, aspnc-a2raq2, aspnc-a2rav1, aspnc-a5aaf4, aspnc-a5ab63, aspnc-a5abc6, aspnc-a5abe5, aspnc-a5abe8, aspnc-a5abf0, aspnc-a5abh9, aspnc-a5abk1, aspnc-a5abt2, aspnc-a5abz1, aspnc-atg15, aspnc-axe1, aspnc-cuti1, aspnc-cuti2, aspnc-faec, aspng-a2q8w0, aspng-a2qs46, aspng-a2qst4, aspng-a2qv27, aspng-a2qzk9, aspng-a2r0p8, aspng-a2r225, aspng-DAPB, aspng-DPP5, aspng-faeb, aspni-APSC, aspni-EstA, aspni-FAEA, aspni-PAPA, aspkw-g7y0v7, aspnc-a2qt47, aspnc-a2qt66, aspnc-a2r199, aspnc-a2r871, aspnc-a2qbp6, aspnc-a2qqa1, aspnc-a2qt70, aspna-g3y5a6, aspna-g3xpw9, aspnc-a2qw57, aspaw-a0a401kcz4, aspna-alba, aspnc-kex1, aspnc-cbpya, aspnc-a2qbg8

Abstract

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.



        

Title: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI
Ref: Proc Natl Acad Sci U S A, 104:10643, 2007 : PubMed
Abstract


ESTHER: Samuel_2007_Proc.Natl.Acad.Sci.U.S.A_104_10643
PubMedSearch: Samuel 2007 Proc.Natl.Acad.Sci.U.S.A 104 10643
PubMedID: 17563350
Gene_locus related to this paper: mets3-a5ujk2, metsm-d2zrn4

Abstract

The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. Metagenomic studies of the gut microbial communities of genetically obese mice and their lean littermates have shown that the former contain an enhanced representation of genes involved in polysaccharide degradation, possess more archaea, and exhibit a greater capacity to promote adiposity when transplanted into germ-free recipients. These findings have led to the hypothesis that M. smithii may be a therapeutic target for reducing energy harvest in obese humans. To explore this possibility, we have sequenced its 1,853,160-bp genome and compared it to other human gut-associated M. smithii strains and other Archaea. We have also examined M. smithii's transcriptome and metabolome in gnotobiotic mice that do or do not harbor Bacteroides thetaiotaomicron, a prominent saccharolytic bacterial member of our gut microbiota. Our results indicate that M. smithii is well equipped to persist in the distal intestine through (i) production of surface glycans resembling those found in the gut mucosa, (ii) regulated expression of adhesin-like proteins, (iii) consumption of a variety of fermentation products produced by saccharolytic bacteria, and (iv) effective competition for nitrogenous nutrient pools. These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota.



        

Title: Evolution of symbiotic bacteria in the distal human intestine
Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P and Gordon JI <9 more author(s)> Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI (- 9)
Ref: PLoS Biol, 5:e156, 2007 : PubMed
Abstract


ESTHER: Xu_2007_PLoS.Biol_5_e156
PubMedSearch: Xu 2007 PLoS.Biol 5 e156
PubMedID: 17579514
Gene_locus related to this paper: 9bace-b6w170, 9bace-c6z6f2, 9bace-e1z049, 9porp-c7xbp3, 9porp-c7xci2, 9porp-c7xdx2, bacv8-a6kwf6, bacv8-a6kzc1, bacv8-a6kze8, bacv8-a6l0d9, bacv8-a6l1d0, bacv8-a6l1u9, bacv8-a6l7p9, bacv8-a6l7w1, bacv8-a6l018, bacv8-a6l378, bacv8-a6l415, bacv8-a6l715, pard8-a6lc23, pard8-a6lca7, pard8-a6ld87, pard8-a6le10, pard8-a6le63, pard8-a6lfj2, pard8-a6lgh2, pard8-a6lgi6, pard8-a6lgn7, pard8-a6lhe1, pard8-a6li91, bacv8-a6l3w9

Abstract

The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.



        

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
Abstract


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, poptr-a0a2k1xzs5, poptr-b9gga9, poptr-b9guw6, poptr-b9hff2

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: Cloning and sequence analysis of the ces10 gene encoding a Sphingomonas paucimobilis esterase
Videira PA, Fialho AM, Marques AR, Coutinho PM, Sa-Correia I
Ref: Applied Microbiology & Biotechnology, 61:517, 2003 : PubMed
Abstract


ESTHER: Videira_2003_Appl.Microbiol.Biotechnol_61_517
PubMedSearch: Videira 2003 Appl.Microbiol.Biotechnol 61 517
PubMedID: 12764567
Gene_locus related to this paper: sphpa-Ces10

Abstract

The ces10 gene of the gellan gum-producing strain Sphingomonas paucimobilis ATCC 31461 was cloned and sequenced. Multi-sequence alignment of the deduced protein indicated that Ces10 belongs to the serine hydrolase family with a potential catalytic triad comprising Ser(153) (within the G-X-S-X-G consensus sequence), His(75) and Asp(125). The mixed block results obtained following pattern search and the low identities detected in a BLAST analysis indicate that Ces10 is significantly different from other characterised bacterial esterases/lipases. Nevertheless, the Ces10 amino acid sequence showed 45% similarity with Rhodococcus sp. heroin esterase and 48% with Bacillus subtilis p-nitrobenzyl esterase. Ces10, with a predicted molecular mass of 30,641 Da, was overproduced in Escherichia coli and purified to homogeneity in a histidine-tagged form. Enzyme assays using p-nitrophenyl-esters (p-NP-esters) with different acyl chain-lengths as the substrate confirmed the anticipated esterase activity. Ces10 exhibited a marked preference for short-chain fatty acids, yielding the highest activity with p-NP-propionate (optimal pH 7.4, optimal temperature 37 degrees C).