Author Report for: Ohm RANo contact information in database for Ohm RA
Varga T, Krizsan K, Foldi C, Dima B, Sanchez-Garcia M, Sanchez-Ramirez S, Szollosi GJ, Szarkandi JG, Papp V and Nagy LG <52 more author(s)> Varga T, Krizsan K, Foldi C, Dima B, Sanchez-Garcia M, Sanchez-Ramirez S, Szollosi GJ, Szarkandi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonin V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Damon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasinski D, Kautmanova I, Kiss B, Kocsube S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukacs Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Racz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomsovsky M, Tulloss RE, Uehling J, Grigoriev IV, Vagvolgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG (- 52) Ref: Nat Ecol Evol, 3:668, 2019 : PubMed ESTHER: Varga_2019_Nat.Ecol.Evol_3_668 PubMedSearch: Varga 2019 Nat.Ecol.Evol 3 668 PubMedID: 30886374 Gene_locus related to this paper: 9aphy-a0a5c3ppg9, 9aphy-a0a371d1b5, 9agam-a0a5c3ngv5, 9aphy-a0a5c3nsu3, 9agar-a0a4s8mrh7, 9agar-a0a4s8mil0 Abstract Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding. Title: Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi Knapp DG, Nemeth JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A and Kovacs GM <6 more author(s)> Knapp DG, Nemeth JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A, Nolan M, Ohm RA, Tamas L, Grigoriev IV, Spatafora JW, Nagy LG, Kovacs GM (- 6) Ref: Sci Rep, 8:6321, 2018 : PubMed ESTHER: Knapp_2018_Sci.Rep_8_6321 PubMedSearch: Knapp 2018 Sci.Rep 8 6321 PubMedID: 29679020 Gene_locus related to this paper: 9pleo-a0a2v1dn29, 9helo-a0a2v1c5l1, 9pleo-a0a2v1dti3, 9helo-a0a2v1bts1, 9helo-a0a2v1cbe5, 9pleo-a0a2v1cxz2, 9pleo-a0a2v1d1n3, 9pleo-a0a2v1db80, 9pleo-a0a2v1ddg5, 9pleo-a0a2v1dij1, 9pleo-a0a2v1dp20, 9pleo-a0a2v1e6x2, 9pleo-a0a2v1ee64, 9helo-a0a2v1cbn2, 9helo-a0a2v1b581, 9pleo-a0a2v1e5g2, corcc-a0a2t2nt04, 9helo-a0a2v1buk5 Abstract Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle. Title: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, LaButti K, Lipzen A and Pujade-Renaud V <7 more author(s)> Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, LaButti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V (- 7) Ref: Front Microbiol, 9:276, 2018 : PubMed ESTHER: Lopez_2018_Front.Microbiol_9_276 PubMedSearch: Lopez 2018 Front.Microbiol 9 276 PubMedID: 29551995 Gene_locus related to this paper: corcc-a0a2t2nss3, corcc-a0a2t2n5c6, corcc-a0a2t2n3a1, corcc-a0a2t2p617, corcc-a0a2t2nt04, corcc-a0a2t2n262 Abstract Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, and Botrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms. Title: Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A and Perotto S <18 more author(s)> Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S (- 18) Ref: New Phytol, 217:1213, 2018 : PubMed ESTHER: Martino_2018_New.Phytol_217_1213 PubMedSearch: Martino 2018 New.Phytol 217 1213 PubMedID: 29315638 Gene_locus related to this paper: amore-a0a2t3axk4, amore-a0a2t3avs4, amore-a0a2t3ay04, amore-a0a2t3aph0 Abstract Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes. Title: Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies Wu B, Xu Z, Knudson A, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C and Hibbett D <7 more author(s)> Wu B, Xu Z, Knudson A, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, Gibbons J, Hibbett D (- 7) Ref: Genome Biol Evol, 10:3250, 2018 : PubMed ESTHER: Wu_2018_Genome.Biol.Evol_10_3250 PubMedSearch: Wu 2018 Genome.Biol.Evol 10 3250 PubMedID: 30398645 Gene_locus related to this paper: 9aphy-a0a5c2t2q2 Abstract Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi. Title: Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins de Bekker C, Ohm RA, Evans HC, Brachmann A, Hughes DP Ref: Sci Rep, 7:12508, 2017 : PubMed ESTHER: de Bekker_2017_Sci.Rep_7_12508 PubMedSearch: de Bekker 2017 Sci.Rep 7 12508 PubMedID: 28970504 Gene_locus related to this paper: 9hypo-a0a2a9pgw2, 9hypo-a0a2a9pfj9, 9hypo-a0a2a9pdz6 Abstract Much can be gained from revealing the mechanisms fungal entomopathogens employ. Especially intriguing are fungal parasites that manipulate insect behavior because, presumably, they secrete a wealth of bioactive compounds. To gain more insight into their strategies, we compared the genomes of five ant-infecting Ophiocordyceps species from three species complexes. These species were collected across three continents, from five different ant species in which they induce different levels of manipulation. A considerable number of (small) secreted and pathogenicity-related proteins were only found in these ant-manipulating Ophiocordyceps species, and not in other ascomycetes. However, few of those proteins were conserved among them, suggesting that several different methods of behavior modification have evolved. This is further supported by a relatively fast evolution of previously reported candidate manipulation genes associated with biting behavior. Moreover, secondary metabolite clusters, activated during biting behavior, appeared conserved within a species complex, but not beyond. The independent co-evolution between these manipulating parasites and their respective hosts might thus have led to rather diverse strategies to alter behavior. Our data indicate that specialized, secreted enterotoxins may play a major role in one of these strategies. Title: Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C and Banfield JF <6 more author(s)> Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF (- 6) Ref: Front Microbiol, 7:238, 2016 : PubMed ESTHER: Mosier_2016_Front.Microbiol_7_238 PubMedSearch: Mosier 2016 Front.Microbiol 7 238 PubMedID: 26973616 Gene_locus related to this paper: 9pezi-a0a150vf31, 9pezi-a0a150uua7, 9pezi-a0a150uvr8, 9pezi-a0a150uzg0, 9pezi-a0a150v0d4, 9pezi-a0a150v5h7, 9pezi-a0a150v662, 9pezi-a0a150v8z3, 9pezi-a0a150v9v5, 9pezi-a0a150vc68, 9pezi-a0a150vcp1, 9pezi-a0a150vd70, 9pezi-a0a150vda0, 9pezi-a0a150vgv5, 9pezi-a0a150vil1, 9pezi-a0a150uu68, 9pezi-a0a150vas8, 9pezi-a0a150vji1, 9pezi-a0a150vii2 Abstract The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches. Title: Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J and Hibbett DS <11 more author(s)> Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, LaButti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS (- 11) Ref: Molecular Biology Evolution, 33:959, 2016 : PubMed ESTHER: Nagy_2016_Mol.Biol.Evol_33_959 PubMedSearch: Nagy 2016 Mol.Biol.Evol 33 959 PubMedID: 26659563 Gene_locus related to this paper: 9homo-a0a164swv2, 9homo-a0a164tl22, 9homo-a0a164vkv1, 9homo-a0a164y4j9, 9homo-a0a164y4l9, 9homo-a0a164ytj2, 9homo-a0a164zeu0, exigl-a0a165as65, exigl-a0a165ck85, 9basi-a0a165cm83, 9aphy-a0a165dbf1, 9aphy-a0a165dbf3, 9basi-a0a165dcb7, 9aphy-a0a165ddj9, exigl-a0a165dj22, exigl-a0a165dmd7, 9aphy-a0a165egr5, 9basi-a0a165ekd3, 9basi-a0a165enc9, 9basi-a0a165end6, 9basi-a0a165epz3, 9basi-a0a165eq46, 9basi-a0a165eq95, 9basi-a0a165eqk7, 9basi-a0a165eup2, 9aphy-a0a165fb02, 9aphy-a0a165fmr9, 9aphy-a0a165g3p1, 9basi-a0a165g673, 9basi-a0a165g6g2, 9aphy-a0a165gec2, 9basi-a0a165gfp7, 9aphy-a0a165h505, 9aphy-a0a165hd72, 9aphy-a0a165hrk1, exigl-a0a165hzc8, 9basi-a0a165i2y7, 9basi-a0a165iru3, 9basi-a0a165is19, 9basi-a0a165is40, exigl-a0a165j2r4, exigl-a0a165j754, 9basi-a0a165jg92, 9basi-a0a165jgb0, exigl-a0a165ke04, exigl-a0a165kpb0, exigl-a0a165l7g6, 9aphy-a0a165lux8, 9aphy-a0a165luy2.1, 9aphy-a0a165luy2.2, exigl-a0a165m310, 9aphy-a0a165mxa5, 9aphy-a0a165mxc8, 9aphy-a0a165mxe4, exigl-a0a165mz73, 9homo-a0a165nfz4, 9homo-a0a165ng04, 9aphy-a0a165nry3, 9homo-a0a165ntf3, 9homo-a0a165p2a0, 9aphy-a0a165ph74, 9homo-a0a165phz5, exigl-a0a165pm12, exigl-a0a165pu90, exigl-a0a165puh2, 9aphy-a0a165q9t4, 9homo-a0a165qeb7, 9homo-a0a165qeh8, 9aphy-a0a165qqm2, 9aphy-a0a165quj0, 9aphy-a0a165qul3, exigl-a0a165qxy0, 9aphy-a0a165r6t2, 9aphy-a0a165r8g4, 9aphy-a0a165tfc7, 9homo-a0a165tgm2, 9homo-a0a165tzv4, 9homo-a0a165tzw4, 9homo-a0a165uez3, 9homo-a0a165ugh4, 9homo-a0a165ugp4, 9homo-a0a165ugq6, 9homo-a0a165uh51, 9aphy-a0a165umj9, 9homo-a0a165us14, 9homo-a0a165xi11, 9homo-a0a165xmw5, 9homo-a0a165xmx9, 9homo-a0a165xsk7, 9homo-a0a165y3k8, 9homo-a0a165yhg3, 9homo-a0a165ymb3, 9homo-a0a165yt77, 9homo-a0a165ytu4, 9homo-a0a165zr30, 9homo-a0a166a1g9, 9homo-a0a166a1h1, exigl-a0a166abe4, 9homo-a0a166akq6, exigl-a0a166al33, 9homo-a0a166arm1, 9homo-a0a166as45, 9homo-a0a166as65, 9homo-a0a166as77, exigl-a0a166auh4, 9homo-a0a166azk8, exigl-a0a166azz6, 9homo-a0a166bss2, 9homo-a0a166bsu9, 9homo-a0a166bui6, 9homo-a0a166crl5, 9homo-a0a166d8q4, 9homo-a0a166dss7, 9homo-a0a166dtg8, 9homo-a0a166du49, 9homo-a0a166du64, 9homo-a0a166e1z2, 9homo-a0a166eec5, 9homo-a0a166eux5, 9homo-a0a166evw5, 9homo-a0a166ey75, 9homo-a0a166eyq0, 9homo-a0a166ez78, 9homo-a0a166eze7, 9homo-a0a166fh25, 9homo-a0a166g4k8, 9homo-a0a166gct1, 9homo-a0a166gf56, 9homo-a0a166gsr8, 9homo-a0a166j6i1, 9homo-a0a166jiu0, 9homo-a0a166jr36, 9homo-a0a166kia8, 9homo-a0a166ks21, 9homo-a0a166kvn8, 9homo-a0a166kxf0, 9homo-a0a166kxg2, 9homo-a0a166lcs7, 9homo-a0a166lw48, 9homo-a0a166lyz4, 9homo-a0a166puu7.1, 9homo-a0a166puu7.2, 9homo-a0a166puz0, 9homo-a0a166pv75, 9homo-a0a166pva0, 9homo-a0a166pvf7, 9homo-a0a166px11, 9homo-a0a166q635, 9basi-a0a167gl88, 9basi-a0a167gl97, 9basi-a0a167gla5, 9basi-a0a167hca0, 9basi-a0a167hrt3, 9basi-a0a167hru7, 9basi-a0a167k219, 9basi-a0a167k232, 9basi-a0a167k265, 9basi-a0a167l6m6, 9basi-a0a167lrl7, 9basi-a0a167lt70, 9basi-a0a167mtk7, 9basi-a0a167n1z0, 9basi-a0a167p9x5, 9basi-a0a167qks1, 9basi-a0a167qkt4, 9basi-a0a167qky5, 9basi-a0a167qln8, 9basi-a0a167rpp7, 9homo-a0a167u8e3, 9homo-a0a167v1m8, 9homo-a0a166hqx0, 9homo-a0a166l842, exigl-a0a165n4f2, exigl-a0a165q512, 9agam-a0a165nq75, 9agam-a0a166cv75, 9agam-a0a165mvt4, 9agam-a0a164t8q2, 9agam-a0a166flp0 Abstract Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot. Title: Comparative genomics of biotechnologically important yeasts Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Goker M, Salamov AA, Wisecaver JH, Long TM and Jeffries TW <29 more author(s)> Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Goker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW (- 29) Ref: Proc Natl Acad Sci U S A, 113:9882, 2016 : PubMed ESTHER: Riley_2016_Proc.Natl.Acad.Sci.U.S.A_113_9882 PubMedSearch: Riley 2016 Proc.Natl.Acad.Sci.U.S.A 113 9882 PubMedID: 27535936 Gene_locus related to this paper: wicaa-a0a1e3nx95, cybjn-a0a1e4s739, 9asco-a0a1q2yku6, ogapd-w1qjr8, 9asco-a0a1e3pdp5, lipst-a0a1e3qdq0, 9asco-a0a1e4tg55 Abstract Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation. Title: Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C and Berbee ML <4 more author(s)> Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML (- 4) Ref: Genome Biol Evol, 7:1590, 2015 : PubMed ESTHER: Chang_2015_Genome.Biol.Evol_7_1590 PubMedSearch: Chang 2015 Genome.Biol.Evol 7 1590 PubMedID: 25977457 Gene_locus related to this paper: gonpr-a0a139axi8 Abstract As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya. Title: Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J and Hibbett DS <10 more author(s)> Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J, Lipzen A, Tritt A, Sun H, Haridas S, LaButti K, Ohm RA, Kues U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS (- 10) Ref: Fungal Genet Biol, 76:78, 2015 : PubMed ESTHER: Floudas_2015_Fungal.Genet.Biol_76_78 PubMedSearch: Floudas 2015 Fungal.Genet.Biol 76 78 PubMedID: 25683379 Gene_locus related to this paper: 9agar-a0a0d6zyq5, 9agar-a0a0d7a2p9, 9agar-a0a0d7a2v2, 9agar-a0a0d7abt2, 9agar-a0a0d7acd3, 9agar-a0a0d7acx0, 9agar-a0a0d7acx9, 9agar-a0a0d7adg2, 9agar-a0a0d7a6d0, 9agar-a0a0d7aen7, 9agar-a0a0d7aez7, 9agar-a0a0d7ahq5, 9agar-a0a0d7akr6, 9agar-a0a0d7al29, 9agar-a0a0d7an16, 9agar-a0a0d7ann7, 9agar-a0a0d7anv1, 9homo-a0a0d7atv2, 9homo-a0a0d7ay28, 9homo-a0a0d7ayz7, 9homo-a0a0d7b1w8, 9homo-a0a0d7b2p0, 9homo-a0a0d7b4n4, 9homo-a0a0d7b624, 9homo-a0a0d7b7r3, 9homo-a0a0d7b7w3, 9homo-a0a0d7bac5, 9homo-a0a0d7bav7, 9homo-a0a0d7bbx7, 9homo-a0a0d7bdn7, 9homo-a0a0d7bgj9, 9homo-a0a0d7biw2, 9homo-a0a0d7bqi1, 9homo-a0a0d7bv80, 9agar-a0a0d7b6f6, 9agar-a0a0d7b976, 9agar-a0a0d7aeu9, 9agar-a0a0d7ag53, 9agar-a0a0d7b8a5 Abstract Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. Title: Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation de Bekker C, Ohm RA, Loreto RG, Sebastian A, Albert I, Merrow M, Brachmann A, Hughes DP Ref: BMC Genomics, 16:620, 2015 : PubMed ESTHER: de Bekker_2015_BMC.Genomics_16_620 PubMedSearch: de Bekker 2015 BMC.Genomics 16 620 PubMedID: 26285697 Gene_locus related to this paper: 9hypo-a0a0l9sfr4, 9hypo-a0a2a9pgw2, 9hypo-a0a2a9pfj9, 9hypo-a0a2a9pdz6 Abstract BACKGROUND: Adaptive manipulation of animal behavior by parasites functions to increase parasite transmission through changes in host behavior. These changes can range from slight alterations in existing behaviors of the host to the establishment of wholly novel behaviors. The biting behavior observed in Carpenter ants infected by the specialized fungus Ophiocordyceps unilateralis s.l. is an example of the latter. Though parasitic manipulation of host behavior is generally assumed to be due to the parasite's gene expression, few studies have set out to test this. Title: Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species Gostincar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H and Gunde-Cimerman N <7 more author(s)> Gostincar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H, Han J, Sharma A, Chiniquy J, Ngan CY, Lipzen A, Barry K, Grigoriev IV, Gunde-Cimerman N (- 7) Ref: BMC Genomics, 15:549, 2014 : PubMed ESTHER: Gostincar_2014_BMC.Genomics_15_549 PubMedSearch: Gostincar 2014 BMC.Genomics 15 549 PubMedID: 24984952 Gene_locus related to this paper: aurpu-a0a1a7mdx5, 9pezi-a0a074w0m0, 9pezi-a0a074wgq7, aurpu-a0a074xfg8, 9pezi-a0a074y586, 9pezi-a0a074yqf6, 9pezi-a0a074w5k8, aurpu-a0a074x6a3, 9pezi-a0a074z3s4, 9pezi-a0a074x4q0, 9pezi-a0a074w2e2, 9pezi-a0a074x294, aurpu-a0a074y1y2, aurpu-a0a074x9w9, 9pezi-a0a074ydw7, 9pezi-a0a074w1z9, 9pezi-a0a074wvx0, 9pezi-a0a074vkc4, 9pezi-a0a074y2z2, 9pezi-a0a074vlb9, aurpu-a0a074x490, 9pezi-a0a074ydn0, 9pezi-a0a074wng0, 9pezi-a0a074yhi1, 9pezi-a0a074yp94, 9pezi-a0a074wbe1, 9pezi-a0a074wm90, 9pezi-a0a074ww95, aurpu-a0a074xg41, aurpu-a0a074xtu4, 9pezi-a0a074y8g8, aurpu-a0a074ysb8, 9pezi-a0a074zem7, 9pezi-a0a074yvw8, 9pezi-a0a074w278, aurpu-a0a074xxz9, 9pezi-a0a074y9f0, aurpu-a0a074xzv0, 9pezi-a0a074wce5, 9pezi-a0a074wmz5, 9pezi-a0a074vr83, 9pezi-a0a074w4l5, 9pezi-a0a074wwv4, 9pezi-a0a074w5f4, aurpu-a0a074xir3, aurpu-a0a074xnm6, 9pezi-a0a074zhr2, 9pezi-a0a074vzq8, 9pezi-a0a074web5, aurpu-a0a074xz32, 9pezi-a0a074ybl0, aurpu-a0a074xl81, 9pezi-a0a074vaq7, 9pezi-a0a074wuj9, aurpu-a0a074xyu0, 9pezi-a0a074vfi8, 9pezi-a0a074wih8, aurpu-a0a074xj03, 9pezi-a0a074vze0, 9pezi-a0a074w5u8, 9pezi-a0a074wui5, 9pezi-a0a074xhu0, aurpu-a0a074xyg1, 9pezi-a0a074yct6, 9pezi-a0a074zd60, 9pezi-a0a074w686, aurpu-a0a074xr93, 9pezi-a0a074y1r2, 9pezi-a0a074z801, 9pezi-a0a074y6a8, 9pezi-a0a074vg30, aurpu-a0a074wzm8, 9pezi-a0a074y7g9, 9pezi-a0a074vwd1, 9pezi-a0a074whl7, aurpu-a0a074x6c3, 9pezi-a0a074yak1, aurpu-a0a074x5y4, 9pezi-a0a074yaq1, aurpu-a0a074xm87, 9pezi-a0a074wgg7, 9pezi-a0a074vky7, aurpu-a0a074xpr5, 9pezi-a0a074zrg4, 9pezi-a0a074w1f9, aurpu-a0a074xft8, 9pezi-a0a074y5i5, aurpu-a0a074xla0, 9pezi-a0a074w5n7, 9pezi-a0a074wey0, aurpu-a0a074y3b0, 9pezi-a0a074vrn9, 9pezi-a0a074zgu9, aurpu-a0a074xlv7, 9pezi-a0a074wgb6, 9pezi-a0a074wgj7, 9pezi-a0a074vrg4, 9pezi-a0a074ya42, 9pezi-a0a074xnr8, aurpu-a0a074x443, 9pezi-a0a074yex2, 9pezi-a0a074xu89, aurpu-a0a074xxq7, 9pezi-a0a074vih4, aurse-a0a074ydf4, aurse-a0a074yt75, aurpu-a0a074y000 Abstract BACKGROUND: Aureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and the antimycotic aureobasidin A, and as a biocontrol agent in agriculture. It can cause opportunistic human infections, and it inhabits various extreme environments. To promote the understanding of these traits, we performed de-novo genome sequencing of the four varieties of A. pullulans. Title: Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, Albu S, Boyd A, Chow J and Aime MC <8 more author(s)> Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, Albu S, Boyd A, Chow J, Clum A, Heller G, Lipzen A, Nolan M, Sandor L, Zvenigorodsky N, Grigoriev IV, Spatafora JW, Aime MC (- 8) Ref: New Phytol, 202:554, 2014 : PubMed ESTHER: Toome_2014_New.Phytol_202_554 PubMedSearch: Toome 2014 New.Phytol 202 554 PubMedID: 24372469 Gene_locus related to this paper: mixos-g7dyk5, mixos-g7eay5 Abstract Mixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed the genome of M. osmundae, focusing on genes that may provide some insight into its mode of pathogenicity and reproductive biology. Mixia osmundae has the smallest plant pathogenic basidiomycete genome sequenced to date, at 13.6 Mb, with very few repeats, high gene density, and relatively few significant gene family gains. The genome shows that the yeast state of M. osmundae is haploid and the lack of segregation of mating genes suggests that the spores produced on Osmunda spp. fronds are probably asexual. However, our finding of a complete complement of mating and meiosis genes suggests the capacity to undergo sexual reproduction. Analyses of carbohydrate active enzymes suggest that this fungus is a biotroph with the ability to break down several plant cell wall components. Analyses of publicly available sequence data show that other Mixia members may exist on other plant hosts and with a broader distribution than previously known. Title: Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J and Turgeon BG <20 more author(s)> Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG (- 20) Ref: PLoS Genet, 9:e1003233, 2013 : PubMed ESTHER: Condon_2013_PLoS.Genet_9_E1003233 PubMedSearch: Condon 2013 PLoS.Genet 9 E1003233 PubMedID: 23357949 Gene_locus related to this paper: cocsn-m2rnc6, coch5-m2tnl8, coch4-n4xap8, sett2-r0j560, cocsn-m2thl9, coch5-m2v1s2, coch4-n4xzy1, cocsn-m2sqr3, cocsn-m2rnk8, coch4-n4xdv7, coch5-m2uds0, coch5-m2um94, sett2-r0i8c5, coch4-n4wlc8, coch4-n4x9p3, cocsn-m2rh47, cocsn-m2qz08, sett2-r0jqq6, sett2-r0imb6, coch4-n4x7u3, cocsn-m2rv02, cocsn-m2sy95, coch5-m2ubd5, cocsn-m2t3d2, sett2-r0kl84, sett2-r0jts7, coch4-n4x2h3, sett2-r0jxt9, coch4-n4x7r9, cocsn-m2sh75, cocsn-m2t5z2, coch5-m2ucf6, sett2-r0k664, cocsn-m2t3q1, sett2-r0k4b4, cocsn-m2t4i1, coch5-m2th93, cocsn-m2svm8, cocsn-m2s6q4, cocsn-m2s5h5, coch4-n4xf94, sett2-r0kdl8, cocsn-m2qvi9, sett2-r0kfg6, cocsn-m2szq4, sett2-r0j437, coch4-n4x7j4, coch5-m2twk3, coch5-m2usf2, sett2-r0kjt7, sett2-r0k7y2, cocsn-m2th03, sett2-r0iy92, sett2-r0kbr9, sett2-r0k997, coch5-m2sik6, sett2-r0jzj5, cocsn-m2r0j6, coch4-n4x6a4, cocsn-m2s7a5, cocsn-m2sv79, sett2-r0knx4, sett2-r0ksh8, sett2-r0ip86, cocmi-w6yyy3, cocsn-m2sqe4, coch4-n4xzc8, cocvi-w7eyp1, cocmi-w6zf65, cocvi-w7er28, cocca-w6yw25, cocvi-w7e2g6, cocmi-w6z7k5, cocca-w6ys73, cocca-w6ydq2, cocca-w6y7i5, cocmi-w6yyr0, cocca-w6yh47, cocmi-w6zju4, cocca-w6ynq5, cocmi-w6zm44, cocca-w6xx85, cocmi-w6z011, cocca-w6yre4, cocmi-w6z9l3, cocca-w6yfp7, cocmi-w6zlc2, cocca-w6yar2, cocmi-w6yjr7, cocca-w6yhs1, cocca-w6xux8, cocmi-w6z9s8, cocca-w6yq27, cocmi-w6zqk9, cocca-w6xq19, cocca-w6y1r6, cocca-w6ygj2, cocmi-w6zgn4, cocca-w6ybh2, cocmi-w6z710, cocca-w6yk86, cocmi-w6zjz2, cocmi-w6z7f2, cocca-w6xn57, cocca-w6ybq4, cocmi-w6yxn5, cocmi-w6zf08, cocsn-m2rtg8, cocmi-w6zuj7, cocca-w6xtb2, cocca-w6yk97, coch5-m2t2x3, cocmi-w6z646, cocsn-m2sze4, sett2-r0kjg6, cocmi-w6yrn5, sett2-r0k5q0, cocvi-w7ezb7, sett2-r0jtm1, cocmi-w6ywa1, cocsn-m2t3e8, coch5-m2ulw5, coch5-m2urw9, sett2-r0knn5, cocmi-w6ysb2, cocvi-w7eag7, cocca-w6y1v2, sett2-r0i9k2, coch5-m2uul8, cocsn-m2sl21 Abstract The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25x higher than those between inbred lines and 50x lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. Title: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW and Hibbett DS <61 more author(s)> Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Gorecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kues U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Duenas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS (- 61) Ref: Science, 336:1715, 2012 : PubMed ESTHER: Floudas_2012_Science_336_1715 PubMedSearch: Floudas 2012 Science 336 1715 PubMedID: 22745431 Gene_locus related to this paper: aurde-j0d098, aurde-j0dc31, glota-s7rlc1, fompi-s8f7s4, dacsp-m5fpg2, dicsq-r7sm16, dacsp-m5g7q5, dacsp-m5fr12, glota-s7q5w3, fompi-s8f826.1, fompi-s8f826.2, dicsq-r7sy09, glota-s7rt87, dicsq-r7t032, glota-s7rym7, fompi-s8fiv2, dacsp-m5gda3.2, dicsq-r7swi6, dacsp-m5frf2, fompi-s8ebb6, dicsq-r7sln3, dicsq-r7sya6, dacsp-m5g7g1, dicsq-r7syx7, dicsq-r7sx57, dacsp-m5fps7, glota-s7pwi7, dicsq-r7swj6, fompi-s8ejq6, dicsq-r7spc3, glota-s7q258, dacsp-m5ft65, glota-s7q3m7, fompi-s8dkc7, glota-s7q1z1, fompi-s8eqi2, glota-s7q1z8, fompi-s8du50, dacsp-m5gg33, dacsp-m5g3a7, fompi-s8ecd7, fompi-s8dps1, dacsp-m5fwr0, dicsq-r7sub7, glota-s7q8k9, fompi-s8ffc3, dacsp-m5g2f9, fompi-s8ecc2, dacsp-m5g868, fompi-s8f890, dicsq-r7t1a8, fompi-s8ebx4, fompi-s8eb97, glota-s7q222, glota-s7puf0, fompi-s8f6v9, dacsp-m5g0z2, dacsp-m5gdh9, fompi-s8fb37, dacsp-m5fy91, glota-s7q5v6, fompi-s8fl44, dicsq-r7stv9, dicsq-r7szk3, fompi-s8epq9, glota-s7rh56, dacsp-m5gbt1, punst-r7s3x9, punst-r7s0t5, glota-s7q312, glota-s7rhh6, dicsq-r7t117, dicsq-r7slz3 Abstract Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period. Title: 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 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: Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B and Grigoriev IV <18 more author(s)> Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV (- 18) Ref: PLoS Pathog, 8:e1003037, 2012 : PubMed ESTHER: Ohm_2012_PLoS.Pathog_8_E1003037 PubMedSearch: Ohm 2012 PLoS.Pathog 8 E1003037 PubMedID: 23236275 Gene_locus related to this paper: mycpj-q30dw8, sphms-m3db71, bauco-m2n3p9, cocsn-m2rnc6, coch5-m2tnl8, coch4-n4xap8, sett2-r0j560, bauco-m2lw45, cocsn-m2thl9, bauco-m2nan7, sphms-m3asf7, coch5-m2v1s2, mycfi-m3am36, coch4-n4xzy1, mycfi-m3b3x0, cocsn-m2sqr3, cocsn-m2rnk8, mycp1-n1pnd6, bauco-m2n7y7, coch4-n4xdv7, coch5-m2uds0, coch5-m2um94, sett2-r0i8c5, coch4-n4wlc8, coch4-n4x9p3, cocsn-m2rh47, cocsn-m2qz08, sett2-r0jqq6, mycfi-m2yiq2, sett2-r0imb6, sphms-m3b727, coch4-n4x7u3, cocsn-m2rv02, cocsn-m2sy95, coch5-m2ubd5, mycp1-n1per0, mycp1-n1pg49, mycfi-n1q8u1, mycp1-n1pwj1, mycp1-n1pcl8, bauco-m2n330, cocsn-m2t3d2, mycfi-m3b223, sett2-r0kl84, bauco-m2lu86, mycfi-m3b1s8, sett2-r0jts7, mycfi-m3amn9, bauco-m2nf03, mycfi-m3a015, sphms-n1qgv4, coch4-n4x2h3, mycp1-m2y2b1, sett2-r0jxt9, mycfi-m2zg05, sphms-m3cr09, coch4-n4x7r9, mycfi-m2yip7, mycp1-n1pwu7, cocsn-m2sh75, cocsn-m2t5z2, coch5-m2ucf6, sphms-m3c9s8, sphms-m3c383, mycp1-n1ppa8, sett2-r0k664, cocsn-m2t3q1, sett2-r0k4b4, cocsn-m2t4i1, bauco-m2lzw1, coch5-m2th93, cocsn-m2svm8, sphms-m3d7h2, sphms-m3cwc3, mycfi-m3b329, bauco-m2n4x9, cocsn-m2s6q4, mycfi-m3b7x7, mycp1-m2yk59, cocsn-m2s5h5, bauco-m2nfr9, bauco-m2myk4, coch4-n4xf94, mycfi-m3a252, sphms-n1qes8, mycp1-n1pps5, sett2-r0kdl8, cocsn-m2qvi9, sett2-r0kfg6, bauco-m2n1q0, cocsn-m2szq4, sett2-r0j437, coch4-n4x7j4, mycfi-m3b4h3, coch5-m2twk3, coch5-m2usf2, sett2-r0kjt7, mycfi-m2yrk1, bauco-m2n4g8, sett2-r0k7y2, cocsn-m2th03, sett2-r0iy92, sett2-r0kbr9, sett2-r0k997, coch5-m2sik6, bauco-m2n0g0, bauco-m2lkk0, sett2-r0jzj5, sphms-m3bs21, mycfi-m3a3h8, mycp1-n1pw13, cocsn-m2r0j6, mycp1-n1pe19, coch4-n4x6a4, mycp1-m2xhl1, cocsn-m2s7a5, cocsn-m2sv79, mycfi-n1qbd7, mycp1-n1pnh6, sphms-m3cz62, sett2-r0knx4, bauco-m2nlz2, mycp1-n1psn5, sett2-r0ksh8, bauco-m2n3v9, bauco-m2n9y7, mycp1-n1puh9, sett2-r0ip86, sphms-m3c6j1, sphms-n1qnq9, cocsn-m2sqe4, coch4-n4xzc8, mycfi-m3ali0, mycfi-m3a5j4, mycp1-n1phf7, bauco-m2myw5, mycp1-m2y2h4, mycfi-m3as05, sphms-m3ccg5, cocsn-m2rtg8, sphms-n1qny5, mycfi-n1q7c3, mycp1-n1q523, bauco-m2m190, psefd-m3awp8, sphms-n1qfl1, dotsn-n1q1b1, sphms-m3dcu2, bauco-m2m7v7, psefd-m3bad8, bauco-m2nft5, psefd-m3b4x7, sphms-n1qdh4, sphms-m3cq38, bauco-m2mz43, coch5-m2t2x3, cocsn-m2sze4, sphms-n1qfm9, sett2-r0kjg6, sett2-r0k5q0, cocvi-w7ezb7, sett2-r0jtm1, cocmi-w6ywa1, psefd-m3a663, baupa-m2mxl2, cocsn-m2t3e8, coch5-m2ulw5, coch5-m2urw9, sett2-r0knn5, cocca-w6y1v2, baupa-m2nq79, sett2-r0i9k2, coch5-m2uul8, dotsn-n1q415, psefd-n1qcy3, cocsn-m2sl21, baupa-m2luc8, dotsn-est1 Abstract The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress. Title: The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P and Bradshaw RE <29 more author(s)> de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE (- 29) Ref: PLoS Genet, 8:e1003088, 2012 : PubMed ESTHER: de Wit_2012_PLoS.Genet_8_E1003088 PubMedSearch: de Wit 2012 PLoS.Genet 8 E1003088 PubMedID: 23209441 Gene_locus related to this paper: mycpj-q30dw8, mycp1-n1pnd6, mycp1-n1per0, mycp1-n1pg49, mycp1-n1pwj1, mycp1-n1pcl8, mycp1-m2y2b1, mycp1-n1pwu7, mycp1-n1ppa8, mycp1-m2yk59, mycp1-n1pps5, mycp1-n1pw13, mycp1-n1pe19, mycp1-m2xhl1, mycp1-n1pnh6, mycp1-n1psn5, mycp1-n1puh9, mycp1-n1phf7, mycp1-m2y2h4, mycp1-n1q523, dotsn-n1q1b1, dotsn-n1q415, dotsn-est1 Abstract We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an alpha-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation. Title: Genome sequence of the model mushroom Schizophyllum commune Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A and Wosten HA <22 more author(s)> Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kues U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wosten HA (- 22) Ref: Nat Biotechnol, 28:957, 2010 : PubMed ESTHER: Ohm_2010_Nat.Biotechnol_28_957 PubMedSearch: Ohm 2010 Nat.Biotechnol 28 957 PubMedID: 20622885 Gene_locus related to this paper: schcm-d8pqz6, schcm-d8prj2, schcm-d8pug6, schcm-d8pxe8, schcm-d8pxe9, schcm-d8pxz1, schcm-d8q1c7, schcm-d8q2b4, schcm-d8q3j1, schcm-d8q5m5, schcm-d8q7x7.1, schcm-d8q7x7.2, schcm-d8q8y8, schcm-d8q9n6, schcm-d8q697, schcm-d8qip8, schcm-d8q5s5, schcm-d8ppb3, schcm-d8ppb6, schcm-d8pv73, schcm-d8pzm1, schcm-d8q5a7, schcm-d8qif0 Abstract Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals. | |||||||
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