Genomes

Introduction

Protein sequences originating from complete genomes and that can be assigned to CAZy families are listed in the links below. The only genomes that are consistently surveyed in the CAZy database are those released by the NCBI as regular entries in the daily releases of GenBank. In a very limited number of cases, we have included data from RefSeq genomes.

The collection of carbohydrate-active enzymes encoded by the genome of an organism ("CAZome") provides an insight into the nature and extent of the metabolism of complex carbohydrates of the species. The CAZomes of free living organisms typically correspond to 1-5% of the predicted coding sequences. Extremely reduced CAZomes are characteristic of species with a strict intracellular parasitic lifestyle. Because of the massive chemical, structural and functional variability of carbohydrates, CAZome analyses and comparisons highlight significant differences between species.

Although often useful, the simple assignment of a protein sequence to a CAZy family does not constitute a refined functional prediction for genomic annotation. For the later task, we are developping a CAZy-based annotation methodology, which takes into account protein modularity, family and subfamily assignment, relatedness to experimentally characterized enzymes and expertise in the varying substrate specificity of carbohydrate-active enzymes. This methodology, which results in coherent, expert and comparable sets of annotations, is applied to novel genomes and metagenomes on a collaborative basis.

Tables for Direct Genome Access by Kingdom

Bacteria8334
Viruses331
Archaea283
Eukaryota212

Our published work on CAZymes in genomes, metagenomes and transcriptomes

[150] Teixeira et al. (2017) Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). Stud Mycol. 86:1-28 [PMID: 28348446].

[149] Peng et al. (2017) The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi. J. Biotechnol. , 246:1-3 [PMID: 28216099].

[148] Wu et al. (2017) Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels. Appl Microbiol Biotechnol. , 101:2603-2618 [PMID: 28078400].

[147] Patrascu et al. (2017) A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomics. Sci. Rep. , 7:40248 [PMID: 28091525].

[146] Ji et al. (2017) The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria. Environmental Microbiology, 19:1103-1119 [PMID: 27902881].

[145] de Vries et al. (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol. 18(1):28. [PMID: 28196534].

[144] Heiss-Blanquet et al. (2016) Composting-like conditions are more efficient for enrichment and diversity of organisms containing cellulase-encoding genes than submerged cultures. PLoS One 11(12):e0167216 [PMID: 27936240].

[143] Schlegel et al. (2016) Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics, 17:1015 [PMID: 27938347].

[142] Desai et al. (2016) A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339-1353. [PMID: 27863247].

[141] Aranda-Martinez et al. (2016) CAZyme content of Pochonia chlamydosporia reflects that chitin and chitosan modification are involved in nematode parasitism. Environmental Microbiology 18, 4200-4215. [PMID: 27668983].

[140] Abot et al. (2016) CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics. 17:671. [PMID: 27552843].

[139] Miettinen et al. (2016) Draft genome of the white-rot fungus Obba rivulosa 3A-2. Genome Announc, 4(5). pii: e00976-16 [PMID: 27634999].

[138] Peter et al. (2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nature Communications, 7:12662 [PMID: 27601008].

[137] Matos et al. (2016) Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environmental Microbiology, 18(12):4471-4484 [PMID: 27348213].

[136] Zeiner et al. (2016) Comparative analysis of secretome profiles of manganese(II)-oxidizing ascomycete fungi. PLoS One, 11(7):e0157844 [PMID: 27434633].

[135] Eves-van den Akker et al. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol., 17(1):124 [PMID: 27286965].

[134] Redou et al. (2016) Draft genome sequence of the deep-sea ascomycetous filamentous fungus Cadophora malorum Mo12 from the mid-Atlantic ridge reveals its biotechnological potential. Genome Announc. 4(4). pii: e00467-16 [PMID: 27389260].

[133] Redou et al. (2016) Draft genome sequence of the deep-sea basidiomycetous yeast Cryptococcus sp. Mo29 reveals its biotechnological potential. Genome Announc. 4(4). pii: e00461-16 [PMID: 27389259].

[132] Corrochano et al. (2016) Expansion of signal transduction pathways in fungi by whole-genome duplication. Current Biology, 26(12):1577-1584 [PMID: 27238284].

[131] Castell-Miller et al. (2016) Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.). PLoS One, 11(6):e0154122 [PMID: 27253872].

[130] Lebrigand et al. (2016) Comparative genomic analysis of Drechmeria coniospora reveals core and specific genetic requirements for fungal endoparasitism of nematodes. PLoS Genet. 12(5):e1006017. [PMID: 27153332].

[129] Hacquard et al. (2016) Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nature Communications, 7:11362. [PMID: 27150427].

[128] Blanton et al. (2016) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351, aad3311 [PMID: 26912898].

[127] Shah et al. (2016) Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. New Phytol. 209:1705-1719 [PMID: 26527297].

[126] Gazis et al. (2016) The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biology, 120:26-42 [PMID: 26693682].

[125] Doré et al. (2015) Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytol., 208, 1169-1187 [PMID: 26171947].

[124] Kumar et al. (2015) de novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster. PLoS One 10(10):e0140398. [PMID: 26505484].

[123] Chiapello et al. (2015) Deciphering genome content and evolutionary relationships of isolates from the fungus Magnaporthe oryzae attacking different host plants. Genome Biol. Evol. 7(10):2896-2912. [PMID: 26454013].

[122] Wu et al. (2015) Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science, 350(6256):aac5992. [PMID: 26430127].

[121] Ze et al. (2015) Unique organization of extracellular amylases into amylosomes in the resistant starch-utilizing human colonic Firmicutes bacterium Ruminococcus bromii. MBio, 6(5). pii: e01058-15. [PMID: 26419877].

[120] Angelakis et al. (2015) A metagenomic investigation of the duodenal microbiota reveals links with obesity. PLoS One, 10(9):e0137784 [PMID: 26356733].

[119] O’Neill et al. (2015) The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry. Mol Biosyst. 11(10):2808-20 [PMID: 26289754].

[118] Benoit I (2015) Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. Biotechnol Biofuels 8:107 [PMID: 26236396].

[117] Morel et al. (2015) Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep. 5:11571 [PMID: 26108467].

[116] Perlin et al. (2015) Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 16:461 [PMID: 26076695].

[115] Petit et al. (2015) Genome and transcriptome of Clostridium phytofermentans, catalyst for the direct conversion of plant feedstocks to fuels. PLoS One 10(6):e0118285 [PMID: 26035711]

[114] Dhillon et al. (2015) Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci USA 112(11):3451-6 [PMID: 25733908].

[113] Kohler et al. (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 47(4):410-5 [PMID: 25706625].

[112] Karlsson et al. (2015) Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biol Evol. 7(2):465-80 [PMID: 25575496].

[111] Comeau et al. (2014) Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch elm disease. Genome Biol Evol. 7(2):410-30 [PMID: 25539722].

[110] Kopel et al. (2014) Draft genome sequence of Pseudoalteromonas sp. strain PLSV, an ulvan-degrading bacterium. Genome Announc. 2(6). pii: e01257-14 [PMID: 25502665].

[109] Hori et al. (2014) Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood. PLoS Genet. 10(12):e1004759 [PMID: 25474575].

[108] O’Connor et al. (2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci USA 111(47):E5096-104 [PMID: 25385629].

[107] Teixeira et al. (2014) Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. BMC Genomics 15:943 [PMID: 25351875].

[106] Kopel et al. (2014) Draft genome sequences of two ulvan-degrading isolates, strains LTR and LOR, that belong to the Alteromonas genus. Genome Announc. 2(5). pii: e01081-14 [PMID: 25342689].

[105] Navarro et al. (2014) Fast solubilization of recalcitrant cellulosic biomass by the basidiomycete fungus Laetisaria arvalis involves successive secretion of oxidative and hydrolytic enzymes. Biotechnol Biofuels 7(1):143 [PMID: 25320637].

[104] Seedorf et al. (2014) Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159(2):253-66 [PMID: 25284151].

[103] Brouwer et al. (2014) Carbohydrate-related enzymes of important Phytophthora plant pathogens. Fungal Genet Biol. 72:192-200 [PMID: 25192612].

[102] Veneault-Fourrey et al. (2014) Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genet Biol. 72:168-81 [PMID: 25173823].

[101] Kopel et al. (2014) Draft genome sequence of Nonlabens ulvanivorans, an ulvan-degrading bacterium. Genome Announc. 2(4). pii: e00793-14 [PMID: 25125644].

[100] Munir et al. (2014) Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability. PLoS One 9(8):e104260 [PMID: 25101643].

[99] Schellenberg et al. (2014) Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics. BMC Genomics 15:567 [PMID: 24998381].

[98] Dassa et al. (2014) Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS One 9(7):e99221 [PMID: 24992679].

[97] Riley at al. (2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci USA 111(27):9923-8 [PMID: 24958869].

[96] Levasseur et al. (2014) The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 15:486 [PMID: 24942338].

[95] Toome et al. (2014) Draft genome sequence of a rare smut relative, Tilletiaria anomala UBC 951. Genome Announc. 2(3). pii: e00539-14 [PMID: 24926052].

[94] Zhou et al. (2014) Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei. BMC Genomics 15:294 [PMID: 24746234].

[93] Poidevin et al. (2014) Comparative analyses of Podospora anserina secretomes reveal a large array of lignocellulose-active enzymes. Appl Microbiol Biotechnol. 98(17):7457-69 [PMID: 24695830].

[92] Looft et al. (2014) Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. ISME J. 8(8):1566-76 [PMID: 24522263].

[91] Toome et al. (2014) Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. New Phytol. 202(2):554-64 [PMID: 24372469].

[90] Lee et al. (2014) Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. ISME J. 8(3):493-503 [PMID: 24108330].

[89] Tisserant et al. (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci USA 110(50):20117-22 [PMID: 24277808].

[88] Patyshakuliyeva et al. (2013) Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus. BMC Genomics 14:663 [PMID: 24074284].

[87] Cecchini et al. (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One, 8(9): e72766 [PMID: 24066026].

[86] Wegmann et al. (2013) Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota (’Ruminococcus bicirculans’) reveals two chromosomes and a selective capacity to utilize plant glucans. Environ. Microbiol. doi: 10.1111/1462-2920.12217 [PMID: 23919528].

[85] McNulty et al. (2013) Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biology 11(8): e1001637. [PMID: 23976882].

[84] Flot et al. (2013) Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500, 453-457. doi: 10.1038/nature12326 [PMID: 23873043].

[83] Bhattacharya et al. (2013) Genome of the red alga Porphyridium cruentum. Nature Commun., 4:1941. doi: 10.1038/ncomms2931 [PMID: 23770768].

[82] Ji et al. (2013) Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain. Environm. Microbiol. doi: 10.1111/1462-2920.12180 [PMID: 23841906].

[81] El Kaoutari et al. (2013) Abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nature Reviews Microbiology, 11, 497-504 [PMID: 23748339].

[80] Bastien et al. (2013) Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnology for Biofuels, 6(1):78 [PMID: 2367263].

[79] Arfi et al. (2013) Characterization of salt-adapted secreted lignocellulolytic enzymes from the mangrove fungus Pestalotiopsis sp. Nature Commun., 4:1810. doi: 10.1038/ncomms2850 [PMID: 23651998].

[78] Verbeke et al. (2013) Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PLoS One, 8(3): e59362 [PMID: 23555660].

[77] Manning et al. (2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda) 3, 41-63 [PMID: 23316438].

[76] Erickson et al. (2012) Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PLoS One 7(11):e49138 [PMID: 23209564].

[75] Curtis et al. (2012) Algal nuclear genomes reveal evolutionary mosaicism and fate of nucleomorphs. Nature 492:59-65 [PMID: 23201678].

[74] Ohm et al. (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens 8(12): e1003037 [PMID: 23236275].

[73] de Wit et al. (2012) 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. PLoS Genet. 8(11):e1003088 [PMID: 23209441].

[72] Morin et al. (2012) The genome sequence of the Button Mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc. Natl. Acad. Sci. USA 109, 17501-17506 [PMID: 23045686].

[71] Barry et al. (2012) Effects of dietary fiber on the feline gastrointestinal metagenome. J. Proteome Res. 11, 5924-5933 [PMID: 23075436].

[70] Bottacini et al. (2012) Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PLoS One 7(9):e44229 [23028506].

[69] Suzuki et al. (2012) Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics 13, 444 [PMID: 22937793].

[68] O’Connell et al. (2012) Life-style transitions in plant pathogenic Colletotrichum fungi defined by genome and transcriptome analyses. Nature Genetics 44, 1060-1065 [PMID: 22885923].

[67] Dassa et al. (2012) Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics 13, 210 [PMID: 22646801].

[66] Floudas et al. (2012) The Paleozoic origin of white rot wood decay reconstructed using 31 fungal genomes. Science 336, 1715-1719 [PMID: 22745431].

[65] Chen et al. (2012) Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nature Communications 3:913. doi: 10.1038/ncomms1923 [PMID: 22735441].

[64] Cantarel BL, Lombard V, Henrissat B (2012) Complex carbohydrate utilization by the healthy human microbiome. PLoS One 7(6): e28742 [PMID: 22719820].

[63] Abubucker et al. (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8(6): e1002358 [PMID: 22719234].

[62] Olson et al. (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol. 194, 1001-1013 [PMID: 22463738].

[61] Fernandez-Fueyo et al. (2012) Comparative genomics of Ceriporiopisis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc. Natl. Acad. Sci. USA, 109, 5458-5463 [PMID: 22434909].

[60] Ipcho et al. (2012) Transcriptome analysis of Stagonospora nodorum; gene models, effectors, metabolism and pantothenate dispensability. Molec. Plant Pathol. 13, 531–545 [PMID: 22145589].

[59] Zhang et al. (2012) Carbohydrate-active enzymes revealed in Coptotermes formosanus (Isoptera: Rhinotermitidae) transcriptome. Insect Mol Biol. 21, 235-245 [PMID: 22243654].

[58] Price et al. (2012) Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335, 843-847 [PMID: 22344442].

[57] McNulty et al. (2011) The impact of a consortium of fermented milk strains on the human gut microbiome: a study involving monozygotic twins and gnotobiotic mice. Science Transl. Med. 3(106):106ra106 [PMID: 22030749].

[56] Berka et al. (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nature Biotechnol. 29, 922-927 [PMID: 21964414].

[55] De Luca et al. (2011) The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment. PLoS One 6: e23784 [PMID: 21912644].

[54] Manzo et al. (2011) Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation. BMC Microbiol 11, 198 [PMID: 21892951].

[53] Amselem et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics 7, e1002230 [PMID: 21876677].

[52] Klosterman et al. (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog. 7, e1002137 [PMID: 21829347].

[51] Eastwood et al. (2011) The plant cell wall decomposing machinery underlies the functional diversity of forest fungi. Science, 333, 762-765 [PMID: 21764756].

[50] Muegge et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974 [PMID: 21596990].

[49] Duplessis et al. (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc. Natl. Acad. Sci. USA 108, 9166-9171 [PMID: 21536894].

[48] Goodwin et al. (2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity and stealth pathogenesis. PLoS Genetics 7, e1002070. [PMID: 21695235].

[47] Kubicek et al. (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 12, R40 [PMID: 21501500].

[46] Dam et al. (2011) Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res. 39, 3240-3254 [PMID: 21227922].

[45] Sucgang et al. (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol. 12, R20 [PMID: 21356102].

[44] Diguistini et al. (2011) Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc. Natl. Acad. Sci. USA 108, 2504-2509 [PMID: 21262841].

[43] Swanson et al. (2011) Phylogenetic and gene-centric metagenomics of the canine gastrointestinal microbiome reveals similarities with human and mouse gut metagenomes. ISME J 5, 639-649 [PMID: 20962874].

[42] Battaglia et al. (2011) Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics 12, 38 [PMID: 21241472].

[41] Turroni et al. (2010) Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. USA 107, 19514-19519 [PMID: 20974960].

[40] Hemme et al. (2010) Genome announcement: sequencing of multiple clostridia genomes related to biomass conversion and biofuels production. J. Bacteriol. 192, 6494-6496 [PMID: 20889752].

[39] Tasse et al. (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 20, 1605-1612 [PMID: [20841432].

[38] Ohm et al. (2010) Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune. Nature Biotechnol. 28, 957-963 [PMID: 20622885].

[37] Purushe et al. (2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii; insights into their environmental niche. Microbial Ecology 60, 721-729 [PMID: 20585943].

[36] Rincon et al. (2010) Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. (2010) PLoS One 5, e12476 [PMID: 20814577].

[35] Levesque et al. (2010) Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11, R73 [PMID: 20626842].

[34] Turnbaugh et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl. Acad. Sci USA 107, 7503-7508 [PMID: 20363958].

[33] Martin et al. (2010) Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464, 1033-1038 [PMID: 20348908].

[32] Ma et al. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367-373 [PMID: 20237561].

[31] Ventura et al. (2009) The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 5(12) e1000785 [PMID: 20041198].

[30] Coleman et al. (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5, e1000618 [PMID: 19714214].

[29] Yang et al. (2009) The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PloS One 4, e6085 [PMID: 19568419].

[28] Worden et al. (2009) The genomes of Micromonas: global reporters in marine environments. Science 324, 268-272 [PMID: 19359590].

[27] Turnbaugh et al. (2009) A core gut microbiome in obese and lean twins. Nature 457, 480-484 [PMID: 19043404].

[26] McBride et al. (2009) Novel features of the polysaccharide digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl. Environm. Microbiol. 75, 6864-6875 [PMID: 19717629].

[25] Berg Miller et al. (2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 4, e6650. [PMID: 19680555].

[24] Mahowald et al. (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA 106, 5859-5864 [PMID: 19321416].

[23] Ward et al. (2009) Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl. Environ. Microbiol. 75, 2046-2056 [PMID: 19201974].

[22] Brulc et al. (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA 106, 1948-1953 [PMID: 19181843].

[21] Martinez et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA 106, 1954-1959 [PMID: 19193860].

[20] Coutinho et al. (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet. Biol. 46, S161-S169 [PMID: 19618505].

[19] Wortman et al. (2009) The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet. Biol. 46, S2-S13 [PMID: 19146970].

[18] Martin et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452, 88-92 [PMID: 18322534].

[17] Lozupone et al. (2008) The convergence of carbohydrate active gene repertoires in human gut microbes. Proc. Natl. Acad. Sci. USA, 105, 15076-15081 [PMID: 18806222].

[16] Abad et al. (2008) Genome sequence of the metazoan plant-specific nematode Meloidogyne incognita. Nature Biotechnol. 26, 909-915. [PMID: 18660804].

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