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

Bacteria7853
Viruses331
Archaea283
Eukaryota212

Our published work on CAZymes in genomes, metagenomes and transcriptomes

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[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 26289754].

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[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 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 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 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 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 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 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 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 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 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 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 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 25320637].

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[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 25173823].

[101] Kopel et al. (2014) Draft genome sequence of Nonlabens ulvanivorans, an ulvan-degrading bacterium. Genome Announc. 2(4). pii: e00793-14 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 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 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 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 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 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 24926052].

[94] Zhou et al. (2014) Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei. BMC Genomics 15:294 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 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 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 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 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 24277808].

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

[87] Cecchini et al. (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One, 8(9): e72766 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 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. 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 23873043].

[83] Bhattacharya et al. (2013) Genome of the red alga Porphyridium cruentum. Nature Commun., 4:1941. doi: 10.1038/ncomms2931 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 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 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 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 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 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 23316438].

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

[75] Curtis et al. (2012) Algal nuclear genomes reveal evolutionary mosaicism and fate of nucleomorphs. Nature 492:59-65 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 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 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 23045686].

[71] Barry et al. (2012) Effects of dietary fiber on the feline gastrointestinal metagenome. J. Proteome Res. 11, 5924-5933 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 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 22885923].

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

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

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

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

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

[15] Deboy et al. (2008) Insights into plant cell-wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J. Bacteriol. 190, 5455-5463 [PMID: 18556790].

[14] Weiner et al. (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium Saccharophagus degradans strain 2-40T. PLoS Genet., 4(5):e1000087. [PMID: 18516288].

[13] Martinez et al. (2008) Genome sequence analysis of the cellulolytic fungus Trichoderma reesei (syn. Hypocrea jecorina) reveals a surprisingly limited inventory of carbohydrate-active enzymes. Nature Biotechnol. 26, 553-560. [PMID: 18454138].

[12] Espagne et al. (2008) The genome sequence of the model Ascomycete fungus Podospora anserina. Genome Biol. 9:R77 (doi:10.1186/gb-2008-9-5-r77) [PMID: 18460219].

[11] Pel et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnol. 25, 221-231 [PMID: 17259976].

[10] Xu et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology 5, e156 [PMID: 17579514].

[9] Samuel et al. (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl. Acad. Sci. USA 104, 10643-10648. [PMID: 17563350].

[8] Xie et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl. Environm. Microbiol. 73, 3536-3546. [PMID: 17400776].

[7] Geisler-Lee et al (2006) Poplar Carbohydrate-Active Enzymes (CAZymes). Gene identification and expression analyses. Plant Physiol 140, 946-962. [PMID: 16415215].

[6] Tuskan et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313, 1596-1604 [PMID: 16973872].

[5] West CM, van der Wel H, Coutinho P M, Henrissat B (2005) Glycosyltransferase genomics in Dictyostelium discoideum (2005) In Dictyostelium Genomics. W.F. Loomis & A. Kuspa, eds., Horizon Scientific Press 235-264.

[4] Martinez et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnol 22 695-700 [PMID: 15122302].

[3] Coutinho PM, Stam M, Blanc E & Henrissat B (2003) Why so many carbohydrate-active enzymes related genes in plants ? Trends Plant Sci. 8, 563-565 [PMID: 14659702].

[2] Henrissat B, Deleury E, Coutinho PM (2002) Glycogen metabolism loss : a common marker of parasitic behaviour in bacteria ? Trends Genet 18 437-440 [PMID: 12175798].

[1] Henrissat B, Coutinho P M, Davies GJ (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol 47 55-72 [PMID: 11554480].

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