Comprehensive Fungal Genome CAZyme Annotation

Carbohydrate-active enzymes (CAZymes) were classified separately by HMM search of dbCAN HMMs 4.0 [82 (link)] (default cutoff threshold) and BLASTP search of CAZy datebase [83 (link)] (evalue < = 1e-6 && covered fraction ratio > = 0.2, maximum hit number is 500). Then, according to the common results of these 2 methods, a series of more strict thresholds (BLASTP hit number and evalue, S19 Table) of each CAZyme family were determined by median values of 26 fungal genomes. Finally, the blastp results screened with the new threshold were added to the common results, to obtain the final CAZyme annotation. Therefore, the identification process used here is distinct from that employed by the CAZy system [83 (link)], suggesting the possibility of occasional discrepancies with previously published results. Lignocellulolytic Genes were identified mainly by the Swiss-Prot annotation with key words (S20 Table) among the CAZymes. Transcription factors were identified by a set of InterPro codes (S14 Table) which were collected according to TRANSFAC [84 (link)] and FTFD databases [85 (link)].

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Chen L., Gong Y., Cai Y., Liu W., Zhou Y., Xiao Y., Xu Z., Liu Y., Lei X., Wang G., Guo M., Ma X, & Bian Y. (2016). Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PLoS ONE, 11(8), e0160336.

Publication 2016

Carbohydrate Enzymes Fungal genomes Genes Hmms Transcription factors

Corresponding Organization : Huazhong Agricultural University

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Variable analysis

independent variables

HMM search of dbCAN HMMs 4.0 (default cutoff threshold)
BLASTP search of CAZy datebase (evalue <= 1e-6 && covered fraction ratio >= 0.2, maximum hit number is 500)
New threshold values for BLASTP hit number and evalue for each CAZyme family, determined by median values of 26 fungal genomes

dependent variables

Identification of Carbohydrate-active enzymes (CAZymes)
Identification of Lignocellulolytic Genes
Identification of Transcription factors

control variables

Not explicitly mentioned

positive controls

Not mentioned

negative controls

Not mentioned

Annotations

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