Fungal Phylogeny and Ortholog Analysis

Together with L.edodes, 26 fungal species assigned to Basidiomycota or Ascomycota were used in the phylogenetic analysis. The protein sequences of these 26 fungi were compared by BLASTP with e-value < 1e-5 and hit number < 500. Then, the BLASTP result was analyzed by OrthoMCL[73 (link)] with default parameters to get the orthologous genes, and 756 single-copy orthologous genes were determined. Multiple sequence alignments of these 756 genes were calculated by MAFFT v7.158b [74 (link)] software, and were combined into a long sequence for each species. Then, the conserved block regions of the alignment were picked out by Gblocks 0.91b with default parameters [75 (link)] of the software, and the final alignment length was 193323 aa. With the input of this alignment, phylogenetic tree was constructed by RAxML-8.0.26 [76 (link)] software with bootstrap 1000. Three fossil calibration points [77 (link)] were fixed in the molecule clock analysis: the most recent common ancestor (MRCA) of Coprinopsis cinerea, Laccaria bicolor and Schizophyllum commune were diverged at 122.74 MYA; the MRCA of Serpula lacrymans and Coniophora puteana were diverged at 104.23 MYA; the MRCA of Pichia stipitis, Aspergillus niger, Cryphonectria parasitica, Stagonospora nodorum and Trichoderma reesei were diverged at 517.55 MYA. Then, the divergence time of other nodes was calculated by r8s v1.80 [78 (link)] software with TN algorithm, PL method and the smoothing parameter value set to 1.8 through cross-validation. Based on the ultrametric tree, the orthologous gene family expansion was calculated by CAFE version 3 [25 (link)] software.

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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

Ascomycota Aspergillus niger Basidiomycota Coniophora puteana Coprinopsis cinerea Cryphonectria parasitica Fungi Fungi protein Gene Laccaria bicolor Pichia stipitis Protein sequences Regions block Schizophyllum commune Sequence alignments Serpula lacrymans Stagonospora nodorum Tree Trichoderma reesei

Corresponding Organization : Huazhong Agricultural University

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Variable analysis

independent variables

Protein sequences of 26 fungal species assigned to Basidiomycota or Ascomycota

dependent variables

Phylogenetic analysis
Orthologous genes
Divergence time of nodes
Orthologous gene family expansion

control variables

BLASTP with e-value < 1e-5 and hit number < 500
OrthoMCL with default parameters
MAFFT v7.158b for multiple sequence alignments
Gblocks 0.91b with default parameters to pick conserved block regions
RAxML-8.0.26 with bootstrap 1000 for phylogenetic tree construction
Three fossil calibration points for molecule clock analysis
R8s v1.80 with TN algorithm, PL method and smoothing parameter value set to 1.8 for divergence time calculation
CAFE version 3 for orthologous gene family expansion calculation

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