比较基因组学，单拷贝直系同源基因研究物种遗传进化：

一篇查找单拷贝直系同源基因研究真菌遗传进化的方法，可以参考：

Species tree construction and gene family expansion 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] 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] 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] 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]

software with bootstrap 1000. Three fossil calibration points [77] 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] 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] software.

参考文献：

Article Source: Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation 
Chen L, Gong Y, Cai Y, Liu W, Zhou Y, et al. (2016) Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PLOS ONE 11(8): e0160336. https://doi.org/10.1371/journal.pone.0160336