5.5 Phylogenetic tree construction and gene famili...
First，an all-to-all BLASTP alignment was programmed for G.lucidum and other 18 species(BLASTP cut-off e-value＜1e-7)and core genes which were single-copy in all species were extracted.Then，following a certain order，all core genes of each species were concatenated into a super sequence and were made multiple sequence alignment using the MUSCLE Software.The Neighbor Joining tree(NJ)was constructed with 1000 bootstrap replications from aligned sequences by MEGA-5.05［55］.Based on the allto-all BLASTP results，Tribe-MCL tools［56］were used to generate the multigene families with default parameters(inflation parameter=3)in G.lucidum and other 7 Agaricomycotina fungi(F.pinicol，G.trabeum，S.hirstutum，P.chrysosporium，S.commune，L.bicolor，and C.cinerea).The gene families containing genes from only one species were considered as lineage specific.For other gene families(≥2 members)，the evolutionary changes in the protein family size were analyzed using the CAFE program［57］，which assesses the protein family expansion or contraction based on the topology of the phylogenetic tree.(https://www.daowen.com)