2.7 Phylogeny of G.lucidum and multigene families
The phylogenetic tree constructed by concatenated sequences alignments showed that G.lucidum was close to another polyporale fungus Fomitopsis pinicola in the evolutionary relationship among all our analyzed fungi(Figure 5A).In the all-to-all BLASTPanalysis，9278 predicted proteins of G.lucidum showed high sequence similarity with that of F.pinicola(BLASTP，cut-off e-value＜1e-7).Following，9013 and 8872 predicted proteins showed significant sequence similarity to that of Gloeophyllum trabeum and Stereum hirsutum，which were all in polyporales.
Figure 5 Phylogeny tree of 19 fungi and genes in their genomes(https://www.daowen.com)
(A)The Neighbor Joining tree(NJ)was constructed with 1，000 bootstrap replications from a concatenated alignment of 323 single-copy proteins.(B)Bars represent a comparison of the gene content of all these species in the corresponding position in NJ tree.Bars are subdivided to indicate different types of homology relationships.Black：genes that are found only one copy in all these fungi(323 genes)；Orange：genes that were in all species but maybe more copies in some species；Green：genes presenting in more than one fungus but not in all these fungi；White：species-specific genes with no detectable homologs in other species genes.Abbreviations：Aga，Agaricomycotina；Ust，Ustilaginomycotina；Puc，Pucciniomycotina；Eur，Eurotiomycetes；Dot，Dothideomycetes；Sor，Sordariomycetes；Sac，Saccharomycotina；Bas，Basidiomycota；Asc，Ascomycota.
In order to observe gene family expansion in G.lucidum，we performed analyses for multigene families，which were generated from proteins in 8 Agaricomycotina species.In total，10，720 gene families containing at least two members were generated using the Tribe-MCL tool，of which 5947 families have at least one G.lucidum gene and 1487 families have at least 2 G.lucidum genes.The largest gene family had 517 genes and 126 of them were G.lucidum genes.In 3540 lineage specific gene families，287 families were G.lucidum specific；the number was very similar to that of G.trabeum and much lower than other basidiomycetes.L.bicolor had the largest(947)lineage-specific gene families，which may be related to its biggest genome size among our analyzed basidiomycetes.The distributions of genes with different copies or species-specific are shown in Figure 5B.
Besides the lineage specific gene families，the evolutionary changes in the size of each gene family were performed using CAFE program.As a result，we found that among the 7，180 non-lineage specific gene families for G.lucidum，636 of them were expanded and 994 of them had undergone contraction.The function of the most abundant gene families were uncharacterized since lack of available annotation，while the second most abundant gene families code for proteins with a p450 domain.