2.5 Comparative genomics analysis of KEGG annotati...
For made comprehensive comparison in KEGGannotation in fungi，KEGG pathway mapping were performed in 13 basidiomycetes and 5 ascomycetes.To facilitate comparison and show results in one table，we only showed the results of 8 basidiomycetes(7 in agaricomycotina and 1 in ustilaginomycotina)and 2 represented ascomycetes in the following analyses.In the second layer of KEGG pathway terms，we found fungi in Agaricomycotina(including G.lucidum)had much more genes in each pathway than other fungi(Figure 1).G.lucidum had relatively more genes in several pathways of metabolism and biosynthesis，such as“Metabolism of Terpenoids and Polyketides”，“Metabolism of Other Amino Acids”，and“Xenobiotics Biodegradation and Metabolism”.In the third layer of KEGG，in the sub pathways of“Xenobiotics Biodegradation and Metabolism”，we found that G.lucidum and other Agaricomycotina fungi had relatively more proteins involved in several degradation pathways including pathways of aminobenzoate，bisphenol，dioxin and polycyclic aromatic hydrocarbon degradation(Table 2).There were about 190 genes involved 3 of these degradation pathways in G.lucidum(Table 2).These results indicated that G.lucidum had strong ability of degradation.In addition，we also observed that“Metabolism of xenobiotics by cytochrome P450”and“Drug metabolism cytochrome P450”sub-pathways had relative more genes in G.lucidum.
Table 2 The gene distribution of fungi in pathway“Xenobiotics Biodegradation and Metabolism”
*represents G.lucidum having relatively more genes than others.Abbreviations：G.lui，Ganoderma lucidum；F.pin：Fomitopsis pinicola；P.chr：Phanerochaete chrysosporium；S.com：Schizophyllum commune；P.ost：Pleurotus ostreatus；L.bic：Laccaria bicolor；C.cin：Coprinopsis cinerea；M.glo：Malassezia globosa；P.tritici：Pyrenophora tritici-repentis；S.cer：Saccharomyces cerevisiae
In the fourth layer，G.lucidum has 27 KO terms with 1.5-fold genes more than other Agaricomycotina fungi(Table 3).Of them，the term K00490(cytochrome P450)showed relatively more genes in G.lucidum.Since cytochrome P450 is a large group of enzymes involved in many important biosynthesis and metabolism pathways，we further identified and performed comparison about P450 genes at genome level in these fungi.We found that the numbers of P450 genes in fungi of subphylum agaricomycotina are much more than fungi in other subphylum of basidiomycota and in ascomycota(Table 4).G.lucidum has 222 putative P450 genes，which was the most in the 10 represented fungi and the top 3 in all the 18 fungi we analyzed.
Table 3 KO families showing relatively more genes in G.lucidum genome as compared to other fungi
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Continued table
The abbreviations of species were the same with Table 2.The number of genes in G.lucidum of each KO of is 1.5 fold more than the average of the other 10 Agaricomycotina fungi.
Table 4 The gene distribution of fungi in P450 family and GST family
*represents G.lucidum having the most genes than others.The abbreviations of species were the same with Table 2.
Under the“Metabolism of xenobiotics by cytochrome P450”pathway，we found the glutathione S-transferases(GST，EC 2.5.1.18)which are well-known detoxification enzymes［23］were greatly enriched in G.lucidum compared with other fungi.According to the classification of Morel et al.［24］，we investigated the GSTs distribution in six known classes(GTT1，GTT2，URE2p，Omega，EFBγ，MAK16)and a new class(GTE)of all fungi in this study.Under the relatively strict cutoff(BLASTPe-value＜1e—10 and similarity＞30%)，we found 39 GST genes in G.lucidum，which was the highest GST gene numbers among all the fungi we studied.Notably，G.lucidum had 18 genes in the Omega subfamily，which appeared much more than other fungi(Table 4).