2.4 Gene annotation
By homology search，we mapped our predicted proteins to Gene Ontology(GO)，5893(49%)of which were assigned to GO terms.There were 5410，1738 and 4034 genes mapped to the molecular function，cellular component and biological process category，respectively.We also assigned 4737 proteins to the Kyoto Encyclopedia of Genes and Genomes(KEGG)database.KEGG function classification was showed in Figure 1 and“Carbohydrate Metabolism”，“Xenobiotics Biodegradation and Metabolism”，and“Amino Acid Metabolism”were the top 3 categories.Of these predicted genes in G.lucidum，up to 9978，6436 and 9981 showed a significant similarity(BLASTP，cut-off e-value＜1e—7)to documented proteins in the NCBI nr database(Aug 2011)，Swiss-Prot，and TrEMBL，respectively.As a result，about 83% of predicted proteins were similar to sequences in these public databases and only 2094 genes were not similar to current public sequences，some of which might be G.lucidum specific genes.We further classed predicted genes into orthologous group(single-copy in G.lucidum and at least one other species ortholog)，or paralogous group(multi-copy in G.lucidum).There were 4689 orthologous genes and 5510 paralogous genes by the above definition.By the NCBI COG mapping，3509(29%)proteins were assigned to COGs proteins(Figure 2).Similar to the KEGG annotation，some metabolism and biosynthesis categories in COG were highly enriched.
Figure 1 The KEGG function annotaion of G.lucidum
Distribution of Genes in different KEGG categories.(https://www.daowen.com)
Figure 2 The COG function annotaion of G.lucidum
Distribution of Genes in different COG function classification.
Comparing with other published basidiomycetes，G.lucidum has many different biological characteristics，such as saprophytism，multiple triterpenoids and polysaccharides metabolites.To compare and find genes for G.lucidum specific characteristics，we performed comprehensive comparison among G.lucidum and other published fungi genomes in the follow sections.