Differentially expressed genes unique to the brown rot fungal strains tested

  • a Genes are shown by the orthologous group ID generated by OrthoMCL v2.0.

  • b Functions of orthologues were annotated by Blast2Go (v4.0.7), which combined the results of Gene Ontology annotation and InterPro Scan. Functions were further manually confirmed by blastp in Swiss-Prot database.

  • c FC, fold change. Ratios were calculated by comparing the RPKM value (reads per kilobase of transcript per million mapped reads) of early decay (i.e., 0- to 5-mm section) and that of the older section (i.e., 15- to 20-mm or 30- to 35-mm section). The gene list was ranked according to the ratio numbers of G. trabeum.

  • d The RPKM value of the 15- to 20-mm section is listed or used to calculate the ratio.

  • e Nineteen orthologous groups have similar functions for ribosomal structure and were combined to simplify the table.