title: Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus.
abstract: Simple sequence repeats (SSRs) play specific roles in many biological activities. In this paper, we focused on SSRs in the genome of Pleurotus ostreatus, which is a widely cultivated edible mushroom. The distribution curves of SSRs and exons are opposite throughout the genome, which means that SSRs are mostly located in non-coding regions. A comparative analysis of nine fungi suggests that Agaricomycotina fungi have similar SSR distributions. Functional enrichment analysis on the SSR-containing gene set uncovers enriched functions about environmental interactions and important cellular functions for life. Trinucleotide SSRs account for an extremely high fraction of all SSRs, and in exonic regions, they are equivalent to inserting repeating amino acids (RAAs) into the protein sequences. The RAA indel could partly explain some enriched functions of the genes they modify. Agaricomycotina fungi have similar distributions of RAAs, indicating that this may be a potential common mechanism for some specific functions.
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Jibin
authors.initials: J
authors.lastname: Qu
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Chenyang
authors.initials: C
authors.lastname: Huang
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China. Electronic address: zhangjinxia@caas.cn.
authors.forename: Jinxia
authors.initials: J
authors.lastname: Zhang
mesh_terms: D018744:DNA, Plant / Q000032:analysis; D005091:Exons; D018745:Genome, Plant; D018895:Microsatellite Repeats; D020076:Pleurotus / Q000235:genetics*; D018911:Trinucleotide Repeats
chemical_list: D018744:DNA, Plant
keywords: Functional enrichment analysis; Pleurotus ostreatus genome; Repeating amino acid; Simple sequence repeat