Genome-wide SNP in silico detection of Lentinula edodes via whole genome sequencing

• 作 者: CHENXiang;BAODa-Peng;
• 机 构: National Research Center for Edible Fungi Biotechnology and Engineering
• 出 处: 中国菌物学会第五届会员代表大会暨2011年学术年会
• 发表日期: 2011年期

　　Analysis of single nucleotide polymorphisms (SNPs) emerges as an important tool in evolutionary biology and ecology.Here we report the in silico discovery and analysis of SNPs across the whole genome of two protoplast monokaryons (TPMs) of basidiomycete fungi Lentinula edodes via the high-throughput sequencing technology.To our knowledge, this is a novel study in which different protoplast monokaryons are utilized for SNPs detection and analysis.Novel sequence information including 210M and 250M nucleotide bases was generated from TPMs yielding approximately 80% of whole genome sequence.We used surpassed 380K and 41 OK reads of TPMs for the de novo assembly of two contig sets with an overall estimated depth of 5.67-fold and 6.05-fold coverage, respectively.Comparison of the contigs between TPMs identified 108,235 putative SNPs owning a high probability of at least 10-fold coverage.