Whole Genomic SNPs and SSRs Development based on High-Throughput Transcript Sequencing in Sea Cucumber (Apostichopus japonicus)

摘要

As the efficient genomic resources, molecular markers (single nucleotide polymorphism (SNPs) and simple sequence repeats (SSRs)) have become the significant molecular marker of choice for breeding programs and population genetic studies in many species. RNA-Seq has been approved as a cost-effective and efficient way for molecular marker identification and validation. In this study, a large scale of polymorphic functional markers on papillae and skin transcriptome of sea cucumber (Apostichopus japonicas) were obtained by high-throughput sequencing. A total of 166,572 and 171,480 putative SNPs were identified in papillae and skin transcriptome, respectively. These putative SNPs included transitions (papillae/skin, 95,713/98,905) and transversions (papillae/skin, 70,859/72,575). Additionally, 12,201 and 12,149 SSRs were discovered from the papillae and skin transcriptome, respectively. Among SSRs, tri-nucleotide repeats were almost equally in UTRs compared to CDSs and non-CDSs, while di-nucleotide repeats were twice more abundant spread over these two regions. And the distribution rate of tri-nucleotide which around CDS were almost five-fold more abundant than that of di-nucleotide. We also analyzed the A. japonicus genes that contained molecular markers from both tissues transcriptome by Gene ontology (GO). We also found many growth-related genes contained a lot of SNPs and SSRs. These useful molecular markers can be used for genetics, breeding and genetic diversity analysis in the sea cucumber.