Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the gill samples of Takifugu rubripes analyzed by using Illumina HiSeq 2000 platform to identify gene-associated SNPs from the transcriptome of T. rubripes gill. A total of 27,085,235 unique-mapped-reads from 55,061,524 raw data reads were generated. A total of 56,972 putative SNPs were discovered, which were located in 11,327 genes. 35,839 SNPs were transitions (Ts), 21,074 SNPs were transversions (Tv) and 88.1% of 56,972 SNPs were assigned to the 22 chromosomes. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analyses were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 63.4% of SNPs (34/52) were true SNPs. RNA-Seq is a cost-effective way to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies. The results of our study can also offer some useful information as molecular makers to help select and cultivate T. rubripes.