De novo assembly, gene annotation, and molecular marker development using Illumina paired-end transcriptome sequencing in the clam Saxidomus purpuratus

The clam Saxidomus purpuratus is an important economic marine bivalve species in China. In this study, we performed a de novo transcriptome sequencing of S. purpuratus gill tissues to generate a transcriptome dataset by performing Illumina paired-end sequencing on the HiSeq 2500 platform. A total of 10,488,024 raw reads were produced. After removing the inferior sequences, adaptor sequences, and rRNAs, 68,080,636 high-quality reads were obtained, from which 5,115,494 assembled contigs were produced. These contigs were assembled into 120,479 transcripts and 66,388 unigenes with mean lengths of 674.96 and 562.70 bp, respectively. All unigene sequences were compared against the NCBI databases, and 26,781 unigenes were annotated. Both the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that several functional genes were involved in the stress response, immune system, and oxidation reduction process. Meanwhile, 414 simple sequence repeats (SSRs) were identified in the S. purpuratus transcriptome. SSR validation via PCR confirmed that 26 primer pairs had expected products, and 13 primers proved to be polymorphism among 30 individuals. The S. purpuratus transcriptome advances the underlying molecular understanding of this economic shellfish and provides a basis for further exploring S. purpuratus genomics resources.