De novo Whole Genome and Transcriptome Sequencing of the Korean Short-Necked Clam, Ruditapes philippinarum, in Korea

The short-necked clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. In spite of its importance in marine resource, the reference genome of short-necked clam for comprehensive genetic studies is absence. Here, we reported the whole-genome sequencing with de novo assembly from the short-necked clam and whole-transcriptome analysis with total RNA sequencing across its three different tissues (foot, gill, and adductor muscle). Through massive parallel sequencing with short-inset paired-end (PE) and long-insert mate-pair (MP) libraries, and TruSeq synthetic Long-Read (TSLR) libraries, high quality de novo assembly of the short-necked clam genome was constructed as well as the ~2.56 Gb genome sequence (with ~39.7 X coverage). We annotated 15,485 protein coding genes, which are supported by the whole-transcriptome data from three different tissues. In addition, identification of the repetitive elements including simple sequence repeats (SSRs) and non-coding RNAs (ncRNAs), and taxonomy profiling were conducted to provide more inclusive understanding of the short-necked clam genome. Interestingly, we found that the gene family related with the innate immune response (i.e., complement C1q gene) has been remarkably expanded in R. philippinarum. Based on the whole-transcriptome data, we also identified differential expressed genes (DEG) across three tissues and validated tissue-specific expressed genes using real-time PCR. Consequentially, our study established the basic construction of the short-necked clam genome and revealed genetic features of them via next-generation sequencing and comparative genomic analyses.