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 ~74.1 X coverage). We further 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. 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 functional and comparative genomic analyses.
