Sampling, Sequencing, and Genome Size Estimation

The Arg. argo DNA used for sequencing was derived from a single female caught as a bycatch in the fixed nets set along the coast in Oki Island Town, Shimane Prefecture, Japan (36°17′20.6″ ″N 133°12′46.4″″E). Pieces of the gonad (ovary) were collected from an individual female specimen collected in 2018. The shell is registered as a collection of the University Museum, University of Tokyo, Tokyo, Japan (Voucher No. RM33391). The specimen is also registered under Tree of Life Identifiers; xcArgArgo1. Genomic DNA was extracted from the ovaries using a QIAGEN Genomic-tip kit. Pooled DNA was used for the preparation of three paired-end and three mate-pair (3, 6, 10, and 15 kb insert size) libraries, which were sequenced using an Illumina HiSeq 2500 at the National Institute of Genetics, Japan with support from the Platform for Advanced Genome Science (PAGS; supplementary tables S6–S8, Supplementary Material online).

Pieces of the mantle, arm membrane of the first arm, and second arm tip were obtained from the same single individual to extract genomic DNA. Eyes, hearts, and gill hearts were sampled from different Arg. argo individuals. Six transcriptomes of Arg. argo were obtained, and raw data statistics are provided in supplementary table S7, Supplementary Material online. Total RNA was extracted from the tissue samples using TRIzol (Invitrogen) followed by an on-column DNase I treatment using the RNeasy mini kit (Qiagen). The RNA was stored at −80 °C until further transcriptome analyses.

The Arg. argo genome size and heterozygosity were assessed using GenomeScope v2.0 (Ranallo-Benavidez et al. 2020), based on quality-filtered Illumina reads. A heterozygosity rate of 1.44% was estimated from a 32-mer-based assessment of the Arg. argo genome (supplementary fig. S1, Supplementary Material online). Complete microsatellite sequences were estimated and visualized using the Krait v1.3.3 (Du et al. 2018b).

Raw read sequence data are available from the DNA Data Bank of Japan (DDBJ). Genome and transcriptome sequencing reads were deposited in the Sequence Read Archive (Bioproject PRJNA470951). The DDBJ DRA accession numbers are listed in supplementary table S8 (Supplementary material online). To provide these data and information for annotation, we constructed a database, ArgoBase (https://cell-innovation.nig.ac.jp/Aargo/).