Chromosome-level genome assembly and improved gene annotation of the Iwagaki oyster, Crassostrea nippona (version 2)

De novo genome assembly was performed using hifiasm (v0.19.4-r575) in Hi-C mode. Hi-C reads were processed with the Juicer pipeline (v1.6) and subsequently used to scaffold the assembly with 3D-DNA (v180419). The resulting assembly and Hi-C contact maps were manually inspected and curated using Juicebox (v1.11.08), and the adjustments were incorporated into a subsequent round of optimization with 3D-DNA.Gene prediction was conducted using Iso-seq and bulk RNA-seq data from multiple developmental stages and adult tissues of Crassostrea nippona. Briefly, short-read RNA-seq data were aligned to the genome using HISAT2 (v2.2.1) and assembled with Trinity (v2.15.1). The resulting transcripts were integrated with protein homology evidence and de novo gene predictions generated by AUGUSTUS (v3.4.0) within the MAKER pipeline (v3.01.03). Iso-Seq subreads were processed and mapped to the genome using the SMRT Link software (v12.0). Redundant Iso-Seq transcripts were collapsed and full-length transcript models were merged using the TAMA toolkit. Final gene models were generated by integrating the MAKER- and Iso-seq-based annotations using AGAT (v1.3.0).