Genome annotation of Sinonovacula rivularis

Sinonovacula rivularis, an estuarine burrowing bivalve first, was initially identified in the Minjiang Estuary of China.This species demonstrates exceptional adaptability to low-salinity environments andis extensivelycultivated in estuarine regions. Recently, it has been successfully cultivated in saline-alkali ponds in inland provinces such as Gansu Province, highlighting its significant potential for aquaculture. Despite the clarification of its taxonomic status through partial gene fragments, research on its genome remains undeveloped, with a notable absence of high-qualitychromosome-level genome maps. This deficiency hinders comprehensive analysis of its genetic characteristics, adaptive mechanisms, and the advancement of genetic breeding initiatives. To addressthis research, we constructed a chromosomal reference genome for S. rivularis by integrating PacBio HiFi long-read sequencing with Hi-C scaffolding techniques. The assembled genome spans a total length of 1.19Gbp, with a contig N50 of 25.6Mbp. Through chromosomal-level scaffold construction, 19 chromosomes were successfully identified, with at least 97.94% of the genome sequences accurately mapped to the chromosome. In addition, the reference genome analysis identified 536.47 Mb (44.1% of the genome) of repetitive sequences, leading to the annotation of 28,468 protein-coding genes and 4,779 non-coding RNAs. The high-precision, chromosome-level reference genome of Sinonovacula rivularis serves as a crucial genomic resource for the genetic breeding of this species. It also provides a foundational framework for elucidating its adaptation mechanisms to low-salinity environments and for resolving phylogenetic relationships within the genus Sinonovacula.