Telomere-to-Telomere, Haplotype-Resolved Chromosome-Level Genome Assembly and Annotation of Taiwan Hard Clam (Meretrix taiwanica)

Taiwan Hard Clam (Meretrix taiwanica) is an economically important aquaculture species in Taiwan, yet genomic resources for this species have remained fragmented. We present a telomere-to-telomere (T2T), haplotype-resolved, chromosome-level genome assembly for M. taiwanica, generated using PacBio HiFi long reads and Hi-C sequencing. The two haploid assemblies (hap1 and hap2) span 1,006.48 Mb and 1,007.28 Mb, comprising 126 and 66 sequences, respectively, and each containing 19 chromosomes. Hap1 and hap2 exhibit sequence N50 values of 53.87 Mb and 51.57 Mb, with average scaffold lengths of 7.99 Mb and 15.26 Mb, and contain 0.0176% and 0.1313% ambiguous bases. Comparative analyses revealed 81.59% and 83.78% syntenic regions between haplotypes and identified 10,175 structural variations. Repetitive elements constitute 47.06% and 47.02% of the hap1 and hap2 genomes. We annotated 23,320 and 23,598 protein-coding gene models, with median gene lengths of 7,721 bp and 7,657.5 bp, respectively. The mitochondrial genome was assembled at 21,164 bp and encodes 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. Functional annotation covered 16.23% and 16.33% of the nuclear and mitochondrial gene sets. BUSCO analysis indicated genome completeness of 92.4% and 92.5%, and proteome completeness of 95.4% and 94.5% for hap1 and hap2. By providing the first T2T-level reference, this dataset enables precise identification of trait-associated markers for marker-assisted selection (MAS), thereby facilitating genetic improvement of growth and stress-resistance traits. Furthermore, it serves as a robust genomic framework for conservation genomics to assess the genetic diversity of both wild and hatchery populations of this economically vital species.