Whole-Genome Sequencing Reveals a Novel Native Hard Clam Species in Taiwan

Abstract

Extreme climate events have increasingly threatened Taiwan's hard clam industry through thermal stress, salinity fluctuations, and disease outbreaks. However, species identification within the genus Meretrix remains difficult because of their highly similar morphology, limiting biodiversity conservation and selective breeding efforts. This study integrated third-generation long-read sequencing, short-read sequencing, and Hi-C chromosome conformation capture technology to generate the first chromosome-level reference genomes of Taiwanese Meretrix species. Comparative genomics, phylogenetic reconstruction, and fossil-calibrated evolutionary analyses revealed the existence of a previously undescribed native cryptic species, Meretrix sp. MF. Functional genomic analyses further identified species-specific gene expansions associated with growth and immune functions, providing valuable insights into environmental adaptation and disease resistance. The resulting high-quality genomic resources establish an essential foundation for biodiversity conservation, genetic breeding, climate adaptation studies, and sustainable aquaculture development in Taiwan while strengthening the nation's marine genomic research capacity.

Keywords: Hard clam; Whole-genome sequencing; Chromosome-level genome; Cryptic species

Methodology and Implementation Steps

Samples representing Meretrix species were collected from Taiwan and neighboring regions. Chromosome-level genome assemblies were generated by integrating third-generation Nanopore long-read sequencing, next-generation short-read sequencing, and Hi-C chromosome conformation capture technology. Genome assembly was followed by repeat annotation, gene prediction, and functional annotation to establish high-quality reference genomes. Phylogenetic relationships were reconstructed using mitochondrial COXI sequences, while Average Nucleotide Identity (ANI), chromosome synteny analyses, and fossil-calibrated divergence time estimation were performed to evaluate species relationships and evolutionary history. Species-specific genes and enriched biological pathways were further analyzed to identify gene family expansions associated with growth, immunity, and environmental adaptation. These integrated genomic analyses established comprehensive genomic resources for Taiwanese Meretrix species and provided a scientific foundation for biodiversity conservation, selective breeding, and sustainable aquaculture.

Innovation and Cross-Disciplinary Collaboration

This study integrated expertise in genome sequencing, bioinformatics, taxonomy, and marine biotechnology through close collaboration between a genomics research team and a clam taxonomy team. By combining molecular evidence, morphological identification, and extensive field investigations, the project successfully identified a previously undescribed native cryptic species, Meretrix sp. MF1 (Temporarily named Meretrix formosana). Comparative genomic analyses further revealed functional differences between species, showing that the Meretrix sp. MF1 possesses expanded immune-related genes, whereas the Taiwan hard clam exhibits stronger environmental adaptation. These findings provide a scientific foundation for future breeding strategies that combine superior disease resistance with enhanced environmental resilience, supporting sustainable aquaculture and biodiversity conservation.

Expected Results and Contributions

This study established the first chromosome-level reference genomes for Taiwanese Meretrix species and identified a previously undescribed native hard clam species. The resulting genomic resources provide reliable references for species identification, biodiversity conservation, germplasm management, precision breeding, disease resistance improvement, and climate adaptation research. The project further supports marine conservation policies, sustainable aquaculture, and enhances Taiwan's international competitiveness in marine genomics and biodiversity research.