China is the largest producer of pearls, accounted for over 90% of world’s total pearl production. The triangle sail mussel (Hyriopsis cumingii), the most important species for freshwater pearl culture in China, is a well-known mussel recognized for pearl production with high yield and quality. Here, we reported a high-quality chromosome-level genome assembly of H. cumingii. The size of assembled genome was as large as 3.38 Gb with a scaffold N50 length of 3.19 Mb, and 2.04 Gb genome sequences were anchored onto 19 linkage groups. A total of 37,681 protein-coding genes and 50.86% of repeat elements were predicted and annotated. The expansive of 752 gene families compared to the most closely related Dreissena rostriformis, with a divergence time of 18.5 million years, might reveal an extensive set of genes associated to biomineralization, of which 237 genes were under strong positive selection in H. cumingii genome. Notably, the fibrillin gene family exhibited expansion and positive selection simultaneously, and multiple high expression after mantle implantation, suggesting the reason for outstanding biomineralization ability of H. cumingii. Furthermore, one fibrillin gene was confirmed as involving in deposition of calcium carbonate and formation of amorphous crystal during initial biomineralization based on RNA silencing and In vitro carbonate calcium crystallization assay. Fibrillin genes also diverse our attention from calcium deposition guided by matrix protein to interlamellar membrane configuration for understanding pearl formation. These findings provide a valuable genomic resource for carbonate biomineralization studies and fill the gap on freshwater mussel genome for evolutionary studies.

Grass carp (Ctenopharyngodon idella) is an important economic and ecological freshwater fish. Grass carp is a highly adaptive and has been introduced around the world, making it a good model to explore genomic divergence in diverse ecosystems. Habitat colonization often requires extensive adaptation to cope with environmental challenges from temperature and light variations; however, the associated genomic mechanisms underlying evolution are unclear. To evaluate the genetic diversity and selective adaptation in this species, we improved the draft genome of female grass carp using a fine genetic map and performed whole-genome resequencing to generalize genetic differentiations and variations among eight populations across its distributional range in Asia. Population structures analysis using principal component, linkage disequilibrium decay, and admixture analyses revealed that the Asian grass carp comprises two independent and genetically distinct populations, which might have resulted from geographical distributions with contrasting environments. The South Asia population exhibited reduced genetic diversity and a distinct population structure compared with those of the China and Vietnam populations. Genome selected sweep analysis revealed many diverged genomic regions containing genes enriched for the nervous system and epigenetic diversity-related genetic variation. Finally, among 27 candidate genes located in selected regions, the oxytocin gene had the highest Fst value, and is involved in parturition, social behavior, growth, and developmental processes, possibly contributing to the local adaptation of South Asia grass carp. Our results suggested that grass carp genomic divergence has been triggered and maintained by geographic isolation, revealing the genomic basis of adaptation in this species.