Copy number variation landscape in the Hyriopsis cumingii genome: Insights into the genetic basis of biomineralization and shell color phenotypic diversity

Copy number variation (CNV) is one primary source of genomic structural variation and has been extensively linked to economic traits in agriculture. The triangle sail mussel, Hyriopsis cumingii , holds particular importance in freshwater pearl industry of China. In this study, we constructed a comprehensive CNV map using whole-genome resequencing data from three selective breeds of H. cumingii : "Shenzi No. 1" with purple inner shell (PS), "Shenzhe No. 3" with fast growth rate and white inner shell (FS), and the F3 golden strain with golden inner shell (GS). The CNV map contains 42,527 copy number variation regions (CNVR), including 32,488 deletions and 10,039 duplications. In total, 4129 genes overlapping with CNVRs were identified, with most being associated with metabolism and immunity. Based on CNVR data, PCA and neighbor-joining (NJ) analysis revealed distinct genetic differentiation, with GS forming a separate branch from PS and FS. Moreover, V i results demonstrated high level of copy number polymorphism, with 223, 260, and 262 specific genes showing copy number variations in PS, FS and GS, respectively. Notably, CNVs in fibrillin and collagen were verified to be associated with rapid biomineralization, while ferritin and retsat were linked to inner shell color formation. These results suggest that CNVs drive rapid growth and color variation in H. cumingii , providing new genetic resources for understanding its genetic variation. • Constructed the first detailed CNV map for Hyriopsis cumingii with 42,527 regions. • Identified 4129 genes overlapping CNVs, many involved in metabolism and immunity. • Confirmed fibrillin , collagen , retsat , and ferritin genes' roles in biomineralization and coloration. • Provide new genetic resources and markers for molecular breeding of freshwater mussels.