The haplotype-resolved chromosome-level genome assembly of Spinibarbus caldwelli provides insights into environmental adaptability and disease resistance

Abstract

Spinibarbus caldwelli is a cyprinid freshwater fish of significant economic and ecological value that is known for its strong environmental adaptability and disease resistance. As an allotetraploid species with a complex genome structure, the lack of a high-quality reference genome has long hindered in-depth studies on its evolutionary mechanisms and adaptive basis. In this study, we employed PacBio HiFi long-read sequencing in combination with Hi-C technology to generate a high-quality, haplotype-resolved chromosome-level reference genome of S. caldwelli. Two haplotypes (Haplotype 1 and Haplotype 2) were assembled, with total lengths of 1.76 Gb and 1.78 Gb respectively. Based on homologous chromosome alignment and genome collinearity analysis, the genome was partitioned into two subgenomes (A and B), confirming its allotetraploid origin. Further integrated gene family evolution and positive selection analyses revealed that genes within several key functional pathways, such as the Fanconi anemia pathway, p53 signaling pathway, and B-cell receptor signaling pathway, presented significant signals of expansion or positive selection. These pathways represented essential biological processes that support genomic stability and immune defense in S. caldwelli under complex hydrodynamic conditions and potential pathogenic stress. The results offer a valuable theoretical and data foundation for studies on genome stability, immune evolution, polyploid diversification, and molecular breeding in cyprinid fishes.