Whole-genome sequencing of the bronze gudgeon (Coreius heterodon) revealsgenetic diversity and sex markers

The bronze gudgeon (Coreius heterodon), endemic to the Yangtze River. has seen asharp decline in wild populations due to anthropogenetic factors. The lack of genomicdata has hindered its molecular breeding and germplasm optimization, We conductecgenome sequencing using SMRT and BG T7 sequencing, followed by a GWSA toassess genetic diversity and identify sex markers. The genome assembly is 1.024 Ghin size, consisting of 25 chromosomes, with a heterozygosity rate of 0.35%, a repeatsequence proportion of 57.09%, and a GC content of 38.7%.Comparative genomicsanalysis revealed 147 expended gene families related to signal transduction andimmune system. Positively selected genes primarily functioned in DNA replication andrepair mechanisms, with notable genes fanc1, ercc4 and mlh1. Additionally, sex-related SNPs were predominantly located on chromosome 4. Comparative genomicanalysis between C. heterodon and C. guichenoti revealed significant enrichment otstructural variant-affected genes in the Glutamatergic synapse and Long-termpotentiation pathways. These findings provide valuable genetic insights for the futureconservation and breeding of C. heterodon.