4.1 Quality of the assembled genome at the chromosome level
O. bidens is a vital aquaculture fish in East Asia that shows sexual dimorphism in growth and body size, with male fish exhibiting faster and greater growth than females (Lian et al., 2017). This species could be exploited as a monosexual fish in aquaculture and used as a model to address gene function in sexual dimorphism. In combination with the released genome sequences of female O. bidens (Xu et al., 2021), the male O. bidens assembled genome at the chromosome level in the present study will provide valuable genomic resources for gaining critical insight into the regulatory mechanism underlying sexual dimorphism, revealing the sexual complexity and genetic diversity of the species genome.
The quality of the male O. bidens genome assembly was evaluated based on continuity and completeness. In the present study, the maleO. bidens final contig assembly was 992.9 Mb with a contig N50 length of 5.2 Mb. In the released female O. bidens genome (Xu et al., 2021), the contig assembly was 818.75 Mb with an N50 length of 4.71 Mb. Compared with the female O. bidens genome assembly, the N50 length of the current male genome contig was much longer (N50:5.2 Mb). It contained more annotated genes (30,922) than that of the female genome (N50:4.71 Mb and 23,992 annotated genes). Also, more than the female O. bidens genome annotated gene numbers based on theD. rerio NCBI database (22,835, data not shown). The maleO. bidens genome using Hi-C chromatin interaction maps was 886.81 Mb and anchored into 38 chromosomes ranging from 6.51-47.68 Mb, consistent with the 2n = 76 karyotypes. The female O. bidensgenome is 818.78 Mb and anchored into 39 chromosomes ranging from 6.77-42.84 Mb, suggesting that O. bidens harbored different chromosomes in sexual individuals and that the male individuals showed the longest chromosome (LG01, ~ 47.68 Mb). This study provides comparative and evolutionary studies of male and femaleO. bidens using genome sequences and further identifies the genes and regulatory elements related to sexual dimorphism traits.
O. bidens genomes were more abundant than many reported Cyprinid genomes (Table S1). It is said that transposons (RNA and DNA types) and the SSRs content contribute to genome size. Larger genomes exhibit richer transposons in comparison with teleost fish genomes with annotated transposons (Liu et al., 2021), such as the 1.37 Gb zebrafish genome with a repeat content of 52.2% (Howe et al., 2013). The maleO. bidens genome showed repeat elements accounting for 43.23% of the 992.9 Mb genome. Using BUSCO methods to evaluate the completeness of the male O. bidens assembled genome, we found that the maleO. bidens assembly genome contained 97.5% of the complete sequences (Table S3). The high continuity and completeness of the maleO. bidens genome will lay a solid foundation for further studies on population genetics, sex-determining mechanisms, sexual dimorphism, growth regulation, and aquaculture breeding (Fu et al., 2021; Mascali et al., 2022).