Comparative Genomic Study Between Nibea Coibor And Nibea Albiflora

Nibea coibor and Nibea albiflora belong to the family Sciaenidae,order Perciformes,and class Osteichthyes.Both species are economically important species for marine aquaculture in China,and are characterized by their tender and delicious meat.In this study,we used thirdgeneration sequencing technology and Hi-C technology to assemble high-quality haploid genomes of both species and to locate and compare the sex-determining regions of the two species.We aimed to clarify the similarities and differences between the two species in terms of their whole genomes,sex chromosomes,and sex-determining genes,as well as to provide a foundation for genetic breeding and germplasm resource protection research.Our main results are as follows:1.We assembled the haploid genomes of Nibea coibor and Nibea albiflora,which were627.66 Mb and 646.42 Mb,respectively,using Hi Fi data generated by third-generation Pac Bio sequencing technology and Hi-C chromosomal interaction data,and split them into haploid genomes.BUSCO and Mercury evaluations showed that the genome completeness of Nibea coibor and Nibea albiflora were 98.90%,97.78% and 98.8%,99.63%,respectively.The proportion of repetitive sequences in Nibea coibor and Nibea albiflora genomes was similar,at 19.34% and18.66%,respectively.Using the strategy of combining gene prediction methods based on de novo prediction,transcriptome data,and protein homology,we annotated 21,433 and 24,771 genes in the Nibea coibor and Nibea albiflora genomes,respectively.Divergence time estimation showed that the differentiation time of Nibea coibor and Nibea albiflora was 16.9 MYA.2.Through resequencing of individuals of the two species,we identified 83934 and 373521high-quality SNP markers in the sex chromosome of Nibea coibor and Nibea albiflora,respectively.By performing Fst and association analyses,we located the sex-determining region of Nibea coibor in the 12.43-13.25 Mb region of chromosome 18.By mining the genes in this region,we found fam114a2,a gene highly expressed in human testes,and gemin5,a gene highly expressed in mouse spermatocytes and spermatids.Using the same analysis strategy,we finely mapped the sex-determining region of Nibea albiflora to a 75-kb segment(19.06-19.13 Mb)of chromosome 6,which only contained two protein-coding genes,dmrt1 and dmrt3.3.Comparative analysis of the genomes of Nibea coibor,Nibea albiflora,and Larimichthys crocea revealed that the sex chromosomes of Nibea albiflora and Larimichthys crocea are collinear and likely have the same sex-determining gene,while the sex chromosomes of Nibea coibor have undergone transformation.Comparative analysis of the sex chromosomes of Nibea coibor and Nibea albiflora with their corresponding homologous autosomes showed that all four chromosomes had inversions,translocations,and duplications.Repetitive sequence annotation results showed that the sex chromosomes of Nibea albiflora had 20 types of repetitive sequences,totaling 3.27 Mb and accounting for 12.03% of the total chromosome length,while the homologous chromosome 22 of Nibea coibor had only three types of repetitive sequences,comprising only 4%of its chromosome length.Seventeen types of repetitive sequences were detected on the sex chromosomes of Nibea coibor,and 22 types were detected on the homologous chromosome 20 of Nibea albiflora,accounting for 12.16% and 11.07% of their respective chromosome lengths.In this study,we first assembled haplotype-resolved genome sequences of the Nibea coibor and Nibea albiflora,and conducted comparative analysis of their sex chromosomes and sexdetermining regions,revealing changes in repetitive sequences after sex chromosome transformation and laying a solid foundation for subsequent evolutionary analysis.Our study provides a basis for genetic breeding and sex-controlled breeding of these two species.