Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

Abstract

Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.

Chromosome-Level Assembly of Male Opsariichthys bidens Genome Provides Insights into the Regulation of the GnRH Signaling Pathway and Genome Evolution

“…Heterozygous describes the presence of two different alleles for the same gene, and higher genome heterozygosity leads to a more diverse gene composition and more genes encoding secreted proteins in fungi [ 60 ]. In addition, there are usually differences in the annotated gene numbers between female and male genomes in fishes (e.g., 2.4% for bighead carp [ 18 , 61 ] and 3.5% for O. fasciatus [ 23 ]). Furthermore, the large contig N50 length is conducive to gene annotation, and when contig N50 ranged from 5.2 Mb [ 15 ] to 19.3 Mb [ 58 ], the total genome number of female grass carp can reach 11.3% of the annotated genes.…”

“…Using BUSCO methods to evaluate completeness, we found that the male O. bidens assembled genome contained 97.5% of the complete sequences ( Table S3 ). The high continuity and completeness of the male O. bidens genome will lay a solid foundation for further studies on population genetics, sex-determining mechanisms, sexual dimorphism, growth regulation, and aquaculture breeding [ 61 , 63 ].…”

Chromosome-level assembly of male Opsariichthys bidens genome provides insights into the regulation of the GnRH signaling pathway and genome evolution

“…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).…”

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

“…Whereas some carps, eels and hagfish are well adapted to hypoxia conditions. Even closely related fish species that inhabit the same environment exhibit varied adaption to oxygen concentrations ( Burggren et al, 2019 ; Fu et al, 2021 ; Wang et al, 2022 ). In previous studies, body mass was found to play a role in fish hypoxia tolerance ( Verberk et al, 2022 ).…”