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

Beide Fu,Jingou Tong,Ying Zhou,Haiyang Liu,Xiaomu Yu

doi:10.3389/fgene.2021.728177

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.

Highlights

The mechanism about sex determination in fishes is astonishing variable and have occurred independently and repeatedly (Bachtrog et al, 2014; Furman et al, 2020)
The last one without any hits in zebrafish was searched against the NCBI NR database, and its best hit was ubiquitin carboxyl-terminal hydrolase 64E (UCH64E) from Anabarilius grahami. We found that this gene was located in a male-specific region on LG19
We constructed a high-quality reference genome for bighead carp with ultra-long nanopore reads, which could span the entire length of most repeat units

Summary

Introduction

The mechanism about sex determination in fishes is astonishing variable and have occurred independently and repeatedly (Bachtrog et al, 2014; Furman et al, 2020). Both genetic and environmental factors can control sex-determination system in fishes, but only a small perentage of teleost fish have been proved to have sex chromosome (Kottler and Schartl, 2018). For many other fishes with genetic sex determination (GSD), they only have sex-specific regions in their genome. With the development of sequencing technology for epigenetics, methylation difference between male and female fishes were found. Sex-determination system in fish is complicated and needs different level of data to uncover the key modules which played key roles in it (Ortega-Recalde et al, 2020)

Methods

Results

Conclusion