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

Abstract

The hook snout carp Opsariichthys bidens is an important farmed fish in East Asia that shows sexual dimorphism in growth, with males growing faster and larger than females. To understand these complex traits and improve molecular breeding, chromosome-level genome assembly of male O. bidens was performed using Illumina, Nanopore, and Hi-C sequencing. The 992.9 Mb genome sequences with a contig N50 of 5.2 Mb were anchored to 38 chromosomes corresponding to male karyotypes. Of 30,922 functionally annotated genes, 97.5% of BUSCO genes were completely detected. Genome evolution analysis showed that the expanded and contracted gene families in the male O. bidens genome were enriched in 76 KEGG pathways, and 78 expanded genes were involved in the GnRH signaling pathway that regulates the synthesis and secretion of luteinizing hormone and glycoprotein hormones, further acting on male growth by inducing growth hormone. Compared to the released female O. bidens genome, the number of annotated genes in males was much higher (23,992). The male chromosome LG06 exhibited over 97% identity with the female GH14/GH38. Male-specific genes were identified for LG06, where structural variation, including deletions and insertions, occurred at a lower rate, suggesting a centric fusion of acrocentric chromosomes GH14 and GH38. The genome-synteny analysis uncovered significant inter-chromosome conservation between male O. bidens and grass carp, the former originating from ancestral chromosome breakage to increase the chromosome number. Our results provide a valuable genetic resource for studying the regulation of sexual dimorphism, sex-determining mechanisms, and molecular-guided breeding of O. bidens.

Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens)

“…Previous genomic studies showed that the haploid chromosome number of this species varied between sexes, e.g. females had 39 chromosomes while males 38 chromosomes [43] , [95] . However, in our study, the female O. bidens also carried 38 chromosomes, suggesting sex may be not the major determinant of chromosome number variation.…”

“…Carp O. bidens is known for its ability to grow fast and adapt well to both the field and farming environment, making it an ideal species to investigate adaptation and fast evolution [101] , [106] , [14] , [46] . Currently, genomic studies on O. bidens have largely focused on chromosome evolution and adaptive radiation [22] , [43] , [95] . However, little is known about the molecular evolutionary rate of O. bidens and the underlying determinants.…”

New perspectives on the genetic structure of dotted gizzard shad (Konosirus punctatus) based on RAD-seq

“…7 B), as this signaling pathway can take a vital role in the control of reproductive function, growth and development of fishes (Okubo and Nagahama 2008 ). Also, Liu et al ( 2022a , b ) have found that this signaling pathway in male Opsariichthys bidens was able to induce the action of growth hormone in males by regulating the secretion of luteinizing hormone and glycoprotein hormone, making males grow faster than females (Liu et al 2022b ). In addition, we identified the Notch signaling pathway that may be directly related to the adaptive evolution of K. punctatus (Fig.…”

Palmitic acid-modified GnRH-Th epitope peptide immunocastration vaccine (W/O/W adjuvant) can effectively ensure the castration and reduce the smelly smell in boars

“…Boars require castration during the pig breeding process, as male hormones will accumulate in their bodies after growing to a certain age, causing odor and negatively affecting the flavor and taste of pork. The gonadotropin-releasing hormone GnRH plays a crucial role in animal growth and reproduction by stimulating the pituitary synthesis and secretion of gonadotrophic hormone in the head ( 3 ). Multiple factors influence animal reproduction both in vivo and in vitro , including positive and negative feedback, where the hypothalamic–pituitary-gonadal axis plays an important role, while GnRH is the most critical ( 4 , 5 ).…”