Chromosome-Level Assembly of the Chinese Hooksnout Carp (Opsariichthys bidens) Genome Using PacBio Sequencing and Hi-C Technology

Xu, Xiuhong; Guan, Wenzhi; Niu, Bin; Guo, Dandan; Xie, Qingping; Zhan, Wei; Yi, Shaokui; Liu, Bao

doi:10.3389/fgene.2021.788547

Cited by 8 publications

(17 citation statements)

References 42 publications

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, most recently, long-term-cultured spermatogonia stem cell line that could produce sperm in vitro was established in O. bidens (Chen et al, 2022). Regarding the morphological traits of hook snout carp, female individuals have plain bodies, while male individuals have irregular dark bars aside from the body (Lian et al, 2017;Xu et al, 2021). During the reproductive season, male individuals exhibit nuptial coloration on the sides of the body and the surfaces of the head, pectoral, and extended-anal fins with nuptial organs, which facilitates matching with females and improves fertilization and reproductive success rates (Lian et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Although the female hook snout carp genome was presented in data format (Xu et al, 2021), its annotation profile is still lacking. It is limited to serving as a reference for finely mapping and characterizing quantitative trait loci, sex-linked DNA markers, sex control, and genetic breeding of hook snout carp.…”

Section: Introductionmentioning

confidence: 99%

“…It is limited to serving as a reference for finely mapping and characterizing quantitative trait loci, sex-linked DNA markers, sex control, and genetic breeding of hook snout carp. The female hook snout carp genome is 814.71Mb and anchored to 39 chromosomes (2n = 78), the largest number in the Danioninae subfamily (Chen, 1998;Xu et al, 2021). The diploid chromosome number of hook snout carp varies in different populations: 74 for Sichuan in Yangtze River drainages, 76 for Guangdong in Pearl River drainages, and 78 for Japan (Li and Li, 1987).…”

Section: Introductionmentioning

confidence: 99%

“…The diploid chromosome number of hook snout carp varies in different populations: 74 for Sichuan in Yangtze River drainages, 76 for Guangdong in Pearl River drainages, and 78 for Japan (Li and Li, 1987). The female O. bidens individuals whose 78-chromosome genome has been sequenced were collected from Zhejiang in the Yangtze River drainages (Xu et al, 2021). A few fish species show different chromosome numbers due to sex chromosomes.…”

Section: Introductionmentioning

confidence: 99%

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

Liu

Gui

Zhu

et al. 2022

Preprint

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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 male o.bedins 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 than in females (23,992). The male chromosome LG06 exhibited over 97% of identity with the female’s GH14/GH38. Male-specific genes were identified for LG06, where structural variety, 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, and 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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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