1. Introduction
Hook snout carp, Opsariichthys bidens Günther, an endemic Asiatic cyprinid with high economic value, has become a commercially emerging aquaculture fish. O. bidens inhabits the tributaries of rivers and prefers to occupy mountainous streams. It has been cultured in large mountain communities and has significantly increased farmer income in the past two decades (Du, 2021; Fu et al., 2012). The hook snout carp is a small to medium-sized fish distributed across China’s main drainages, including the Jiulongjiang, Huaihe, Yellow, Yangtze, and Pearl rivers, and expansions to Hainan drainages in China, Korea, Japan, and Vietnam (Chen et al., 2018b). The long-distance dispersal distribution of hook snout carp was driven by the uplift of the Qinghai-Tibet Plateau and Pleistocene glacial cycles, causing morphological variations, such as lateral line scales and shaped particular populations (Chen et al., 2018b). Genetic diversity examined via mitochondria-based phylogeny has revealed hook snout carp clustering in five different evolutionary lineages (Perdices et al., 2005), revealing potential candidates for fishery resources for hook snout carp breeding in the future.
O. bidensexhibits sexual dimorphism in growth, with male individuals showing faster growth than females, possibly because of the sexually different systems (Potau et al., 1999). Sex-related genes, such as dazl , dnd ,nanog , piwi , vasa , zp4 , amh ,cyp19a , and dmrt1 , were identified in hook snout carp using transcription analysis (Tang et al., 2022b). In addition, sex-biased miRNAs of O. bidens were investigated (Tang et al., 2022a). 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). This reproductive strategy drives chromosome evolution by altering the strength of sexually antagonistic selection (Kirkpatrick, 2017). However, the presumed sex-related chromosomes of hook snout carp have not been previously identified, hindering the deciphering of the sexual dimorphism mechanism of hook snout carp due to the absence of a fully sequenced genome.
High-quality genome assembly at the chromosome level would be helpful for aquaculture breeding and genetic research. The available genomes were used as references for the genetic architecture of morphological characters and dig-specific markers to help molecular breeding with important traits (Fan et al., 2022). The whole genomes of economically important aquaculture fishes, including the common carp Cyprinus carpio Linnaeus (Xu et al., 2014), half-smooth tongue soleCynoglossus semilaevis (Chen et al., 2014), grass carpCtenopharyngodon idella (Valenciennes)(Wang et al., 2015), Japanese flounder Paralichthys olivaceus (Shao et al., 2017) , yellow catfish Pelteobagrus fulvidraco (Gong et al., 2018), and bighead carp Hypophthalmichthys nobilis (Richardson) (Jian et al., 2021), gibel carp/Prussian carp Carassius gibelio (Wang et al., 2022) have been released. Genetic analyses of complex traits, including sex control, disease resistance, hypoxia tolerance, and feed efficient utilization, have been widely performed, and breeding of a new aquaculture variety is being conducted in fisheries, greatly relying on genome data (Gui et al., 2022).
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. 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). 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. For example, a rocky reef fish, Oplegnathus fasciatus (Temminck and Schlegel), showed 2n = 48 for female individuals and 47 for male individuals because of a centric fusion of male acrocentric chromosomes in the formation of the sex-determining system (Xiao et al., 2019). Sex chromosomes are responsible for sex regulation and determination (Ueno and Takai, 2008). Hook snout carp display a variety of chromosome numbers, providing insight into the evolution of sex-related chromosomes in fish.
Here, we report the chromosome-level genome assembly of male O. bidens using Illumina short-read sequencing, Nanopore long-read sequencing, and the Hi-C technique. The assembled genome of 992.9 Mb was anchored to 38 chromosomes, corresponding to our karyotype analysis. In total, 36,738 functional genes were identified. This allowed us to further discover male hormone release via the gonadotropin-releasing hormone (GnRH) pathway, which plays a vital role in developing secondary sex characteristics in O. bidens . For the first time, we identified a reunion of male chromosomes carrying expanded genes involved in the GnRH pathway by synteny-based chromosome comparison between male and female O. bidens . In addition, the genome of male O. bidens compared to that of C. idella showed that the chromosome broke off to increase the chromosome number during the evolutionary history of fish. The male O. bidens genome provides valuable genomic data for further studies on conservation genetics, sex-determining mechanisms, and all-male and hypoxia-resistant breeding.