4.3 Mechanism underlying O. bidens chromosome number variety
During vertebrate evolution, the entire genome has undergone two rounds (2R) of duplication, and fish-specific genome duplication, namely the third round of whole-genome duplication (3R) approximately 320 million years ago, subsequently developed into new diploids (Meyer and Van de Peer, 2005). Therefore, most teleosts carry about 50 chromosomes in diploid fish species (Jaillon et al., 2004). The 4R has occurred in certain Cyprinidae fish, resulting in palaeopolyploids with 100 chromosomes in their nuclear genome, such as the common carp C. carpio andS. rhinocerous in the tetraploidized chromosome (David et al., 2003; Meyer and Van de Peer, 2005; Wang et al., 2012; Xu et al., 2014). Multiple rounds of whole genome duplication produce redundant genes that provide important genetic material for phenotypic complexity, which would potentially benefit an organism in its molecular functions. Interestingly, the Cyprinid fishO. bidens is an exception, and different populations show various chromosome numbers (between 74 and 78) (Li and Li, 1987). The chromosomal evolution of Cyprinid remains a subject of debate.
Recently, the released genome of female O. bidens has provided an opportunity to investigate the mechanism underlying chromosome changes (Xu et al., 2021). The female O. bidens carried 39 (2n = 78) chromosomes. In comparison, the male O. bidens carried 38 (2n = 76) chromosomes in the present study, suggesting a difference in the regulation of sexual dimorphism in hook snout carp at the chromosomal level. The male O. bidens LG06 chromosome was a reunion of female GH14 and GH38 chromosomes and showed more than 97% sequence similarity between males and females. Male LG06-special genes have two functions in chromosome replication, recombination, and repair, and one well-known DNA polymerase epsilon subunit 2 (pole2). Pole2 is required for cell growth, chromosomal DNA replication, and double-strand break repair (Hashimoto et al., 2003), indicating the fidelity of the reunion chromosomes provided by pole2 gene function. It has been verified thatO. fasciatus, which possesses 2n = 47 in males and 2n = 48 in females, carries a large metacentric Y chromosome (Xiao et al., 2020). Different karyotypes in O. punctatus are responsible for the genome size discrepancy between male and female individuals (Xu et al., 2019). This suggests that O. bidens has a sex-dependent system. In the male O. bidens genome, GnRH-induced hormone-releasing related gene families underwent expansions, and up to seven expanded genes were distributed in the LG06 chromosome, and LG06 was a reunion of female O. bidens GH14 and GH38 chromosomes. Therefore, it is reasonable to regard LG06 as a sexual dimorphic chromosome, and the related molecular mechanisms are worth investigating in future studies.
The hook snout carp displayed an atypical karyotype of 3R. Our genome assembly for male O. bidens led to 38 chromosomes, directly corresponding to male karyotypes (2n = 76). Although different populations carry different chromosome numbers, the fundamental arm number of their karyotypes is 86 (Li and Li, 1987; Li et al., 1985). The leuciscin fishes, including Ochetobius elongatus (Kner),Luciobrama macrocephalus (Lacepède), Elopichthys bambusa(Richardson), Squaliobarbus curriculus (Richardson), and C. idellus, carry 2n = 48 chromosomes, with fundamental arm numbers of 74, 82, 82,90, and 92 (Li et al., 1985). Hook snout carp have similar fundamental arm numbers to Leuciscin fishes, suggesting that the 76 chromosomes of male O. bidens resulted from the 2n = 48 chromosomes of Leuciscin fishes by breakage at centromere sites. Considering that C. idellus is regarded as a primitive species in Leuciscin fish species evolution (Wu et al., 2022), the synteny-based chromosome comparison between male O. bidens and C. idellus showed that out of the 24 chromosomes in C. idellus , one breakage into two chromosomes occurred in 12 chromosomes, providing evidence of added chromosome number via breakage. Our results could serve as a framework for studies on sex-determining mechanisms and genome evolution in fish.