Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

Abstract

The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.

Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species

“…Importantly, although these models reveal a great deal about highly degenerate Y chromosomes, they tell us very little about the earliest stages of Y divergence. Only recently have the initial stages of sex chromosomes formation been studied using genomic approaches [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. These nascent sex chromosome systems offer the opportunity to elucidate the first stages of sex chromosome differentiation, and study the rate and process of Y divergence.…”

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

“… Liu et al (2020) used resequencing to construct a high-density genetic map and QTL mapping of sex traits in pearl oysters. Zhang et al (2017) used a pool-and-sequence method to identify six Y-linked scaffolds in the grass carp genome and verified it in the wild population. In this study, we identified six male-specific regions longer than 10 kb in the bighead carp genome.…”

“…The largest one covered over 480 kb on LG19 and harbored one previously reported male-specific marker and three SNP markers located in sex-related QTL ( Liu et al, 2018 ; Zhou et al, 2020 ). As bighead carp and grass carp belong to the same family, we BLASTed six verified sequences in ctg971, the only verified Y-linked scaffold in the grass carp genome, to the male-specific regions in bighead carp and found that four out of six mapped to the largest region on chromosome 19 ( Figure 5 ; Zhang et al, 2017 ). These results further support the common origin of sex-specific regions in the diploid endemic clade of East Asia Cyprinidae ( Liu et al, 2018 ).…”

“…With more than 1,600 species distributed in different continents, Cyprinidae is one of the largest family of freshwater fishes in the world ( Nelson, 2006 ). But sex determination studies have been conducted only in few species of this large group ( Zhang et al, 2017 ; Liu et al, 2018 ). As a model experimental species in Cyprinidae, wild zebrafish has been found to have ZZ/ZX sex determination (SD) system and after human selection the strain in labs lost their GSD system ( Kossack and Draper, 2019 ).…”

“…As a model experimental species in Cyprinidae, wild zebrafish has been found to have ZZ/ZX sex determination (SD) system and after human selection the strain in labs lost their GSD system ( Kossack and Draper, 2019 ). However, previous studies have shown that many fishes use XX/XY sex determination system in this large group ( Zhang et al, 2017 ; Feng et al, 2018 ; Liu et al, 2018 ; Zhou et al, 2020 ), but these studies are far away from understanding the sex-determination system, which needs the help from genomic, transcriptomic and epigenetic data.…”