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

Aidi Zhang,Libo He,Rong Huang,Yaping Wang,Yongming Li,Liangming Chen,Zuoyan Zhu,Lv Xiong,Lanjie Liao

doi:10.1038/s41598-017-08476-y

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.

Highlights

Sex determination and differentiation are important issues in biology research
The sexual proportion statistics confirmed that grass carp has a heteromorphic XX/XY sex chromosome system
No ubq-y ortholog was detected in zebrafish despite being in the same Cyprinidae family. These findings indicated that their divergence from zebrafish followed by independent divergence of the sex chromosomes in these two species

Summary

Introduction

Sex determination and differentiation are important issues in biology research. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Bidon et al compared two in silico approaches and found that the method based on differences in the average read depth of autosomal versus sex chromosomal scaffolds was more efficient than that was based on similarity searching of known Y-linked genes[19]. With the former method, a 1.9 Mb region of Y chromosome was identified from the Polar bear (Ursus groenlandicus) genome. In the present study, basing on our previous male grass carp genome data, we tested the suitability and reliability of the sequencing read depth approach of pooled DNAs in the identification of sex markers in fish. Our findings will provide valuable insights into the evolution of fish sex chromosome

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Results

Conclusion