Synteny search identifies carnivore Y chromosome for evolution of male specific genes

Abstract

The explosively accumulated mammalian genomes have provided a valuable resource to characterize the evolution of the Y chromosome. Unexpectedly, the Y-chromosome sequence has been characterized in only a small handful of species, with a majority of them being model organisms. Thus, identification of Y-linked scaffolds from unordered genome sequences is becoming more important. Here, we used a syntenic-based approach to generate the scaffolds of male specific region in Y chromosome (MSY) from the genome sequence of 6 male carnivore species. Our results identified 14, 15, 9, 28, 14 and 11 Y-linked scaffolds in polar bear, pacific walrus, red panda, cheetah, ferret and tiger, covering 1.55Mbp, 2.62Mbp, 964Kb, 1.75Mb, 2.17Mbp and 1.84Mb MSY, respectively. All of the candidate Y-linked scaffolds in three selected species (red panda, polar bear and tiger) were successfully verified using PCR. We re-annotated these Y-linked scaffolds plus with domestic dog and cat MSY, a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified. These 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts, indicating less purifying selection for MSY genes. Taken together, our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genome and provides a preliminary evolutionary study for carnivore MSY genes. This article is protected by copyright. All rights reserved.

Sex Determination Using RNA-Sequencing Analyses in Early Prenatal Pig Development

“…The importance of these Y-linked genes during male development has been elucidated for mammals [31][32][33][34]. These genes are located in the non-recombining region of the Y chromosome (NRY), which is also known as the male-specific Y (MSY) region, transmitted from fathers to sons without recombination with the X chromosome [35]. The MSY region contains only 27 genes coding for distinct proteins, as the SRY, EIF1AY, KDM5D, ZFY, EIF2S3Y, and DDX3Y [31,35,36].…”

Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas

“…Previously, we de novo sequenced a wild male red panda genome (15), which enabled us to develop Y chromosome SNPs. Using a genome synteny searching strategy and the female dog genome (boxer breed) and the dog male-specific Y chromosome sequences (Doberman breed) as the reference, Fan et al recently identified a set of nine male-specific Y chromosome scaffolds with a total length of 964 kb from the male red panda genome assembly (table S5) (31). Using the 964-kb male-specific Y chromosome scaffolds as the reference, we aligned the whole-genome resequencing reads of 18 male red pandas to the reference genome using BWA and then performed SNP calling using SAMtools and GATK.…”

The Red Fox Y-Chromosome in Comparative Context

“…In total, 22 scaffolds of 5 Kbp or longer were found to contain an MSY gene or gene fragment. Putative Y-chromosome orthologs were identified for all 11 core carnivore MSY genes [31].…”

“…Research in well-developed mammalian genomic models such as dog and cat [6,7,35] facilitated the identification of red fox orthologs of carnivore MSY genes. Out of 18 dog MSY genes analyzed, 17 were identified in putative Y-linked red fox scaffolds, including all 11 of the core carnivore MSY genes [31]. The only dog protein that was not assigned a position in the fox scaffolds was TSPY .…”

“…The two known Y-chromosome scaffolds comprise only 1 Mbp of sequence, whereas the male-specific region of the Y-chromosome (MSY) is approximately 2.5 Mbp in many other carnivores [6], suggesting that additional sequence may be present in the assembly. Likewise, the two Y-scaffolds contain only nine predicted genes [27,28], including only four of the 11 MSY genes consistently observed across carnivore species [31]. Therefore, additional analysis is required to identify Y-chromosome sequence, including genes, present in the red fox draft genome.…”