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Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses

Bidon, Tobias, Schreck, Nancy, Hailer, Frank, Nilsson, Maria A. and Janke, Axel 2015. Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses. Genome Biology and Evolution 7 (7) , pp. 2010-2022. 10.1093/gbe/evv103

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Abstract

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Publisher: Oxford University Press
ISSN: 1759-6653
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 23 May 2015
Last Modified: 11 Mar 2019 13:10
URI: http://orca.cf.ac.uk/id/eprint/76873

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