Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses
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...
Published in: | Genome Biology and Evolution |
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Language: | English |
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Oxford University Press
2015
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Online Access: | https://orca.cardiff.ac.uk/id/eprint/76873/ https://doi.org/10.1093/gbe/evv103 https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf |
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ftunivcardiff:oai:https://orca.cardiff.ac.uk:76873 2023-06-11T04:17:29+02:00 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. Janke, Axel 2015-07-01 application/pdf https://orca.cardiff.ac.uk/id/eprint/76873/ https://doi.org/10.1093/gbe/evv103 https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf en eng Oxford University Press https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf Bidon, Tobias, Schreck, Nancy, Hailer, Frank https://orca.cardiff.ac.uk/view/cardiffauthors/A21394518.html orcid:0000-0002-2340-1726 orcid:0000-0002-2340-1726, 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 https://doi.org/10.1093/gbe%2Fevv103 file https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf doi:10.1093/gbe/evv103 cc_by QH426 Genetics QL Zoology Article PeerReviewed 2015 ftunivcardiff https://doi.org/10.1093/gbe/evv103 2023-05-04T22:33:50Z 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. Article in Journal/Newspaper Ursus maritimus Cardiff University: ORCA (Online Research @ Cardiff) Genome Biology and Evolution 7 7 2010 2022 |
institution |
Open Polar |
collection |
Cardiff University: ORCA (Online Research @ Cardiff) |
op_collection_id |
ftunivcardiff |
language |
English |
topic |
QH426 Genetics QL Zoology |
spellingShingle |
QH426 Genetics QL Zoology Bidon, Tobias Schreck, Nancy Hailer, Frank Nilsson, Maria A. Janke, Axel Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
topic_facet |
QH426 Genetics QL Zoology |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Bidon, Tobias Schreck, Nancy Hailer, Frank Nilsson, Maria A. Janke, Axel |
author_facet |
Bidon, Tobias Schreck, Nancy Hailer, Frank Nilsson, Maria A. Janke, Axel |
author_sort |
Bidon, Tobias |
title |
Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
title_short |
Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
title_full |
Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
title_fullStr |
Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
title_full_unstemmed |
Genome-wide search identifies 1.9 Mb from the polar bear Y chromosome for evolutionary analyses |
title_sort |
genome-wide search identifies 1.9 mb from the polar bear y chromosome for evolutionary analyses |
publisher |
Oxford University Press |
publishDate |
2015 |
url |
https://orca.cardiff.ac.uk/id/eprint/76873/ https://doi.org/10.1093/gbe/evv103 https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf |
genre |
Ursus maritimus |
genre_facet |
Ursus maritimus |
op_relation |
https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf Bidon, Tobias, Schreck, Nancy, Hailer, Frank https://orca.cardiff.ac.uk/view/cardiffauthors/A21394518.html orcid:0000-0002-2340-1726 orcid:0000-0002-2340-1726, 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 https://doi.org/10.1093/gbe%2Fevv103 file https://orca.cardiff.ac.uk/id/eprint/76873/1/Bidon%20et%20al.%202015%20GBE%20-%20Polar%20bear%20Y%20chr%20identification.pdf doi:10.1093/gbe/evv103 |
op_rights |
cc_by |
op_doi |
https://doi.org/10.1093/gbe/evv103 |
container_title |
Genome Biology and Evolution |
container_volume |
7 |
container_issue |
7 |
container_start_page |
2010 |
op_container_end_page |
2022 |
_version_ |
1768376710029377536 |