The Red Fox Y-Chromosome in Comparative Context.
Identifieur interne : 000518 ( PubMed/Curation ); précédent : 000517; suivant : 000519The Red Fox Y-Chromosome in Comparative Context.
Auteurs : Halie M. Rando [États-Unis] ; William H. Wadlington [États-Unis] ; Jennifer L. Johnson [États-Unis] ; Jeremy T. Stutchman [États-Unis] ; Lyudmila N. Trut [Russie] ; Marta Farré [Royaume-Uni] ; Anna V. Kukekova [États-Unis]Source :
- Genes [ 2073-4425 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Carnivora, Chromosome Y, Loups, Renards, Variations de nombre de copies de segment d'ADN.
- Animaux, Chats, Chiens, Femelle, Génome, Mâle, Phylogénie.
English descriptors
- KwdEn :
- MESH :
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
DOI: 10.3390/genes10060409
PubMed: 31142040
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pubmed:31142040Le document en format XML
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<term>Dogs</term>
<term>Female</term>
<term>Foxes (genetics)</term>
<term>Genome</term>
<term>Male</term>
<term>Phylogeny</term>
<term>Wolves (genetics)</term>
<term>Y Chromosome (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Carnivora (génétique)</term>
<term>Chats</term>
<term>Chiens</term>
<term>Chromosome Y (génétique)</term>
<term>Femelle</term>
<term>Génome</term>
<term>Loups (génétique)</term>
<term>Mâle</term>
<term>Phylogénie</term>
<term>Renards (génétique)</term>
<term>Variations de nombre de copies de segment d'ADN (génétique)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Carnivora</term>
<term>DNA Copy Number Variations</term>
<term>Foxes</term>
<term>Wolves</term>
<term>Y Chromosome</term>
</keywords>
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<front><div type="abstract" xml:lang="en">While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (<i>Felis</i>
<i>catus</i>
), dog (<i>Canis</i>
<i>lupus</i>
<i>familiaris</i>
), and grey wolf (<i>Canis</i>
<i>lupus</i>
<i>lupus</i>
), providing the opportunity to examine the red fox (<i>Vulpes</i>
<i>vulpes</i>
) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific <i>k</i>
-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of <i>BCORY2</i>
and <i>UBE1Y</i>
than has been reported in related species and fewer copies of <i>SRY</i>
than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.</div>
</front>
</TEI>
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<DateCompleted><Year>2019</Year>
<Month>12</Month>
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<Abstract><AbstractText>While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (<i>Felis</i>
<i>catus</i>
), dog (<i>Canis</i>
<i>lupus</i>
<i>familiaris</i>
), and grey wolf (<i>Canis</i>
<i>lupus</i>
<i>lupus</i>
), providing the opportunity to examine the red fox (<i>Vulpes</i>
<i>vulpes</i>
) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific <i>k</i>
-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of <i>BCORY2</i>
and <i>UBE1Y</i>
than has been reported in related species and fewer copies of <i>SRY</i>
than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rando</LastName>
<ForeName>Halie M</ForeName>
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<AffiliationInfo><Affiliation>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. rando2@illinois.edu.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. rando2@illinois.edu.</Affiliation>
</AffiliationInfo>
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<Initials>WH</Initials>
<AffiliationInfo><Affiliation>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA. wwadlington@ufl.edu.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Johnson</LastName>
<ForeName>Jennifer L</ForeName>
<Initials>JL</Initials>
<AffiliationInfo><Affiliation>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. jjohnso@illinois.edu.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Trut</LastName>
<ForeName>Lyudmila N</ForeName>
<Initials>LN</Initials>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Farré</LastName>
<ForeName>Marta</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK. m.farre-belmonte@kent.ac.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kukekova</LastName>
<ForeName>Anna V</ForeName>
<Initials>AV</Initials>
<AffiliationInfo><Affiliation>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. avk@illinois.edu.</Affiliation>
</AffiliationInfo>
</Author>
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<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002415" MajorTopicYN="N">Cats</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D056915" MajorTopicYN="N">DNA Copy Number Variations</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004285" MajorTopicYN="N">Dogs</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005589" MajorTopicYN="N">Foxes</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019596" MajorTopicYN="N">Wolves</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014998" MajorTopicYN="N">Y Chromosome</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">BCORY2</Keyword>
<Keyword MajorTopicYN="Y">MSY</Keyword>
<Keyword MajorTopicYN="Y">UBE1Y</Keyword>
<Keyword MajorTopicYN="Y">Vulpes vulpes</Keyword>
<Keyword MajorTopicYN="Y">Y-chromosome</Keyword>
<Keyword MajorTopicYN="Y">Y-chromosome genes</Keyword>
<Keyword MajorTopicYN="Y">carnivore</Keyword>
<Keyword MajorTopicYN="Y">copy-number variation</Keyword>
<Keyword MajorTopicYN="Y">next-generation sequencing</Keyword>
<Keyword MajorTopicYN="Y">sex chromosomes</Keyword>
</KeywordList>
<CoiStatement>The authors declare no conflict of interest.</CoiStatement>
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