The Red Fox Y-Chromosome in Comparative Context
Identifieur interne : 002239 ( Ncbi/Merge ); précédent : 002238; suivant : 002240The Red Fox Y-Chromosome in Comparative Context
Auteurs : Halie M. Rando [États-Unis] ; William H. Wadlington ; Jennifer L. Johnson ; Jeremy T. Stutchman ; Lyudmila N. Trut ; Marta Farré ; Anna V. KukekovaSource :
- 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 (
Url:
DOI: 10.3390/genes10060409
PubMed: 31142040
PubMed Central: 6627929
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PMC:6627929Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Red Fox Y-Chromosome in Comparative Context</title>
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<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
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<author><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H." last="Wadlington">William H. Wadlington</name>
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(J.L.J.);<email>stutchm2@illinois.edu</email>
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<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
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<author><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N." last="Trut">Lyudmila N. Trut</name>
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<author><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name>
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<author><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V." last="Kukekova">Anna V. Kukekova</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
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<series><title level="j">Genes</title>
<idno type="eISSN">2073-4425</idno>
<imprint><date when="2019">2019</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Carnivora (genetics)</term>
<term>Cats</term>
<term>DNA Copy Number Variations (genetics)</term>
<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>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Carnivora</term>
<term>Chromosome Y</term>
<term>Loups</term>
<term>Renards</term>
<term>Variations de nombre de copies de segment d'ADN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Cats</term>
<term>Dogs</term>
<term>Female</term>
<term>Genome</term>
<term>Male</term>
<term>Phylogeny</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Chats</term>
<term>Chiens</term>
<term>Femelle</term>
<term>Génome</term>
<term>Mâle</term>
<term>Phylogénie</term>
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<front><div type="abstract" xml:lang="en"><p>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 (<italic>Felis catus</italic>
), dog (<italic>Canis lupus familiaris</italic>
), and grey wolf (<italic>Canis lupus lupus</italic>
), providing the opportunity to examine the red fox (<italic>Vulpes vulpes</italic>
) 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 <italic>k</italic>
-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 <italic>BCORY2</italic>
and <italic>UBE1Y</italic>
than has been reported in related species and fewer copies of <italic>SRY</italic>
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.</p>
</div>
</front>
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</TEI>
<double pmid="31142040"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Red Fox Y-Chromosome in Comparative Context</title>
<author><name sortKey="Rando, Halie M" sort="Rando, Halie M" uniqKey="Rando H" first="Halie M." last="Rando">Halie M. Rando</name>
<affiliation wicri:level="2"><nlm:aff id="af1-genes-10-00409">Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H." last="Wadlington">William H. Wadlington</name>
<affiliation><nlm:aff id="af3-genes-10-00409">Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA;<email>wwadlington@ufl.edu</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Johnson, Jennifer L" sort="Johnson, Jennifer L" uniqKey="Johnson J" first="Jennifer L." last="Johnson">Jennifer L. Johnson</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stutchman, Jeremy T" sort="Stutchman, Jeremy T" uniqKey="Stutchman J" first="Jeremy T." last="Stutchman">Jeremy T. Stutchman</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N." last="Trut">Lyudmila N. Trut</name>
<affiliation><nlm:aff id="af4-genes-10-00409">Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia;<email>trut@bionet.nsc.ru</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name>
<affiliation><nlm:aff id="af5-genes-10-00409">School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;<email>m.farre-belmonte@kent.ac.uk</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V." last="Kukekova">Anna V. Kukekova</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
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<idno type="doi">10.3390/genes10060409</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Red Fox Y-Chromosome in Comparative Context</title>
<author><name sortKey="Rando, Halie M" sort="Rando, Halie M" uniqKey="Rando H" first="Halie M." last="Rando">Halie M. Rando</name>
<affiliation wicri:level="2"><nlm:aff id="af1-genes-10-00409">Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H." last="Wadlington">William H. Wadlington</name>
<affiliation><nlm:aff id="af3-genes-10-00409">Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA;<email>wwadlington@ufl.edu</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Johnson, Jennifer L" sort="Johnson, Jennifer L" uniqKey="Johnson J" first="Jennifer L." last="Johnson">Jennifer L. Johnson</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stutchman, Jeremy T" sort="Stutchman, Jeremy T" uniqKey="Stutchman J" first="Jeremy T." last="Stutchman">Jeremy T. Stutchman</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N." last="Trut">Lyudmila N. Trut</name>
<affiliation><nlm:aff id="af4-genes-10-00409">Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia;<email>trut@bionet.nsc.ru</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name>
<affiliation><nlm:aff id="af5-genes-10-00409">School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;<email>m.farre-belmonte@kent.ac.uk</email>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V." last="Kukekova">Anna V. Kukekova</name>
<affiliation><nlm:aff id="af2-genes-10-00409">Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;<email>jjohnso@illinois.edu</email>
(J.L.J.);<email>stutchm2@illinois.edu</email>
(J.T.S.);<email>avk@illinois.edu</email>
(A.V.K.)</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Genes</title>
<idno type="eISSN">2073-4425</idno>
<imprint><date when="2019">2019</date>
</imprint>
</series>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><p>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 (<italic>Felis catus</italic>
), dog (<italic>Canis lupus familiaris</italic>
), and grey wolf (<italic>Canis lupus lupus</italic>
), providing the opportunity to examine the red fox (<italic>Vulpes vulpes</italic>
) 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 <italic>k</italic>
-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 <italic>BCORY2</italic>
and <italic>UBE1Y</italic>
than has been reported in related species and fewer copies of <italic>SRY</italic>
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.</p>
</div>
</front>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Red Fox Y-Chromosome in Comparative Context.</title>
<author><name sortKey="Rando, Halie M" sort="Rando, Halie M" uniqKey="Rando H" first="Halie M" last="Rando">Halie M. Rando</name>
<affiliation wicri:level="2"><nlm:affiliation>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. rando2@illinois.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H" last="Wadlington">William H. Wadlington</name>
<affiliation wicri:level="2"><nlm:affiliation>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA. wwadlington@ufl.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031</wicri:regionArea>
<placeName><region type="state">Floride</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Johnson, Jennifer L" sort="Johnson, Jennifer L" uniqKey="Johnson J" first="Jennifer L" last="Johnson">Jennifer L. Johnson</name>
<affiliation wicri:level="2"><nlm: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.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Stutchman, Jeremy T" sort="Stutchman, Jeremy T" uniqKey="Stutchman J" first="Jeremy T" last="Stutchman">Jeremy T. Stutchman</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. stutchm2@illinois.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N" last="Trut">Lyudmila N. Trut</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia. trut@bionet.nsc.ru.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk</wicri:regionArea>
<wicri:noRegion>630090 Novosibirsk</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK. m.farre-belmonte@kent.ac.uk.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ</wicri:regionArea>
<wicri:noRegion>Kent CT2 7NJ</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V" last="Kukekova">Anna V. Kukekova</name>
<affiliation wicri:level="2"><nlm: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.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:31142040</idno>
<idno type="pmid">31142040</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">The Red Fox Y-Chromosome in Comparative Context.</title>
<author><name sortKey="Rando, Halie M" sort="Rando, Halie M" uniqKey="Rando H" first="Halie M" last="Rando">Halie M. Rando</name>
<affiliation wicri:level="2"><nlm:affiliation>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. rando2@illinois.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H" last="Wadlington">William H. Wadlington</name>
<affiliation wicri:level="2"><nlm:affiliation>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA. wwadlington@ufl.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031</wicri:regionArea>
<placeName><region type="state">Floride</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Johnson, Jennifer L" sort="Johnson, Jennifer L" uniqKey="Johnson J" first="Jennifer L" last="Johnson">Jennifer L. Johnson</name>
<affiliation wicri:level="2"><nlm: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.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Stutchman, Jeremy T" sort="Stutchman, Jeremy T" uniqKey="Stutchman J" first="Jeremy T" last="Stutchman">Jeremy T. Stutchman</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. stutchm2@illinois.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N" last="Trut">Lyudmila N. Trut</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia. trut@bionet.nsc.ru.</nlm:affiliation>
<country xml:lang="fr">Russie</country>
<wicri:regionArea>Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk</wicri:regionArea>
<wicri:noRegion>630090 Novosibirsk</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK. m.farre-belmonte@kent.ac.uk.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ</wicri:regionArea>
<wicri:noRegion>Kent CT2 7NJ</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V" last="Kukekova">Anna V. Kukekova</name>
<affiliation wicri:level="2"><nlm: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.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Genes</title>
<idno type="ISSN">2073-4425</idno>
<imprint><date when="2019" type="published">2019</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Carnivora (genetics)</term>
<term>Cats</term>
<term>DNA Copy Number Variations (genetics)</term>
<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>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Carnivora</term>
<term>Chromosome Y</term>
<term>Loups</term>
<term>Renards</term>
<term>Variations de nombre de copies de segment d'ADN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Cats</term>
<term>Dogs</term>
<term>Female</term>
<term>Genome</term>
<term>Male</term>
<term>Phylogeny</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Chats</term>
<term>Chiens</term>
<term>Femelle</term>
<term>Génome</term>
<term>Mâle</term>
<term>Phylogénie</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<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>
</pubmed>
</double>
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