The Red Fox Y-Chromosome in Comparative Context
Identifieur interne : 000155 ( Pmc/Checkpoint ); précédent : 000154; suivant : 000156The 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.
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
Affiliations:
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<record><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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31142040</idno><idno type="pmc">6627929</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627929</idno><idno type="RBID">PMC:6627929</idno><idno type="doi">10.3390/genes10060409</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000C95</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C95</idno><idno type="wicri:Area/Pmc/Curation">000C95</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000C95</idno><idno type="wicri:Area/Pmc/Checkpoint">000155</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000155</idno></publicationStmt><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></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></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><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Compeau, P E C" uniqKey="Compeau P">P.E.C. Compeau</name></author><author><name sortKey="Pevzner, P A" uniqKey="Pevzner P">P.A. Pevzner</name></author><author><name sortKey="Tesler, G" uniqKey="Tesler G">G. Tesler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Henson, J" uniqKey="Henson J">J. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genes (Basel)</journal-id><journal-id journal-id-type="iso-abbrev">Genes (Basel)</journal-id><journal-id journal-id-type="publisher-id">genes</journal-id><journal-title-group><journal-title>Genes</journal-title></journal-title-group><issn pub-type="epub">2073-4425</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31142040</article-id><article-id pub-id-type="pmc">6627929</article-id><article-id pub-id-type="doi">10.3390/genes10060409</article-id><article-id pub-id-type="publisher-id">genes-10-00409</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The Red Fox Y-Chromosome in Comparative Context</article-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0001-7688-1770</contrib-id><name><surname>Rando</surname><given-names>Halie M.</given-names></name><xref ref-type="aff" rid="af1-genes-10-00409">1</xref><xref ref-type="aff" rid="af2-genes-10-00409">2</xref><xref rid="c1-genes-10-00409" ref-type="corresp">*</xref></contrib><contrib contrib-type="author"><name><surname>Wadlington</surname><given-names>William H.</given-names></name><xref ref-type="aff" rid="af3-genes-10-00409">3</xref></contrib><contrib contrib-type="author"><name><surname>Johnson</surname><given-names>Jennifer L.</given-names></name><xref ref-type="aff" rid="af2-genes-10-00409">2</xref></contrib><contrib contrib-type="author"><name><surname>Stutchman</surname><given-names>Jeremy T.</given-names></name><xref ref-type="aff" rid="af2-genes-10-00409">2</xref></contrib><contrib contrib-type="author"><name><surname>Trut</surname><given-names>Lyudmila N.</given-names></name><xref ref-type="aff" rid="af4-genes-10-00409">4</xref></contrib><contrib contrib-type="author"><name><surname>Farré</surname><given-names>Marta</given-names></name><xref ref-type="aff" rid="af5-genes-10-00409">5</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0001-7027-3715</contrib-id><name><surname>Kukekova</surname><given-names>Anna V.</given-names></name><xref ref-type="aff" rid="af2-genes-10-00409">2</xref></contrib></contrib-group><aff id="af1-genes-10-00409"><label>1</label>Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA</aff><aff id="af2-genes-10-00409"><label>2</label>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.)</aff><aff id="af3-genes-10-00409"><label>3</label>Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA;<email>wwadlington@ufl.edu</email></aff><aff id="af4-genes-10-00409"><label>4</label>Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia;<email>trut@bionet.nsc.ru</email></aff><aff id="af5-genes-10-00409"><label>5</label>School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;<email>m.farre-belmonte@kent.ac.uk</email></aff><author-notes><corresp id="c1-genes-10-00409"><label>*</label>Correspondence: <email>rando2@illinois.edu</email></corresp></author-notes><pub-date pub-type="epub"><day>28</day><month>5</month><year>2019</year></pub-date><pub-date pub-type="collection"><month>6</month><year>2019</year></pub-date><volume>10</volume><issue>6</issue><elocation-id>409</elocation-id><history><date date-type="received"><day>13</day><month>4</month><year>2019</year></date><date date-type="accepted"><day>20</day><month>5</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 by the authors.</copyright-statement><copyright-year>2019</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><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></abstract><kwd-group><kwd>Y-chromosome</kwd><kwd>carnivore</kwd><kwd><italic>Vulpes vulpes</italic></kwd><kwd>sex chromosomes</kwd><kwd>MSY</kwd><kwd>Y-chromosome genes</kwd><kwd>copy-number variation</kwd><kwd><italic>BCORY2</italic></kwd><kwd><italic>UBE1Y</italic></kwd><kwd>next-generation sequencing</kwd></kwd-group></article-meta></front><floats-group><fig id="genes-10-00409-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Average per-fox depth in males and females along dog chromosome X (CFAX). Bars represent the standard deviation of mean estimates, while the grey shading indicates the confidence interval based on smoothing with geom_smooth() in ggplot2 [<xref rid="B51-genes-10-00409" ref-type="bibr">51</xref>]. (<bold>A</bold>) Averages were calculated in 1-Mbp intervals. (<bold>B</bold>) Averages were calculated in 100-Kbp windows and are shown only for the region from chrX 6 Mbp to 7 Mbp. The two genes flanking the pseudoautosomal boundary on CFAX, <italic>SHROOM2</italic> (pseudoautosomal) and <italic>WWC3</italic> (X-chromosomal), are indicated as rectangles along the <italic>x</italic>-axis.</p></caption><graphic xlink:href="genes-10-00409-g001"></graphic></fig><fig id="genes-10-00409-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>The distribution of male-specific sequence among scaffolds. This histogram indicates the percent of valid, single-copy <italic>k</italic>-mers unmatched in the female reads across all scaffolds evaluated.</p></caption><graphic xlink:href="genes-10-00409-g002"></graphic></fig><fig id="genes-10-00409-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Comparison of male and female coverage of windows. (<bold>A</bold>) In each window, the percent of the mapped reads coming from the male and from the female resequencing data was calculated. Due to the depth of coverage in the male resequencing data being slightly higher, there is some displacement of the autosomal and X-chromosome curves off 50% and 33/67%, respectively. The expected pattern of density distribution is apparent, with males and females contributing roughly equal numbers of reads to most windows. Very small peaks are apparent at 0% and 100% that correspond to primarily male contribution. (<bold>B</bold>) Zoomed-in depiction of only the small peaks that represent 75% or more contribution from a single sex.</p></caption><graphic xlink:href="genes-10-00409-g003"></graphic></fig><fig id="genes-10-00409-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Based on copy number variation (CNV) between males and females and male-specific sequence motifs, the windows form three clusters. The percent of reads mapping to each window that originated in males (as estimated with CNV-Seq) was plotted against the percent of male-specific 18-mers comprising each scaffold (as estimated with YGS.pl). Percentages were normalized based on standard score. (<bold>A</bold>) Windows from scaffolds with predicted chromosomal origins are plotted, and chromosomal origin is indicated by color. (<bold>B</bold>) Windows from all 12,625 scaffolds analyzed are included, and chromosomal origin, when known, is indicated by color. (<bold>C</bold>) Each window is color-coded according to the cluster to which it was assigned by <italic>k</italic>-means clustering.</p></caption><graphic xlink:href="genes-10-00409-g004"></graphic></fig><fig id="genes-10-00409-f005" orientation="portrait" position="float"><label>Figure 5</label><caption><p>Depth of coverage of Y-scaffolds by male and female resequencing reads. Depth was averaged in males and females over 5000-bp windows for scaffolds longer than 50 Kbp, or for windows 10% of the scaffold length for shorter scaffolds. Microsatellite marker positions [<xref rid="B28-genes-10-00409" ref-type="bibr">28</xref>] are indicated along the top with stars; gene positions as identified in <xref rid="genes-10-00409-t003" ref-type="table">Table 3</xref> are indicated along the bottom. Only scaffolds containing genes are shown. Axes vary depending on the observed depth (<italic>y</italic>) and the length of the scaffold (<italic>x</italic>).</p></caption><graphic xlink:href="genes-10-00409-g005"></graphic></fig><fig id="genes-10-00409-f006" orientation="portrait" position="float"><label>Figure 6</label><caption><p>Estimated depth of coverage along <italic>BCORY1</italic> on scaffold360 (<bold>A</bold>) and <italic>BCORY2</italic> on scaffold310 (<bold>B</bold>). When the position of the codons could not be estimated from the BLAST results, the position is indicated below line at <italic>y</italic> = 0. Male and female depth is indicated separately. Each point represents an amino acid, with the depth estimated off of the surrounding 15 bp (approximately two codons on either side). Dotted lines indicate intervals of 2.5×, or approximately one copy.</p></caption><graphic xlink:href="genes-10-00409-g006"></graphic></fig><fig id="genes-10-00409-f007" orientation="portrait" position="float"><label>Figure 7</label><caption><p>Depth of coverage in the predicted exons of MSY genes. Based on research in dogs and cats [<xref rid="B6-genes-10-00409" ref-type="bibr">6</xref>], <italic>DDX3Y</italic>, <italic>USP9Y</italic>, <italic>UTY</italic>, and <italic>UBE1Y</italic> (top two rows) were predicted to be single-copy in males, whereas <italic>HSFY, SRY</italic>, and <italic>CUL4BY</italic> (bottom two rows) were predicted to be multi-copy in males. The depth of coverage suggests a single copy (as indicated by the lower dotted line) for all of these genes, except <italic>UBE1Y</italic> and <italic>CUL4BY</italic>, which appeared to be present at a high copy number. When a codon’s position could not be estimated from the BLAST results, that region of the amino acid is indicated below 0.</p></caption><graphic xlink:href="genes-10-00409-g007"></graphic></fig><table-wrap id="genes-10-00409-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-10-00409-t002_Table 2</object-id><label>Table 2</label><caption><p>Wolf MSY genes compared to the red fox genome. When dog X-chromosomal protein sequences were available, they were compared to the red fox draft genome using translated BLAST (tblastn). In the remaining cases, the sequences of the regions of the wolf reference genome [<xref rid="B42-genes-10-00409" ref-type="bibr">42</xref>] that contained the MSY genes [<xref rid="B14-genes-10-00409" ref-type="bibr">14</xref>] were compared to the draft red fox genome using standard nucleotide BLAST (blastn). Other than <italic>DYNG</italic>, which was initially reported in dogs [<xref rid="B6-genes-10-00409" ref-type="bibr">6</xref>], these genes have not been identified on the Y-chromosome of dogs or cats. NCBI refers to the databases maintained by the National Center for Biotechnology Information.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gene</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Source</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Chromosome of Sequence Probe</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Sequence Used</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>AP1S2Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">NCBI dog protein </td><td align="center" valign="middle" rowspan="1" colspan="1">ChrX</td><td align="center" valign="middle" rowspan="1" colspan="1">XP_005641196</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>DYNG</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Wolf reference sequence</td><td align="center" valign="middle" rowspan="1" colspan="1">Y-linked scaffold</td><td align="center" valign="middle" rowspan="1" colspan="1">scaffold_2411:21000-65000</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TMSB4Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Wolf reference sequence</td><td align="center" valign="middle" rowspan="1" colspan="1">Y-linked scaffold</td><td align="center" valign="middle" rowspan="1" colspan="1">scaffold_3047:10000-13000</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><italic>WWC3Y</italic></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">NCBI dog protein</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ChrX</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">XP_548855.3</td></tr></tbody></table></table-wrap><table-wrap id="genes-10-00409-t003" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-10-00409-t003_Table 3</object-id><label>Table 3</label><caption><p>Positions of carnivore MSY genes on the red fox scaffolds. The approximate positions of each gene in the red fox genome was determined with BLAST.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gene Name</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Status</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Scaffold #</th><th colspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">Approximate Position Range</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>AMELY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">549</td><td align="center" valign="middle" rowspan="1" colspan="1">18,297</td><td align="center" valign="middle" rowspan="1" colspan="1">26,696</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>AP1S2</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">372</td><td align="center" valign="middle" rowspan="1" colspan="1">67,637</td><td align="center" valign="middle" rowspan="1" colspan="1">77,342</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>BCORY2</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">7152</td><td align="center" valign="middle" rowspan="1" colspan="1">38,910</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>BCORY1</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">360</td><td align="center" valign="middle" rowspan="1" colspan="1">112,755</td><td align="center" valign="middle" rowspan="1" colspan="1">137,091</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td rowspan="8" align="center" valign="middle" colspan="1"><italic>CUL4BY</italic></td><td rowspan="8" align="center" valign="middle" colspan="1">Fragmented</td><td align="center" valign="middle" rowspan="1" colspan="1">653</td><td align="center" valign="middle" rowspan="1" colspan="1">15,446</td><td align="center" valign="middle" rowspan="1" colspan="1">15,604</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">2441</td><td align="center" valign="middle" rowspan="1" colspan="1">2922</td><td align="center" valign="middle" rowspan="1" colspan="1">3038</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">2986</td><td align="center" valign="middle" rowspan="1" colspan="1">5148</td><td align="center" valign="middle" rowspan="1" colspan="1">5270</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">948</td><td align="center" valign="middle" rowspan="1" colspan="1">15,791</td><td align="center" valign="middle" rowspan="1" colspan="1">15,883</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">931</td><td align="center" valign="middle" rowspan="1" colspan="1">6211</td><td align="center" valign="middle" rowspan="1" colspan="1">6294</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">573</td><td align="center" valign="middle" rowspan="1" colspan="1">6191</td><td align="center" valign="middle" rowspan="1" colspan="1">14,432</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">2407</td><td align="center" valign="middle" rowspan="1" colspan="1">5919</td><td align="center" valign="middle" rowspan="1" colspan="1">6035</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">367</td><td align="center" valign="middle" rowspan="1" colspan="1">113,983</td><td align="center" valign="middle" rowspan="1" colspan="1">124,732</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>DYNG</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">367</td><td align="center" valign="middle" rowspan="1" colspan="1">25,206</td><td align="center" valign="middle" rowspan="1" colspan="1">66,258</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>DDX3Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">203,960</td><td align="center" valign="middle" rowspan="1" colspan="1">210,475</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>EIF1AY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">596,932</td><td align="center" valign="middle" rowspan="1" colspan="1">597,039</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>EIF2S3Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">135,297</td><td align="center" valign="middle" rowspan="1" colspan="1">168,226</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>FLJ36031Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Not found</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>HSFY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">647,018</td><td align="center" valign="middle" rowspan="1" colspan="1">648,668</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>KDM5D</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">486,476</td><td align="center" valign="middle" rowspan="1" colspan="1">499,109</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td rowspan="2" align="center" valign="middle" colspan="1"><italic>OFD1</italic></td><td rowspan="2" align="center" valign="middle" colspan="1">Fragmented</td><td align="center" valign="middle" rowspan="1" colspan="1">758</td><td align="center" valign="middle" rowspan="1" colspan="1">9373</td><td align="center" valign="middle" rowspan="1" colspan="1">9579</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">732</td><td align="center" valign="middle" rowspan="1" colspan="1">3168</td><td align="center" valign="middle" rowspan="1" colspan="1">2995</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>RBMYL</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">444</td><td align="center" valign="middle" rowspan="1" colspan="1">13,493</td><td align="center" valign="middle" rowspan="1" colspan="1">22,483</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>RPS4Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">636,415</td><td align="center" valign="middle" rowspan="1" colspan="1">636,457</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>SRY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">431</td><td align="center" valign="middle" rowspan="1" colspan="1">74,758</td><td align="center" valign="middle" rowspan="1" colspan="1">75,417</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TETY1</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Not found</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TETY2</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">6025</td><td align="center" valign="middle" rowspan="1" colspan="1">6288</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TMSB4Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">372</td><td align="center" valign="middle" rowspan="1" colspan="1">50,666</td><td align="center" valign="middle" rowspan="1" colspan="1">53,690</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TSPY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Not found</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td rowspan="2" align="center" valign="middle" colspan="1"><italic>TXLNGY</italic></td><td rowspan="2" align="center" valign="middle" colspan="1">Fragmented</td><td align="center" valign="middle" rowspan="1" colspan="1">444</td><td align="center" valign="middle" rowspan="1" colspan="1">50,789</td><td align="center" valign="middle" rowspan="1" colspan="1">50,884</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">360</td><td align="center" valign="middle" rowspan="1" colspan="1">8239</td><td align="center" valign="middle" rowspan="1" colspan="1">21,762</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td rowspan="5" align="center" valign="middle" colspan="1"><italic>UBE1Y</italic></td><td rowspan="5" align="center" valign="middle" colspan="1">Fragmented</td><td align="center" valign="middle" rowspan="1" colspan="1">504</td><td align="center" valign="middle" rowspan="1" colspan="1">28,869</td><td align="center" valign="middle" rowspan="1" colspan="1">42,400</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">612</td><td align="center" valign="middle" rowspan="1" colspan="1">22,935 </td><td align="center" valign="middle" rowspan="1" colspan="1">23,670</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">703</td><td align="center" valign="middle" rowspan="1" colspan="1">16,522</td><td align="center" valign="middle" rowspan="1" colspan="1">25,924</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">828</td><td align="center" valign="middle" rowspan="1" colspan="1">5048</td><td align="center" valign="middle" rowspan="1" colspan="1">14,951</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">1224</td><td align="center" valign="middle" rowspan="1" colspan="1">6911</td><td align="center" valign="middle" rowspan="1" colspan="1">7033</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>USP9Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">238,257</td><td align="center" valign="middle" rowspan="1" colspan="1">355,974</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>UTY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">39,840</td><td align="center" valign="middle" rowspan="1" colspan="1">178,019</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>WWC3Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">303,473</td><td align="center" valign="middle" rowspan="1" colspan="1">425,370</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><italic>ZFY</italic></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Present</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">310</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">55,006</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">67,293</td></tr></tbody></table></table-wrap><table-wrap id="genes-10-00409-t004" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-10-00409-t004_Table 4</object-id><label>Table 4</label><caption><p>Dog orthologs of red fox predicted genes. The best-hit canine protein sequence was selected using protein BLAST (blastp) against NCBI protein database. When the best-hit gene is not located on the dog Y-chromosome, its chromosomal position is also indicated. The overlap column describes whether the position of the predicted gene in the red fox genome overlaps the position assigned using the dog version of the gene as a query against the fox genome.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Predicted Gene</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Scaffold</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Start</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">End</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Dog Best Hit Name</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Accession Number</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Overlap</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011272</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">28,248</td><td align="center" valign="middle" rowspan="1" colspan="1">178,019</td><td align="center" valign="middle" rowspan="1" colspan="1">UTY</td><td align="center" valign="middle" rowspan="1" colspan="1">NM_001284484.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011273</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">185,825</td><td align="center" valign="middle" rowspan="1" colspan="1">186,022</td><td align="center" valign="middle" rowspan="1" colspan="1">RPS20 (chr20)</td><td align="center" valign="middle" rowspan="1" colspan="1">XM_542128.5</td><td align="center" valign="middle" rowspan="1" colspan="1">No</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011274</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">202,921</td><td align="center" valign="middle" rowspan="1" colspan="1">215,729</td><td align="center" valign="middle" rowspan="1" colspan="1">DDX3Y</td><td align="center" valign="middle" rowspan="1" colspan="1">JX964855.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011275</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">236,816</td><td align="center" valign="middle" rowspan="1" colspan="1">355,974</td><td align="center" valign="middle" rowspan="1" colspan="1">USP9Y</td><td align="center" valign="middle" rowspan="1" colspan="1">JX964851.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011276</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">466,274</td><td align="center" valign="middle" rowspan="1" colspan="1">499,306</td><td align="center" valign="middle" rowspan="1" colspan="1">KDM5D</td><td align="center" valign="middle" rowspan="1" colspan="1">NM_001113458.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V011277</td><td align="center" valign="middle" rowspan="1" colspan="1">292</td><td align="center" valign="middle" rowspan="1" colspan="1">647,015</td><td align="center" valign="middle" rowspan="1" colspan="1">648,668</td><td align="center" valign="middle" rowspan="1" colspan="1">HSFY</td><td align="center" valign="middle" rowspan="1" colspan="1">JX964870.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V012194</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">54,922</td><td align="center" valign="middle" rowspan="1" colspan="1">67,302</td><td align="center" valign="middle" rowspan="1" colspan="1">ZFY</td><td align="center" valign="middle" rowspan="1" colspan="1">JX964866.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V012195</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">165,975</td><td align="center" valign="middle" rowspan="1" colspan="1">168,466</td><td align="center" valign="middle" rowspan="1" colspan="1">EIF2S3 (chrX)</td><td align="center" valign="middle" rowspan="1" colspan="1">XM_537983.6</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V012196</td><td align="center" valign="middle" rowspan="1" colspan="1">310</td><td align="center" valign="middle" rowspan="1" colspan="1">218,169</td><td align="center" valign="middle" rowspan="1" colspan="1">450,681</td><td align="center" valign="middle" rowspan="1" colspan="1">WWC3 (chrX)</td><td align="center" valign="middle" rowspan="1" colspan="1">XM_548855.6</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Vulp_V014417</td><td align="center" valign="middle" rowspan="1" colspan="1">431</td><td align="center" valign="middle" rowspan="1" colspan="1">74,746</td><td align="center" valign="middle" rowspan="1" colspan="1">75,342</td><td align="center" valign="middle" rowspan="1" colspan="1">SRY</td><td align="center" valign="middle" rowspan="1" colspan="1">KP081776.1</td><td align="center" valign="middle" rowspan="1" colspan="1">Yes</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Vulp_V018159</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">703</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">14,088</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">19,601</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">UBE1Y</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">JX964860.1</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Yes</td></tr></tbody></table></table-wrap><table-wrap id="genes-10-00409-t005" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-10-00409-t005_Table 5</object-id><label>Table 5</label><caption><p>Clusters identified with <italic>k</italic>-means clustering. The centers of the clusters identified by <italic>k</italic>-means clustering are based on a Cartesian plot of the two metrics. The chromosome type most consistent with each cluster’s position is indicated. As expected, because the scores are normalized, the centroid for the autosomes is at approximately (0,0), whereas the centroid for the X-chromosome is to the left of 0 (i.e., the normalized CNV-Seq score is negative), and the centroid for the Y-chromosome is to the right (i.e., the normalized CNV-Seq score is positive).</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Cluster</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Normalized Percent Mapped Reads Contributed by Males (CNV-Seq)</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Normalized Percent 18-mers Unique to Males (YGS.pl)</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Windows</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Scaffolds</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Most Likely Chromosome Type</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">1</td><td align="center" valign="middle" rowspan="1" colspan="1">11.173</td><td align="center" valign="middle" rowspan="1" colspan="1">1.178</td><td align="center" valign="middle" rowspan="1" colspan="1">752</td><td align="center" valign="middle" rowspan="1" colspan="1">180</td><td align="center" valign="middle" rowspan="1" colspan="1">Y-Chromosome</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">2</td><td align="center" valign="middle" rowspan="1" colspan="1">0.173</td><td align="center" valign="middle" rowspan="1" colspan="1">−0.326</td><td align="center" valign="middle" rowspan="1" colspan="1">461,795</td><td align="center" valign="middle" rowspan="1" colspan="1">11,263</td><td align="center" valign="middle" rowspan="1" colspan="1">Autosome</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">3</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">−3.822</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">−0.399</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">23,200</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">305</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">X-Chromosome</td></tr></tbody></table></table-wrap><table-wrap id="genes-10-00409-t006" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-10-00409-t006_Table 6</object-id><label>Table 6</label><caption><p>Summary of gene status in horse, cat, grey wolf, dog, and red fox based on the current literature. Grey shading indicates genes for which copy number estimates were available in all five taxa, and an estimated copy number is provided in these cells. Wolf estimates for <italic>AMELY, FLJ36031Y</italic>, and <italic>RPS4Y</italic> were determined by BLAST against the wolf reference genome using the same parameters used in the fox versus cat analysis (<xref ref-type="app" rid="app1-genes-10-00409">Table S2</xref>). Starred gene names (*) indicate the 11 core carnivore Y-chromosome genes [<xref rid="B31-genes-10-00409" ref-type="bibr">31</xref>]. +/- indicate binary presence/absence of gene based on current literature. ++ indicates genes that are multicopy but with no estimate of copy number specified. The question mark (?) indicates uncertainty about gene status. +* indicates ambiguity in the literature about which copy of a duplicated gene was observed.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gene/Gene Family</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Horse</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Cat</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Red Fox</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Wolf</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Dog</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>AMELY</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">?</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>AP1S2Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>BCORY1</italic></td><td rowspan="2" align="center" valign="middle" colspan="1">+*</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td rowspan="2" align="center" valign="middle" colspan="1">+*</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>BCORY2</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>CUL4BY *</italic></td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">9</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">3+</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~25</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~10</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">++</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TXLNGY *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>DDX3Y *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>DYNG</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>EIF1AY *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>EIF2S3Y *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>FLJ36031Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>HSFY</italic></td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">3</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">11</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~1</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>KDM5D *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>OFD1</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>RBMYL *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>RPS4Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>SRY *</italic></td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~4</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">3</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">7</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TETY1</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td rowspan="2" align="center" valign="middle" colspan="1">+*</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TETY2</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TMSB4Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>TSPY</italic></td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">13</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">10</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">-</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~100</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">25+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>UBE1Y/UBA1Y *</italic></td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">8+</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">~36</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">2</td><td align="center" valign="middle" style="background:#D9D9D9" rowspan="1" colspan="1">1</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>USP9Y *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>UTY *</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>WWC3Y</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">+</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><italic>ZFY</italic></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">+</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">+</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">+</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">+</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">+</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">References</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B32-genes-10-00409" ref-type="bibr">32</xref>,<xref rid="B44-genes-10-00409" ref-type="bibr">44</xref>]</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B6-genes-10-00409" ref-type="bibr">6</xref>,<xref rid="B7-genes-10-00409" ref-type="bibr">7</xref>,<xref rid="B31-genes-10-00409" ref-type="bibr">31</xref>,<xref rid="B35-genes-10-00409" ref-type="bibr">35</xref>,<xref rid="B44-genes-10-00409" ref-type="bibr">44</xref>,<xref rid="B72-genes-10-00409" ref-type="bibr">72</xref>]</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><xref rid="genes-10-00409-t002" ref-type="table">Table 2</xref> and <xref rid="genes-10-00409-t003" ref-type="table">Table 3</xref></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B14-genes-10-00409" ref-type="bibr">14</xref>]; <xref ref-type="app" rid="app1-genes-10-00409">Table S2</xref></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B6-genes-10-00409" ref-type="bibr">6</xref>,<xref rid="B7-genes-10-00409" ref-type="bibr">7</xref>,<xref rid="B44-genes-10-00409" ref-type="bibr">44</xref>]</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Illinois</li></region></list><tree><noCountry><name sortKey="Farre, Marta" sort="Farre, Marta" uniqKey="Farre M" first="Marta" last="Farré">Marta Farré</name><name sortKey="Johnson, Jennifer L" sort="Johnson, Jennifer L" uniqKey="Johnson J" first="Jennifer L." last="Johnson">Jennifer L. Johnson</name><name sortKey="Kukekova, Anna V" sort="Kukekova, Anna V" uniqKey="Kukekova A" first="Anna V." last="Kukekova">Anna V. Kukekova</name><name sortKey="Stutchman, Jeremy T" sort="Stutchman, Jeremy T" uniqKey="Stutchman J" first="Jeremy T." last="Stutchman">Jeremy T. Stutchman</name><name sortKey="Trut, Lyudmila N" sort="Trut, Lyudmila N" uniqKey="Trut L" first="Lyudmila N." last="Trut">Lyudmila N. Trut</name><name sortKey="Wadlington, William H" sort="Wadlington, William H" uniqKey="Wadlington W" first="William H." last="Wadlington">William H. Wadlington</name></noCountry><country name="États-Unis"><region name="Illinois"><name sortKey="Rando, Halie M" sort="Rando, Halie M" uniqKey="Rando H" first="Halie M." last="Rando">Halie M. Rando</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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