Sequences, Annotation and Single Nucleotide Polymorphism of the Major Histocompatibility Complex in the Domestic Cat
Identifieur interne : 000694 ( Pmc/Curation ); précédent : 000693; suivant : 000695Sequences, Annotation and Single Nucleotide Polymorphism of the Major Histocompatibility Complex in the Domestic Cat
Auteurs : Naoya Yuhki [États-Unis] ; James C. Mullikin [États-Unis] ; Thomas Beck [États-Unis] ; Robert Stephens [États-Unis] ; Stephen J. O'Brien [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2008.
Abstract
Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a chromosomal inversion were annotated in detail. Gene annotation of this MHC was completed and identified 183 possible coding regions, 147 human homologues, possible functional genes and 36 pseudo/unidentified genes) by GENSCAN and BLASTN, BLASTP RepeatMasker programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens) lacking the functional DP, DQ regions, nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and LMP2/LMP7,TAP1/TAP2), 52 class III genes, nineteen class I genes/gene fragments (FLAI-A to FLAI-S). Three class I genes (FLAI-H, I-K, I-E) may encode functional classical class I antigens based on deduced amino acid sequence and promoter structure. The second region spans 0.362 Mbp sequence encoding no class I genes and 18 cross-species conserved genes, excluding class I, II and their functionally related/associated genes, namely framework genes, including three olfactory receptor genes. One previously identified feline endogenous retrovirus, a baboon retrovirus derived sequence (ECE1) and two new endogenous retrovirus sequences, similar to brown bat endogenous retrovirus (FERVmlu1, FERVmlu2) were found within a 140 Kbp interval in the middle of class I region. MHC SNPs were examined based on comparisons of this BAC sequence and MHC homozygous 1.9× WGS sequences and found that 11,654 SNPs in 2.84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in the WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp).
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DOI: 10.1371/journal.pone.0002674
PubMed: 18629345
PubMed Central: 2453318
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Mullikin</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Beck, Thomas" sort="Beck, Thomas" uniqKey="Beck T" first="Thomas" last="Beck">Thomas Beck</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>SAIC-Frederick, Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>SAIC-Frederick, Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Stephens, Robert" sort="Stephens, Robert" uniqKey="Stephens R" first="Robert" last="Stephens">Robert Stephens</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>SAIC-Frederick, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>SAIC-Frederick, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="O Brien, Stephen J" sort="O Brien, Stephen J" uniqKey="O Brien S" first="Stephen J." last="O'Brien">Stephen J. O'Brien</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a chromosomal inversion were annotated in detail. Gene annotation of this MHC was completed and identified 183 possible coding regions, 147 human homologues, possible functional genes and 36 pseudo/unidentified genes) by GENSCAN and BLASTN, BLASTP RepeatMasker programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens) lacking the functional DP, DQ regions, nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and LMP2/LMP7,TAP1/TAP2), 52 class III genes, nineteen class I genes/gene fragments (FLAI-A to FLAI-S). Three class I genes (FLAI-H, I-K, I-E) may encode functional classical class I antigens based on deduced amino acid sequence and promoter structure. The second region spans 0.362 Mbp sequence encoding no class I genes and 18 cross-species conserved genes, excluding class I, II and their functionally related/associated genes, namely framework genes, including three olfactory receptor genes. One previously identified feline endogenous retrovirus, a baboon retrovirus derived sequence (ECE1) and two new endogenous retrovirus sequences, similar to brown bat endogenous retrovirus (FERVmlu1, FERVmlu2) were found within a 140 Kbp interval in the middle of class I region. MHC SNPs were examined based on comparisons of this BAC sequence and MHC homozygous 1.9× WGS sequences and found that 11,654 SNPs in 2.84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in the WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp).</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Klein, J" uniqKey="Klein J">J Klein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Younger, Rm" uniqKey="Younger R">RM Younger</name></author><author><name sortKey="Amadou, C" uniqKey="Amadou C">C Amadou</name></author><author><name sortKey="Bethel, G" uniqKey="Bethel G">G Bethel</name></author><author><name sortKey="Ehlers, A" uniqKey="Ehlers A">A Ehlers</name></author><author><name sortKey="Fischer Lindahl, K" uniqKey="Fischer Lindahl K">K Fischer 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18629345</article-id><article-id pub-id-type="pmc">2453318</article-id><article-id pub-id-type="publisher-id">07-PONE-RA-02440R2</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0002674</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Genetics and Genomics/Animal Genetics</subject><subject>Genetics and Genomics/Comparative Genomics</subject><subject>Genetics and Genomics/Genetics of the Immune System</subject><subject>Genetics and Genomics/Genome Projects</subject></subj-group></article-categories><title-group><article-title>Sequences, Annotation and Single Nucleotide Polymorphism of the Major Histocompatibility Complex in the Domestic Cat</article-title><alt-title alt-title-type="running-head">MHC Structure and SNP Analysis</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yuhki</surname><given-names>Naoya</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mullikin</surname><given-names>James C.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Beck</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Stephens</surname><given-names>Robert</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>O'Brien</surname><given-names>Stephen J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America</addr-line></aff><aff id="aff3"><label>3</label><addr-line>SAIC-Frederick, Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></aff><aff id="aff4"><label>4</label><addr-line>SAIC-Frederick, Advanced Biomedical Computing Center, National Cancer Institute at Frederick, Frederick, Maryland, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Ellegren</surname><given-names>Hans</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">University of Uppsala, Sweden</aff><author-notes><corresp id="cor1">* E-mail: <email>yuhki@ncifcrf.gov</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: NY SJO. Performed the experiments: NY TB. Analyzed the data: NY JCM TB RS. Contributed reagents/materials/analysis tools: NY. Wrote the paper: NY TB.</p></fn></author-notes><pub-date pub-type="collection"><year>2008</year></pub-date><pub-date pub-type="epub"><day>16</day><month>7</month><year>2008</year></pub-date><volume>3</volume><issue>7</issue><elocation-id>e2674</elocation-id><history><date date-type="received"><day>9</day><month>10</month><year>2007</year></date><date date-type="accepted"><day>12</day><month>6</month><year>2008</year></date></history><permissions><copyright-statement>This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.</copyright-statement><copyright-year>2008</copyright-year><license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.</license-p></license></permissions><abstract><p>Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a chromosomal inversion were annotated in detail. Gene annotation of this MHC was completed and identified 183 possible coding regions, 147 human homologues, possible functional genes and 36 pseudo/unidentified genes) by GENSCAN and BLASTN, BLASTP RepeatMasker programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens) lacking the functional DP, DQ regions, nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and LMP2/LMP7,TAP1/TAP2), 52 class III genes, nineteen class I genes/gene fragments (FLAI-A to FLAI-S). Three class I genes (FLAI-H, I-K, I-E) may encode functional classical class I antigens based on deduced amino acid sequence and promoter structure. The second region spans 0.362 Mbp sequence encoding no class I genes and 18 cross-species conserved genes, excluding class I, II and their functionally related/associated genes, namely framework genes, including three olfactory receptor genes. One previously identified feline endogenous retrovirus, a baboon retrovirus derived sequence (ECE1) and two new endogenous retrovirus sequences, similar to brown bat endogenous retrovirus (FERVmlu1, FERVmlu2) were found within a 140 Kbp interval in the middle of class I region. MHC SNPs were examined based on comparisons of this BAC sequence and MHC homozygous 1.9× WGS sequences and found that 11,654 SNPs in 2.84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in the WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp).</p></abstract><counts><page-count count="17"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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