The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene
Although IgD first appeared, along with IgM, in the cartilaginous fishes and has been retained throughout subsequent vertebrate evolution, it has been lost in a diverse group of vertebrate species. We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene with...
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| description | Although IgD first appeared, along with IgM, in the cartilaginous fishes and has been retained throughout subsequent vertebrate evolution, it has been lost in a diverse group of vertebrate species. We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene within 13.5 kb downstream of the IgM gene. We report here that, by conducting BLAST searches of rabbit Ig heavy chain genomic DNA with known mammalian IgD exons, we identified the remnant of the rabbit Cδ gene approximately 21 kb downstream of the IgM gene. The remnant Cδ locus lacks the δCH1 and hinge exons, but contains truncated δCH2 and δCH3 exons, as well as largely intact, but non-functional, secretory and transmembrane exons. In addition, we report that the Cδ gene probably became non-functional in leporids at least prior to the divergence of rabbits and hares ~12 million years ago. |
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We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene within 13.5 kb downstream of the IgM gene. We report here that, by conducting BLAST searches of rabbit Ig heavy chain genomic DNA with known mammalian IgD exons, we identified the remnant of the rabbit Cδ gene approximately 21 kb downstream of the IgM gene. The remnant Cδ locus lacks the δCH1 and hinge exons, but contains truncated δCH2 and δCH3 exons, as well as largely intact, but non-functional, secretory and transmembrane exons. In addition, we report that the Cδ gene probably became non-functional in leporids at least prior to the divergence of rabbits and hares ~12 million years ago.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0182029</identifier><identifier>PMID: 28832642</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Base Sequence ; Biological evolution ; Biology and Life Sciences ; Deoxyribonucleic acid ; Divergence ; DNA ; European rabbit ; Evolution ; Exons ; Genes ; Genetic aspects ; Identification ; Immunoglobulin D ; Immunoglobulin D - genetics ; Immunoglobulin M ; Immunoglobulins ; Immunology ; Lymphocytes ; Mammals ; Phylogeny ; Rabbits ; Research and Analysis Methods ; Sequence Homology, Amino Acid ; Vertebrates</subject><ispartof>PloS one, 2017-08, Vol.12 (8), p.e0182029-e0182029</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Lanning et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Lanning et al 2017 Lanning et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-5921b8596fed8213ab6935522f1687c140095b06986aec5e173586cf4984a9333</citedby><cites>FETCH-LOGICAL-c593t-5921b8596fed8213ab6935522f1687c140095b06986aec5e173586cf4984a9333</cites><orcidid>0000-0002-1079-5439</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568218/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568218/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28832642$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Yu, Kefei</contributor><creatorcontrib>Lanning, Dennis K</creatorcontrib><creatorcontrib>Esteves, Pedro J</creatorcontrib><creatorcontrib>Knight, Katherine L</creatorcontrib><title>The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Although IgD first appeared, along with IgM, in the cartilaginous fishes and has been retained throughout subsequent vertebrate evolution, it has been lost in a diverse group of vertebrate species. We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene within 13.5 kb downstream of the IgM gene. We report here that, by conducting BLAST searches of rabbit Ig heavy chain genomic DNA with known mammalian IgD exons, we identified the remnant of the rabbit Cδ gene approximately 21 kb downstream of the IgM gene. The remnant Cδ locus lacks the δCH1 and hinge exons, but contains truncated δCH2 and δCH3 exons, as well as largely intact, but non-functional, secretory and transmembrane exons. In addition, we report that the Cδ gene probably became non-functional in leporids at least prior to the divergence of rabbits and hares ~12 million years ago.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>European rabbit</subject><subject>Evolution</subject><subject>Exons</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Identification</subject><subject>Immunoglobulin D</subject><subject>Immunoglobulin D - genetics</subject><subject>Immunoglobulin M</subject><subject>Immunoglobulins</subject><subject>Immunology</subject><subject>Lymphocytes</subject><subject>Mammals</subject><subject>Phylogeny</subject><subject>Rabbits</subject><subject>Research and Analysis Methods</subject><subject>Sequence Homology, Amino Acid</subject><subject>Vertebrates</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUk1v1DAUjBCIlsI_QBCJSzns4u_Yl0rVUmClSr2Us-U4z6lXWXuxE6T-e7zdtOqiygfbzzPz3lhTVR8xWmLa4G-bOKVghuUuBlgiLAki6lV1ihUlC0EQff3sfFK9y3mDEKdSiLfVCZGSEsHIabW6vYM6wTaYMNbR1WO5Xk0p7sCEOpm29WN9fpPu7RgH00-5tlPwdhqm_LVe99_rHgK8r944M2T4MO9n1e8fV7erX4vrm5_r1eX1wnJFxwVXBLeSK-GgkwRT0wpFOSfEYSEbixlCirdIKCkMWA64oVwK65iSzChK6Vn1-aC7G2LWs_-si0ssFENUFcT6gOii2ehd8luT7nU0Xj8UYuq1SaO3A2jFDWuUsoyzjjlGFAJusHXcMQBjWNG6mLtN7RY6C2FMZjgSPX4J_k738a_mXBR7sgiczwIp_pkgj3rrs4VhMAHi9DA3wQITxQv0y3_Ql93NqN4UAz64WPravai-5AgLwXnTFNTyBVRZHWy9LWFxvtSPCOxAsCnmnMA9ecRI76P2OIzeR03PUSu0T8__54n0mC36D6Oyzd4</recordid><startdate>20170823</startdate><enddate>20170823</enddate><creator>Lanning, Dennis K</creator><creator>Esteves, Pedro J</creator><creator>Knight, Katherine L</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-1079-5439</orcidid></search><sort><creationdate>20170823</creationdate><title>The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene</title><author>Lanning, Dennis K ; Esteves, Pedro J ; Knight, Katherine L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-5921b8596fed8213ab6935522f1687c140095b06986aec5e173586cf4984a9333</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Deoxyribonucleic acid</topic><topic>Divergence</topic><topic>DNA</topic><topic>European rabbit</topic><topic>Evolution</topic><topic>Exons</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Identification</topic><topic>Immunoglobulin D</topic><topic>Immunoglobulin D - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lanning, Dennis K</au><au>Esteves, Pedro J</au><au>Knight, Katherine L</au><au>Yu, Kefei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-08-23</date><risdate>2017</risdate><volume>12</volume><issue>8</issue><spage>e0182029</spage><epage>e0182029</epage><pages>e0182029-e0182029</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Although IgD first appeared, along with IgM, in the cartilaginous fishes and has been retained throughout subsequent vertebrate evolution, it has been lost in a diverse group of vertebrate species. We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene within 13.5 kb downstream of the IgM gene. We report here that, by conducting BLAST searches of rabbit Ig heavy chain genomic DNA with known mammalian IgD exons, we identified the remnant of the rabbit Cδ gene approximately 21 kb downstream of the IgM gene. The remnant Cδ locus lacks the δCH1 and hinge exons, but contains truncated δCH2 and δCH3 exons, as well as largely intact, but non-functional, secretory and transmembrane exons. In addition, we report that the Cδ gene probably became non-functional in leporids at least prior to the divergence of rabbits and hares ~12 million years ago.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28832642</pmid><doi>10.1371/journal.pone.0182029</doi><orcidid>https://orcid.org/0000-0002-1079-5439</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Base Sequence Biological evolution Biology and Life Sciences Deoxyribonucleic acid Divergence DNA European rabbit Evolution Exons Genes Genetic aspects Identification Immunoglobulin D Immunoglobulin D - genetics Immunoglobulin M Immunoglobulins Immunology Lymphocytes Mammals Phylogeny Rabbits Research and Analysis Methods Sequence Homology, Amino Acid Vertebrates |
| title | The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene |
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