Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with di...
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| creator | Jaratlerdsiri, Weerachai Deakin, Janine Godinez, Ricardo M Shan, Xueyan Peterson, Daniel G Marthey, Sylvain Lyons, Eric McCarthy, Fiona M Isberg, Sally R Higgins, Damien P Chong, Amanda Y John, John St Glenn, Travis C Ray, David A Gongora, Jaime |
| description | The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs. |
| doi_str_mv | 10.1371/journal.pone.0114631 |
| format | Article |
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The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0114631</identifier><identifier>PMID: 25503521</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptive immunity ; Alligators ; Alligators and Crocodiles - genetics ; Alligators and Crocodiles - virology ; Analysis ; Animals ; Antigen presentation ; Aquatic reptiles ; Artificial chromosomes ; Bacterial artificial chromosomes ; Biochemistry ; Bioinformatics ; Biology and Life Sciences ; Biotechnology ; Birds ; Chromosomes ; Chromosomes, Artificial, Bacterial - genetics ; Clusters ; Contig Mapping ; Crocodiles ; Crocodylidae ; Crocodylus porosus ; Gene clusters ; Gene order ; Gene sequencing ; Genes ; Genes, MHC Class I - genetics ; Genes, MHC Class II - genetics ; Genomes ; Genomics ; Immunity ; Life Sciences ; Major histocompatibility complex ; Molecular biology ; Plant pathology ; Reptiles & amphibians ; Retroelements - genetics ; Retroviridae - genetics ; Saline water ; Science ; Six gene ; Species Specificity ; Synteny ; Vertebrates ; Zebrafish</subject><ispartof>PloS one, 2014-12, Vol.9 (12), p.e114631</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Jaratlerdsiri 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>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>2014 Jaratlerdsiri et al 2014 Jaratlerdsiri et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c726t-11df5ad9e23cf7ca47252f15b328bb675f4be0bd91d64e9d7f78389f5209f5e13</citedby><cites>FETCH-LOGICAL-c726t-11df5ad9e23cf7ca47252f15b328bb675f4be0bd91d64e9d7f78389f5209f5e13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263668/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263668/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25503521$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01194095$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Jaratlerdsiri, Weerachai</creatorcontrib><creatorcontrib>Deakin, Janine</creatorcontrib><creatorcontrib>Godinez, Ricardo M</creatorcontrib><creatorcontrib>Shan, Xueyan</creatorcontrib><creatorcontrib>Peterson, Daniel G</creatorcontrib><creatorcontrib>Marthey, Sylvain</creatorcontrib><creatorcontrib>Lyons, Eric</creatorcontrib><creatorcontrib>McCarthy, Fiona M</creatorcontrib><creatorcontrib>Isberg, Sally R</creatorcontrib><creatorcontrib>Higgins, Damien P</creatorcontrib><creatorcontrib>Chong, Amanda Y</creatorcontrib><creatorcontrib>John, John St</creatorcontrib><creatorcontrib>Glenn, Travis C</creatorcontrib><creatorcontrib>Ray, David A</creatorcontrib><creatorcontrib>Gongora, Jaime</creatorcontrib><title>Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.</description><subject>Adaptive immunity</subject><subject>Alligators</subject><subject>Alligators and Crocodiles - genetics</subject><subject>Alligators and Crocodiles - virology</subject><subject>Analysis</subject><subject>Animals</subject><subject>Antigen presentation</subject><subject>Aquatic reptiles</subject><subject>Artificial chromosomes</subject><subject>Bacterial artificial chromosomes</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Birds</subject><subject>Chromosomes</subject><subject>Chromosomes, Artificial, Bacterial - genetics</subject><subject>Clusters</subject><subject>Contig Mapping</subject><subject>Crocodiles</subject><subject>Crocodylidae</subject><subject>Crocodylus porosus</subject><subject>Gene clusters</subject><subject>Gene order</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, MHC Class I - genetics</subject><subject>Genes, MHC Class II - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Immunity</subject><subject>Life Sciences</subject><subject>Major histocompatibility complex</subject><subject>Molecular biology</subject><subject>Plant pathology</subject><subject>Reptiles & amphibians</subject><subject>Retroelements - genetics</subject><subject>Retroviridae - genetics</subject><subject>Saline water</subject><subject>Science</subject><subject>Six gene</subject><subject>Species Specificity</subject><subject>Synteny</subject><subject>Vertebrates</subject><subject>Zebrafish</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl-L00AUxYMo7rr6DUQDgrAPrZm_SV6EUtQWKgu6-jpMZu60s6SZ7sykut_eqc0ujShIIBkmv3Mu996TZS9RMUWkRO9uXO872U53roNpgRDlBD3KzlFN8ITjgjw-OZ9lz0K4KQpGKs6fZmeYsYIwjM6z67nb7qSX0e4hX0PntpDLZHsXIOQe9iDbXNsQbadiHqLvVew95LbL4wbyINv4Q0bwufJOOW1byD8v5s-zJ0a2AV4M34vs28cP1_PFZHX1aTmfrSaqxDxOENKGSV0DJsqUStISM2wQawiumoaXzNAGikbXSHMKtS5NWZGqNgwX6QWIXGSvj7671gUxDCQIxFNvtKYlScTySGgnb8TO2630d8JJK35fOL8W0kerWhC0oYYrQxGuJSVaVaqkRdNQjRijVOLk9X6o1jdb0Aq66GU7Mh3_6exGrN1eUMwJ51UyuDwabP6QLWYrcbhLW6xpUbP9obU3QzHvbnsI8R_tDdRapg5sZ1wqrLY2KDGjqEpg2nOipn-h0qNha1WKj0l7GwsuR4LERPgZ17IPQSy_fvl_9ur7mH17wm5StuImuLaP1nVhDNIjmGIVggfzMC5UiEP676chDukXQ_qT7NXphh5E93EnvwDu6_64</recordid><startdate>20141211</startdate><enddate>20141211</enddate><creator>Jaratlerdsiri, Weerachai</creator><creator>Deakin, Janine</creator><creator>Godinez, Ricardo M</creator><creator>Shan, Xueyan</creator><creator>Peterson, Daniel G</creator><creator>Marthey, Sylvain</creator><creator>Lyons, Eric</creator><creator>McCarthy, Fiona M</creator><creator>Isberg, Sally R</creator><creator>Higgins, Damien P</creator><creator>Chong, Amanda Y</creator><creator>John, John St</creator><creator>Glenn, Travis C</creator><creator>Ray, David A</creator><creator>Gongora, Jaime</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>IOV</scope><scope>ISR</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>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20141211</creationdate><title>Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC</title><author>Jaratlerdsiri, Weerachai ; Deakin, Janine ; Godinez, Ricardo M ; Shan, Xueyan ; Peterson, Daniel G ; Marthey, Sylvain ; Lyons, Eric ; McCarthy, Fiona M ; Isberg, Sally R ; Higgins, Damien P ; Chong, Amanda Y ; John, John St ; Glenn, Travis C ; Ray, David A ; Gongora, Jaime</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c726t-11df5ad9e23cf7ca47252f15b328bb675f4be0bd91d64e9d7f78389f5209f5e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adaptive immunity</topic><topic>Alligators</topic><topic>Alligators and Crocodiles - 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genetics</topic><topic>Retroviridae - genetics</topic><topic>Saline water</topic><topic>Science</topic><topic>Six gene</topic><topic>Species Specificity</topic><topic>Synteny</topic><topic>Vertebrates</topic><topic>Zebrafish</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jaratlerdsiri, Weerachai</creatorcontrib><creatorcontrib>Deakin, Janine</creatorcontrib><creatorcontrib>Godinez, Ricardo M</creatorcontrib><creatorcontrib>Shan, Xueyan</creatorcontrib><creatorcontrib>Peterson, Daniel G</creatorcontrib><creatorcontrib>Marthey, Sylvain</creatorcontrib><creatorcontrib>Lyons, Eric</creatorcontrib><creatorcontrib>McCarthy, Fiona M</creatorcontrib><creatorcontrib>Isberg, Sally R</creatorcontrib><creatorcontrib>Higgins, Damien P</creatorcontrib><creatorcontrib>Chong, Amanda Y</creatorcontrib><creatorcontrib>John, John St</creatorcontrib><creatorcontrib>Glenn, Travis C</creatorcontrib><creatorcontrib>Ray, David A</creatorcontrib><creatorcontrib>Gongora, Jaime</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</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>Jaratlerdsiri, Weerachai</au><au>Deakin, Janine</au><au>Godinez, Ricardo M</au><au>Shan, Xueyan</au><au>Peterson, Daniel G</au><au>Marthey, Sylvain</au><au>Lyons, Eric</au><au>McCarthy, Fiona M</au><au>Isberg, Sally R</au><au>Higgins, Damien P</au><au>Chong, Amanda Y</au><au>John, John St</au><au>Glenn, Travis C</au><au>Ray, David A</au><au>Gongora, Jaime</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-12-11</date><risdate>2014</risdate><volume>9</volume><issue>12</issue><spage>e114631</spage><pages>e114631-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25503521</pmid><doi>10.1371/journal.pone.0114631</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2014-12, Vol.9 (12), p.e114631 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1635249473 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adaptive immunity Alligators Alligators and Crocodiles - genetics Alligators and Crocodiles - virology Analysis Animals Antigen presentation Aquatic reptiles Artificial chromosomes Bacterial artificial chromosomes Biochemistry Bioinformatics Biology and Life Sciences Biotechnology Birds Chromosomes Chromosomes, Artificial, Bacterial - genetics Clusters Contig Mapping Crocodiles Crocodylidae Crocodylus porosus Gene clusters Gene order Gene sequencing Genes Genes, MHC Class I - genetics Genes, MHC Class II - genetics Genomes Genomics Immunity Life Sciences Major histocompatibility complex Molecular biology Plant pathology Reptiles & amphibians Retroelements - genetics Retroviridae - genetics Saline water Science Six gene Species Specificity Synteny Vertebrates Zebrafish |
| title | Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC |
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