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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...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263668/ https://www.ncbi.nlm.nih.gov/pubmed/25503521 http://dx.doi.org/10.1371/journal.pone.0114631 |
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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_facet | 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 | Jaratlerdsiri, Weerachai |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-4263668 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42636682014-12-19 Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC 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 PLoS One Research Article 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. Public Library of Science 2014-12-11 /pmc/articles/PMC4263668/ /pubmed/25503521 http://dx.doi.org/10.1371/journal.pone.0114631 Text en © 2014 Jaratlerdsiri et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article 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 Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title | Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title_full | Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title_fullStr | Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title_full_unstemmed | Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title_short | Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC |
title_sort | comparative genome analyses reveal distinct structure in the saltwater crocodile mhc |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263668/ https://www.ncbi.nlm.nih.gov/pubmed/25503521 http://dx.doi.org/10.1371/journal.pone.0114631 |
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