Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC

Weerachai Jaratlerdsiri, Janine Deakin, Ricardo M. Godinez, Xueyan Shan, Daniel G. Peterson, Sylvain Marthey, Eric H Lyons, Fiona M McCarthy, Sally R. Isberg, Damien P. Higgins, Amanda Y. Chong, John St John, Travis C. Glenn, David A. Ray, Jaime Gongora

Research output: Contribution to journalArticle

9 Citations (Scopus)

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 crocodilianavian 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.

Original languageEnglish (US)
Article numbere114631
JournalPLoS One
Volume9
Issue number12
DOIs
StatePublished - Dec 11 2014

Fingerprint

Crocodylus porosus
Alligators and Crocodiles
major histocompatibility complex
Major Histocompatibility Complex
Genes
Genome
genome
Crocodylia
genes
MHC Class II Genes
MHC Class I Genes
Vertebrates
vertebrates
Alligator (Alligatoridae)
Birds
Chromosomes
genomics
Bacterial Artificial Chromosomes
Scaffolds
antigen presentation

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Jaratlerdsiri, W., Deakin, J., Godinez, R. M., Shan, X., Peterson, D. G., Marthey, S., ... Gongora, J. (2014). Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS One, 9(12), [e114631]. https://doi.org/10.1371/journal.pone.0114631

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 H; McCarthy, Fiona M; Isberg, Sally R.; Higgins, Damien P.; Chong, Amanda Y.; St John, John; Glenn, Travis C.; Ray, David A.; Gongora, Jaime.

In: PLoS One, Vol. 9, No. 12, e114631, 11.12.2014.

Research output: Contribution to journalArticle

Jaratlerdsiri, W, Deakin, J, Godinez, RM, Shan, X, Peterson, DG, Marthey, S, Lyons, EH, McCarthy, FM, Isberg, SR, Higgins, DP, Chong, AY, St John, J, Glenn, TC, Ray, DA & Gongora, J 2014, 'Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC', PLoS One, vol. 9, no. 12, e114631. https://doi.org/10.1371/journal.pone.0114631
Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S et al. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS One. 2014 Dec 11;9(12). e114631. https://doi.org/10.1371/journal.pone.0114631
Jaratlerdsiri, Weerachai ; Deakin, Janine ; Godinez, Ricardo M. ; Shan, Xueyan ; Peterson, Daniel G. ; Marthey, Sylvain ; Lyons, Eric H ; McCarthy, Fiona M ; Isberg, Sally R. ; Higgins, Damien P. ; Chong, Amanda Y. ; St John, John ; Glenn, Travis C. ; Ray, David A. ; Gongora, Jaime. / Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. In: PLoS One. 2014 ; Vol. 9, No. 12.
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