Characterisation and comparative analyses of the saltwater crocodile MHC — ASN Events
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Characterisation and comparative analyses of the saltwater crocodile MHC (#227)

Weerachai Jaratlerdsiri 1 , Janine Deakin 1 , Ricardo M Godinez 2 , Xueyan Shan 3 , Daniel G Peterson 4 , Sylvain Marthey 5 , Eric Lyons 6 , Fiona M McCarthy 7 , Amanda Y Chong 1 , John St John 8 , Travis C Glenn 9 , David A Ray 10 , Damien P Higgins 1 , Sally R Isberg 11 , Jaime Gongora 1
  1. Faculty of Veterinary Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
  2. Department of Organismic and Evolutionary Biology, Universityof Oxford, Cambridge, Massachusetts, USA
  3. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, USA
  4. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, USA
  5. Animal Genetics and Integrative Biology, INRA, Jouy-en-Josas, France
  6. School of Plant Science, University of Arizona, Tucson, USA
  7. School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, USA
  8. Department of Biomolecular Engineering, University of California, Santa Cruz, USA
  9. Department of Environmental Health Science and Georgia Genomics Facility, University of Georgia, Athens, USA
  10. Department of Biological Sciences, Texas Tech University , Texas, USA
  11. Center for Crocodile Research, Noonamah, NT, Australia
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, in particular self-recognition and protection against disease. The MHC is generally divided into classes I, II and III, which are subregions containing genes of similar function across many species, but different gene number and organisation. Although crocodilians occupy the evolutionary mid-point between mammals and birds, thus providing a unique evolutionary link between these groups, research on the MHC genomic region within this lineage has been relatively unexplored. To address this, we characterised the MHC region of the saltwater crocodile by screening, sequencing ofBACs and then comparing the scaffolds from these with genome sequence data from the American alligator and Indian Gharial as well as other vertebrates. Six MHC regions from BACS spanning ~452 kb were identified as containing nine MHC class I, six MHC class II, four TAP and TRIM genes, and a single actin pseudogene. These MHC class I and class II genes were greater in length than their counterparts in the chicken B locus (2.5-11 times) suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses of the saltwater crocodile scaffolds showed separate regions for MHC class I and II and, when compared to two other genomes from the alligator and gharial, there were large syntenic areas among them (> 80% identity) with similar gene order. The close proximity of MHC class I and TAP in the saltwater crocodile suggests an ancestral structure of tetrapod MHC, while the linkage between MHC class I and TRIM39 observed in this species is consistent with newly-rearranged structure in human MHC. This organisation has not been observed in birds suggesting that rearrangement occurred after the divergence of crocodilians and birds from the common ancestor ~240 million years ago. These findings support instability of the saltwater crocodile MHC that differs from that expected in tetrapod ancestors.