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Immunogenetics

, Volume 66, Issue 7–8, pp 479–492 | Cite as

Genomic V exons from whole genome shotgun data in reptiles

  • D. N. Olivieri
  • B. von Haeften
  • C. Sánchez-Espinel
  • J. Faro
  • F. Gambón-Deza
Original Paper

Abstract

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

Keywords

Immunologic repertoire Reptile evolution Immunoglobulin (IG) T cell receptor (TR) Variable (V) gene 

Notes

Acknowledgments

This work was partially supported by the European Union 7th Framework Programme [FP7/REGPOT-2012-2013.1] under grant agreement no. 316265, BIOCAPS. JF acknowledges the support of PIRSES-GA-2012-317893 (7th FP, EC).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • D. N. Olivieri
    • 1
  • B. von Haeften
    • 2
  • C. Sánchez-Espinel
    • 3
  • J. Faro
    • 4
    • 5
    • 6
  • F. Gambón-Deza
    • 5
    • 7
  1. 1.School of Computer EngineeringUniversity of VigoOurenseSpain
  2. 2.Area of Immunology, Faculty of BiologyUniversity of VigoVigoSpain
  3. 3.Nanoimmunotech SLVigoSpain
  4. 4.Immunology, Faculty of Biology, and Biomedical Research Center (CINBIO)University of VigoVigoSpain
  5. 5.Instituto Biomédico de VigoVigoSpain
  6. 6.Instituto Gulbenkian de CienciaOeirasPortugal
  7. 7.Servicio Gallego de Salud (SERGAS), Unidad de InmunologiaHospital do MeixoeiroVigoSpain

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