Genomic V exons from whole genome shotgun data in reptiles

Immunogenetics volume 66, pages479–492(2014)Cite this article

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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).

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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).

Author information

Affiliations

  1. School of Computer Engineering, University of Vigo, 32004, Ourense, Spain

    D. N. Olivieri

  2. Area of Immunology, Faculty of Biology, University of Vigo, 36310, Vigo, Spain

    B. von Haeften

  3. Nanoimmunotech SL, Pza. Fernando Conde, Montero Ríos 9, 3620, Vigo, Spain

    C. Sánchez-Espinel

  4. Immunology, Faculty of Biology, and Biomedical Research Center (CINBIO), University of Vigo, 36310, Vigo, Spain

    J. Faro

  5. Instituto Biomédico de Vigo, 36310, Vigo, Spain

    J. Faro & F. Gambón-Deza

  6. Instituto Gulbenkian de Ciencia, 2781-901, Oeiras, Portugal

    J. Faro

  7. Servicio Gallego de Salud (SERGAS), Unidad de Inmunologia, Hospital do Meixoeiro, 36210, Vigo, Spain

    F. Gambón-Deza

Authors
  1. D. N. Olivieri
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  2. B. von Haeften
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  3. C. Sánchez-Espinel
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  4. J. Faro
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  5. F. Gambón-Deza
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Correspondence to D. N. Olivieri.

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Olivieri, D.N., von Haeften, B., Sánchez-Espinel, C. et al. Genomic V exons from whole genome shotgun data in reptiles. Immunogenetics 66, 479–492 (2014). https://doi.org/10.1007/s00251-014-0784-3

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Keywords

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