Abstract
BackgroundCrocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. The recent sequencing of three crocodilian genomes provides an opportunity for a more detailed and accurate representation of the ERV diversity that is present in these species. Here we investigate the diversity, distribution and evolution of ERVs from the genomes of three key crocodilian species, and outline the key processes driving crocodilian ERV proliferation and evolution.ResultsERVs and ERV related sequences make up less than 2% of crocodilian genomes. We recovered and described 45 ERV groups within the three crocodilian genomes, many of which are species specific. We have also revealed a new class of ERV, ERV4, which appears to be common to crocodilians and turtles, and currently has no characterised exogenous counterpart. For the first time, we formally describe the characteristics of this ERV class and its classification relative to other recognised ERV and retroviral classes. This class shares some sequence similarity and sequence characteristics with ERV3, although it is phylogenetically distinct from the other ERV classes. We have also identified two instances of gene capture by crocodilian ERVs, one of which, the capture of a host KIT-ligand mRNA has occurred without the loss of an ERV domain.ConclusionsThis study indicates that crocodilian ERVs comprise a wide variety of lineages, many of which appear to reflect ancient infections. In particular, ERV4 appears to have a limited host range, with current data suggesting that it is confined to crocodilians and some lineages of turtles. Also of interest are two ERV groups that demonstrate evidence of host gene capture. This study provides a framework to facilitate further studies into non-mammalian vertebrates and highlights the need for further studies into such species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-014-0071-2) contains supplementary material, which is available to authorized users.
Highlights
Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed
Overview of recovered ERVs The estimated ERV content of crocodilian genomes ranges from 1.22% in G. gangeticus, to 1.88% in A. mississippiensis [21]
This is in agreement with previous studies that have identified a large number of ERV1 and ERV4 insertions across crocodilian species [2,4]
Summary
Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. ERVs has focussed on fragments from the protease and reverse transcriptase (pro-pol) genes [1,2,3,4], or longer sequences recovered from a single species [5] These methodologies are highly reliant on sequence conservation for recovery of ERV data, with the PCR surveys focussing on conserved domains, and likely to have missed more divergent, degraded or rarer ERVs. These methodologies are highly reliant on sequence conservation for recovery of ERV data, with the PCR surveys focussing on conserved domains, and likely to have missed more divergent, degraded or rarer ERVs This in turn may result in an underestimation of the true ERV complement of these species, limiting understanding of the impact that these elements may have had on genome evolution, and species biology
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