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Open Access Research

Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia

Amanda Yoon-Yee Chong1, Sarah Jane Atkinson1, Sally Isberg2 and Jaime Gongora1*

Author Affiliations

1 RMC Gunn Building, B19, Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia

2 Porosus Pty Ltd, PO Box 86, Palmerston, NT, 0831, Australia

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Mobile DNA 2012, 3:20  doi:10.1186/1759-8753-3-20

Published: 5 December 2012

Abstract

Background

Endogenous retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the nuclear DNA of a germ-line cell. Here we present the results of a survey into the ERV complement of Crocodylus porosus, the saltwater crocodile, representing 45 individuals from 17 sampling locations in the Northern Territory of Australia. These retroelements were compared with published ERVs from other species of Crocodylia (Crocodilians; alligators, caimans, gharials and crocodiles) as well as representatives from other vertebrates. This study represents one of the first in-depth studies of ERVs within a single reptilian species shedding light on the diversity of ERVs and proliferation mechanisms in crocodilians.

Results

Analyses of the retroviral pro-pol gene region have corroborated the presence of two major clades of ERVs in C. porosus and revealed 18 potentially functional fragments out of the 227 recovered that encode intact pro-pol ORFs. Interestingly, we have identified some patterns of diversification among those ERVs as well as a novel sequence that suggests the presence of an additional retroviral genus in C. porosus. In addition, considerable diversity but low genetic divergence within one of the C. porosus ERV lineages was identified.

Conclusions

We propose that the ERV complement of C. porosus has come about through a combination of recent infections and replication of ancestral ERVs. Strong purifying selection acting on these clades suggests that this activity is recent or still occurring in the genome of this species. The discovery of potentially functional elements is an interesting development that warrants further investigation.

Keywords:
Crocodylia; Endogenous retrovirus; Crocodylus porosus