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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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Analyses of the retroviral <jats:italic>pro<\/jats:italic>-<jats:italic>pol<\/jats:italic> gene region have corroborated the presence of two major clades of ERVs in <jats:italic>C<\/jats:italic>. <jats:italic>porosus<\/jats:italic> and revealed 18 potentially functional fragments out of the 227 recovered that encode intact <jats:italic>pro<\/jats:italic>-<jats:italic>pol<\/jats:italic> 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 <jats:italic>C<\/jats:italic>. <jats:italic>porosus<\/jats:italic>. In addition, considerable diversity but low genetic divergence within one of the <jats:italic>C<\/jats:italic>. <jats:italic>porosus<\/jats:italic> ERV lineages was identified.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We propose that the ERV complement of <jats:italic>C<\/jats:italic>. <jats:italic>porosus<\/jats:italic> 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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1759-8753-3-20","type":"journal-article","created":{"date-parts":[[2012,12,5]],"date-time":"2012-12-05T18:11:38Z","timestamp":1354731098000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia"],"prefix":"10.1186","volume":"3","author":[{"given":"Amanda Yoon-Yee","family":"Chong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah Jane","family":"Atkinson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sally","family":"Isberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaime","family":"Gongora","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,12,5]]},"reference":[{"key":"59_CR1","doi-asserted-by":"publisher","first-page":"5177","DOI":"10.1073\/pnas.93.11.5177","volume":"93","author":"R Lower","year":"1996","unstructured":"Lower R, Lower J, Kurth R: The viruses in all of us: Characteristics and biological significance of human endogenous retrovirus sequences. 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