Distribution of Endogenous Retroviruses in Crocodilians

Jaratlerdsiri, Weerachai; Rodríguez-Zárate, Clara J.; Isberg, Sally R.; Damayanti, Chandramaya Siska; Miles, Lee G.; Chansue, Nantarika; Moran, Chris; Melville, Lorna; Gongora, Jaime

doi:10.1128/jvi.00668-09

Cited by 12 publications

(21 citation statements)

References 24 publications

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“…Unsurprisingly, ERV1 and ERV4 were the predominant lineages in the genomes, with 15 and 22 groups respectively. This is in agreement with previous studies that have identified a large number of ERV1 and ERV4 insertions across crocodilian species [2,4]. The crocodilian ERVs displayed very weak associations with ERVs from other taxa and exogenous retroviral genera, suggesting that ancient ERV insertions represent intermediates or novel lineages between the currently recognised taxa.…”

Section: Discussionsupporting

confidence: 92%

“…While these criteria may bias analyses to insertions that are better preserved or more recently integrated, it also reduces the amount of sequence divergence and evolutionary 'noise' that may be introduced by the inclusion of highly degraded sequences. BLASTX [62] was used to classify the predicted pol sequences into the major ERV classes based on similarity to pro-pol and pol fragments recovered from previous studies [1][2][3][4][5]; Chong et al, unpublished data]. Sequences that showed no similarity to known crocodilian ERV fragments where then compared to other published sequences in GenBank and Repbase using the NCBI BLAST suite [63] and Censor [64].…”

Section: Definition Of Erv Groupsmentioning

confidence: 99%

“…Crocodilians have been shown to harbour a number of divergent ERV lineages that show little similarity to ERVs from other vertebrates. Until now, the characterisation of these crocodilian 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 therefore likely to have missed more divergent, degraded or rarer ERVs.…”

Section: Introductionmentioning

confidence: 99%

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Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

et al. 2014

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Background: 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. 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. Results: ERVs 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. Conclusions: This 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.

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Section: Discussionsupporting

confidence: 92%

Section: Definition Of Erv Groupsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

et al. 2014

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“…Y. Chong Á S. R. Kjeldsen Á J. Gongora (&) Faculty of Veterinary Science, The University of Sydney, Sydney, Australia e-mail: jaime.gongora@sydney.edu.au [8]. PCR amplification, bacterial cloning, and sequencing were carried out as previously described [2,3] using universal primers targeting the region between highly conserved, functional, retroviral motifs from the pro-pol region [9].…”

Section: Methodsmentioning

confidence: 99%

“…Crocodilians (Crocodylia) have been shown to harbour a particularly diverse range of ERVs, including the newly described ERV4 [2][3][4][5][6]. Previously, we have assessed ERV diversity through PCR surveys across species and within populations [2,3], and through interrogation of genomic data of key crocodilian species [6].…”

Section: Introductionmentioning

confidence: 99%

Surveys of endogenous retroviruses (ERVs) in the freshwater crocodile (Crocodylus johnstoni) suggest that ERVs in Crocodylus spp. vary between species

2015

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Endogenous retroviruses (ERVs) are one of many families of transposable elements present in vertebrate genomes. We have examined the ERV complement of the freshwater crocodile (Crocodylus johnstoni) in order to investigate the diversity of ERVs present and possibility of ERV or retroviral activity in a diseased individual of this species. Amplification and sequencing of the highly conserved retroviral pro-pol domains revealed high levels of sequence variation in these ERVs. Phylogenetic analyses of these ERVs and those previously identified in other crocodilian species suggest that although many crocodilians share the same ERV lineages, the relative numbers of retroelement insertions from each of these lineages may vary greatly between species. The data generated in this study provide evidence for the presence of a unique and varied complement of ERVs in crocodilians. This study has also demonstrated the presence of species-specific evolution in ancient retroviral infections.

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A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture

2010

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Historically, views and measurements of biodiversity have had a narrow focus, for instance, characterizing the attributes of observable patterns but affording less attention to processes. Here, we explore the question: how does a systems thinking view - one where the world is seen as elements and processes that connect and interact in dynamic ways to form a whole - affect the way we understand biodiversity and practice conservation? We answer this question by illustrating the systemic properties of biodiversity at multiple levels, and show that biodiversity is a collection of dynamic systems linking seemingly disparate biological and cultural components and requiring an understanding of the system as a whole. We conclude that systems thinking calls traditional views of species, ecosystem function, and human relationships with the rest of biodiversity into question. Finally, we suggest some of the ways in which this view can impact the science and practice of conservation, particularly through affecting our conservation targets and strategies.

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Distribution of Endogenous Retroviruses in Crocodilians

Cited by 12 publications

References 24 publications

Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

Surveys of endogenous retroviruses (ERVs) in the freshwater crocodile (Crocodylus johnstoni) suggest that ERVs in Crocodylus spp. vary between species

A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture

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