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Background <p>The evolutionary history of retroviruses and their impact on vertebrate evolution remains poorly understood, particularly in non-mammalian hosts. In this study, we explore retroviruses associated with Amphibia through analysis of 169 RNA sequencing datasets from 102 amphibian species. Using a BLAST-based approach, we identified retroviral transcripts from assembled transcriptomes and phylogenetically characterise both their <i>pol</i> and <i>env</i> regions to elucidate their evolutionary history.</p> Results <p>We identified the transcription of 18 novel and two previously described retroviruses with closest relatives in <i>gammaretrovirus</i>, <i>epsilonretrovirus</i>, <i>betaretrovirus</i> and <i>spumaretrovirinae</i>. Despite their differing <i>pol</i> phylogenies, we found that all amphibian retroviruses belong to the gamma-type envelope group (GTE). This suggests a common selection pressure for amphibian retroviruses to retain GTEs. Within these GTEs we also observed a new clade of alpharetrovirus-like envelopes in amphibians which form a sister clade to avian alpharetrovirus envelopes. Furthermore, we observe correlations between amphibian taxonomical order and retroviral diversity, with <i>Gymnophiona</i> (caecilians) harbouring the widest diversity of retroviruses whilst <i>Anura</i> (frogs and toads) harbour the fewest. Through mapping these transcribed retroviruses to their respective genomes (seven available) supplemented with observing ORF intactness, we determined that 14 of the 20 retroviruses are likely endogenous in origin yet are still transcribed in many amphibian tissues. These amphibian endogenous retroviruses (ERVs) have high genomic copy numbers: most (5/7) ERVs investigated have &gt; 100 copies, and one of which has 9,219 integrations within the <i>Ichthyophis bannanicus</i> caecilian genome. This high retroviral load in amphibian genomes may suggest that these retroviruses have low pathogenicity, or may reflect a lack of transposon control mechanisms in amphibian cells.</p> Conclusions <p>Through the characterisation of metatranscriptomic and genomic data from retroviruses in this study, we provide insights into their evolution in amphibians and exemplify the diversity of <i>Retroviridae</i> in vertebrate genomes. The identification of novel retroviral clades, widespread transcription of endogenous retroviruses in amphibians and abundance of ERV copies suggests that <i>Retroviridae</i> have played a significant role in amphibian evolution.</p>

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Transcriptome mining reveals diversity and evolution of circulating and endogenous amphibian retroviruses

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月10日

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  • Emma F. Harding,
  • Banjo Webster,
  • Tanu Sridhar,
  • Lewis K. Mercer,
  • Peter A. White

摘要

Background

The evolutionary history of retroviruses and their impact on vertebrate evolution remains poorly understood, particularly in non-mammalian hosts. In this study, we explore retroviruses associated with Amphibia through analysis of 169 RNA sequencing datasets from 102 amphibian species. Using a BLAST-based approach, we identified retroviral transcripts from assembled transcriptomes and phylogenetically characterise both their pol and env regions to elucidate their evolutionary history.

Results

We identified the transcription of 18 novel and two previously described retroviruses with closest relatives in gammaretrovirus, epsilonretrovirus, betaretrovirus and spumaretrovirinae. Despite their differing pol phylogenies, we found that all amphibian retroviruses belong to the gamma-type envelope group (GTE). This suggests a common selection pressure for amphibian retroviruses to retain GTEs. Within these GTEs we also observed a new clade of alpharetrovirus-like envelopes in amphibians which form a sister clade to avian alpharetrovirus envelopes. Furthermore, we observe correlations between amphibian taxonomical order and retroviral diversity, with Gymnophiona (caecilians) harbouring the widest diversity of retroviruses whilst Anura (frogs and toads) harbour the fewest. Through mapping these transcribed retroviruses to their respective genomes (seven available) supplemented with observing ORF intactness, we determined that 14 of the 20 retroviruses are likely endogenous in origin yet are still transcribed in many amphibian tissues. These amphibian endogenous retroviruses (ERVs) have high genomic copy numbers: most (5/7) ERVs investigated have > 100 copies, and one of which has 9,219 integrations within the Ichthyophis bannanicus caecilian genome. This high retroviral load in amphibian genomes may suggest that these retroviruses have low pathogenicity, or may reflect a lack of transposon control mechanisms in amphibian cells.

Conclusions

Through the characterisation of metatranscriptomic and genomic data from retroviruses in this study, we provide insights into their evolution in amphibians and exemplify the diversity of Retroviridae in vertebrate genomes. The identification of novel retroviral clades, widespread transcription of endogenous retroviruses in amphibians and abundance of ERV copies suggests that Retroviridae have played a significant role in amphibian evolution.