Cargando…
The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed
Endogenous viral sequences are essentially ‘fossil records’ that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain...
Autores principales: | , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014472/ https://www.ncbi.nlm.nih.gov/pubmed/27774276 http://dx.doi.org/10.1093/ve/vev002 |
_version_ | 1782452294238863360 |
---|---|
author | Filloux, Denis Murrell, Sasha Koohapitagtam, Maneerat Golden, Michael Julian, Charlotte Galzi, Serge Uzest, Marilyne Rodier-Goud, Marguerite D’Hont, Angélique Vernerey, Marie Stephanie Wilkin, Paul Peterschmitt, Michel Winter, Stephan Murrell, Ben Martin, Darren P. Roumagnac, Philippe |
author_facet | Filloux, Denis Murrell, Sasha Koohapitagtam, Maneerat Golden, Michael Julian, Charlotte Galzi, Serge Uzest, Marilyne Rodier-Goud, Marguerite D’Hont, Angélique Vernerey, Marie Stephanie Wilkin, Paul Peterschmitt, Michel Winter, Stephan Murrell, Ben Martin, Darren P. Roumagnac, Philippe |
author_sort | Filloux, Denis |
collection | PubMed |
description | Endogenous viral sequences are essentially ‘fossil records’ that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21–24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species. |
format | Online Article Text |
id | pubmed-5014472 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-50144722016-10-21 The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed Filloux, Denis Murrell, Sasha Koohapitagtam, Maneerat Golden, Michael Julian, Charlotte Galzi, Serge Uzest, Marilyne Rodier-Goud, Marguerite D’Hont, Angélique Vernerey, Marie Stephanie Wilkin, Paul Peterschmitt, Michel Winter, Stephan Murrell, Ben Martin, Darren P. Roumagnac, Philippe Virus Evol Research Article Endogenous viral sequences are essentially ‘fossil records’ that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21–24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species. Oxford University Press 2015-05-26 /pmc/articles/PMC5014472/ /pubmed/27774276 http://dx.doi.org/10.1093/ve/vev002 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Filloux, Denis Murrell, Sasha Koohapitagtam, Maneerat Golden, Michael Julian, Charlotte Galzi, Serge Uzest, Marilyne Rodier-Goud, Marguerite D’Hont, Angélique Vernerey, Marie Stephanie Wilkin, Paul Peterschmitt, Michel Winter, Stephan Murrell, Ben Martin, Darren P. Roumagnac, Philippe The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title | The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title_full | The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title_fullStr | The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title_full_unstemmed | The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title_short | The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
title_sort | genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014472/ https://www.ncbi.nlm.nih.gov/pubmed/27774276 http://dx.doi.org/10.1093/ve/vev002 |
work_keys_str_mv | AT fillouxdenis thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT murrellsasha thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT koohapitagtammaneerat thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT goldenmichael thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT juliancharlotte thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT galziserge thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT uzestmarilyne thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT rodiergoudmarguerite thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT dhontangelique thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT vernereymariestephanie thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT wilkinpaul thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT peterschmittmichel thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT winterstephan thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT murrellben thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT martindarrenp thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT roumagnacphilippe thegenomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT fillouxdenis genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT murrellsasha genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT koohapitagtammaneerat genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT goldenmichael genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT juliancharlotte genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT galziserge genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT uzestmarilyne genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT rodiergoudmarguerite genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT dhontangelique genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT vernereymariestephanie genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT wilkinpaul genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT peterschmittmichel genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT winterstephan genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT murrellben genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT martindarrenp genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed AT roumagnacphilippe genomesofmanyyamspeciescontaintranscriptionallyactiveendogenousgeminiviralsequencesthatmaybefunctionallyexpressed |