title: The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed.
abstract: 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 variousNicotianaspecies. 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. TheNicotianageminivirus-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 genusBegomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in theDioscoreaspp. of the Enantiophyllum clade. We used fluorescencein situhybridization to confirm that the EGV1 sequences are integrated in theD. alatagenome 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 EnantiophyllumDioscoreaspp. 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 inD. alataof 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.
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Denis
authors: D
authors: Filloux
authors: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors: Sasha
authors: S
authors: Murrell
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France; Department of Pest Management, Faculty of Natural Resources, Prince of Songkla University, Hat Yai campus, Thailand 90120.
authors: Maneerat
authors: M
authors: Koohapitagtam
authors: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa.
authors: Michael
authors: M
authors: Golden
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Charlotte
authors: C
authors: Julian
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Serge
authors: S
authors: Galzi
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Marilyne
authors: M
authors: Uzest
authors: CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France.
authors: Marguerite
authors: M
authors: Rodier-Goud
authors: CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France.
authors: Angélique
authors: A
authors: D'Hont
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Marie Stephanie
authors: MS
authors: Vernerey
authors: Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
authors: Paul
authors: P
authors: Wilkin
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Michel
authors: M
authors: Peterschmitt
authors: DSMZ Plant Virus Department, Messeweg 11/12, 38102, Braunschweig, Germany.
authors: Stephan
authors: S
authors: Winter
authors: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; Department of Medicine, University of California, San Diego, La Jolla, CA.
authors: Ben
authors: B
authors: Murrell
authors: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa.
authors: Darren P
authors: DP
authors: Martin
authors: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors: Philippe
authors: P
authors: Roumagnac
keywords: endogenous viral sequences; functional protein expression; geminivirus; selection analysis; yam