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Vally V, Jouen E, Pecheur B, Carval D, De Lapeyre L, Teycheney PY, Roussel V, Fabre S, Pages C, Adreit H, Carlier J, Rieux A. First report of black leaf streak disease in bananas caused by Pseudocercospora fijiensis on Mauritius island. Plant Dis 2023. [PMID: 37966471 DOI: 10.1094/pdis-09-23-1787-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Pseudocercospora fijiensis, the causal agent of the black leaf streak disease of bananas (plants in the genus Musa) (BLSD), is considered to be the major economic threat to export-banana cultivation (de Bellaire, Fouré, Abadie, & Carlier, 2010). The disease has a worldwide distribution throughout the humid tropical regions and has been previously reported in the Southwestndian Ocean (SWIO) area: in 1993 in Mayotte and Comoros islands (DR Jones & Mourichon, 1993), in 2000 in Madagascar (Jones, 2003; Rivas, Zapater, Abadie, & Carlier, 2004) and in 2018 in Reunion Island (Rieux et al., 2019). In Mauritius, the presence of Pseudocercospora fijiensis was suspected in 1996 (Soomary & Benimadhu, 1998) but has never been confirmed, as symptoms could have been confounded with Pseudocercospora musae or Pseudocercospora eumusae, two causal agents of others leaf spot diseases of banana which were previously described in Mauritius in 1959 (Orieux & Felix, 1968) and 2000 (Carlier, Zapater, Lapeyre, Jones, & Mourichon, 2000), respectively. In March 2022, typical BLSD symptoms were observed at relatively low prevalence in a Cavendish crop located in the "Balance John" area (site S1 on Fig. S1-A) of Mauritius island. Typical early symptoms (stages 2) were 1- to 4-mm long brown streaks at the abaxial leaf surface, and typical older streaks (stages 3 and 4) were also observed (Fig. S1-B). These symptoms were mixed with symptoms of ELSD caused by P. eumusae. Since both species cannot be clearly distinguished only on the description of symptoms, conidial sporulation on stages 2 was checked in the laboratory (Ngando et al., 2015) since P. eumusae does not produce conidia on these young stages. In April 2022, banana leaves bearing symptoms of leaf spot diseases were collected in 7 different sites (Fig. S1-A). All leaf fragments were sent to the CIRAD laboratories where molecular diagnosis was performed following the protocol developed by Arzanlou et al. (2007). In brief, genomic DNA was extracted from ground leaf fragments displaying symptoms using the DNeasy® Plant Mini Kit (Qiagen®, Courtaboeuf, France). At each site, a total of 6 lesions cut from 6 different leaves were pooled. The DNA extracts were added as templates for real-time PCR assay designed to specifically detect the presence of P. fijiensis, P. musae and P. eumusae using MFbf/MFbrtaq/MFbp, MEbf/MEbrtaq/FMep and MMbf/Mmbrtaq/FMep primers and probes, respectively (Arzanlou et al., 2007). Both positive and negative controls were included in the assay and every sample reaction was duplicated. P. fijiensis was detected from 2 out of 7 sites (S2 and S7, see Fig.S2-B). P. eumusae was detected at all sites while P. musae was found in one site only (S6). Interestingly, our results also showed coinfection by P. fijiensis - P. eumusae & P. musae - P. eumusae on several sites. The presence of P. fijiensis was further confirmed by several investigations performed on conidia isolated from S2 samples including i) morphological observations of conidia displaying P. fijiensis type description (Pérez-Vicente, Carreel, Roussel, Carlier, & Abadie (2021), Fig. S2-A), ii) DNA sequencing of 16S ribosomal gene with ITS1 & ITS4 primers (GenBank accessions Nos. OR515818-OR515810) with BLAST results displaying percentages of identity > 99.70% with type strains and iii) Koch's postulates were fulfilled by artificial inoculation of detached leaf pieces as described in Pérez-Vicente, Carreel, Roussel, Carlier, & Abadie (2021) (Fig. S2-D). In brief, for the artificial inoculation, symptoms obtained after inoculation of both a strain isolated in Mauritius (S2-MAU) and a positive control (T+) were compared and shown to be typical of P. fijiensis species for the 3 replicates. To the best of our knowledge, this is the first official report of P. fijiensis and BLSD in Mauritius Island. This revelation holds significant importance for both the agricultural and scientific communities, shedding light on the potential spread and impact of this devastating pathogen in previously unaffected regions. From a global perspective, this discovery underscores the interconnectedness of agricultural ecosystems and the need for vigilance in monitoring and responding to emerging plant diseases in an increasingly interconnected world (Vega et al. 2022). Future investigations will be required to monitor the spread of BLSD on the island, describe the genetic structure of populations and identify routes of invasion at the SWOI scale.
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Affiliation(s)
- Vivian Vally
- Food and Agricultural Research and Extension Institute, Plant Pathology Division, Reduit, Mauritius;
| | - Emmanuel Jouen
- CIRAD, AMIS, 7 chemin de l'IRAT, Ligne Paradis, Saint Pierre, Réunion, 97410
- 40 rue ArchambaudAppt 10Saint Pierre, Réunion, 97410;
| | - Bernard Pecheur
- Food and Agricultural Research and Extension Institute, Plant Pathology Division, Reduit Mauritius, Reduit, Mauritius, 80835;
| | | | | | | | | | - Sandrine Fabre
- CIRAD BIOS, 206941, Montpellier, Languedoc-Roussillon, France;
| | - Christine Pages
- CIRAD Biological Systems Department, 206941, Montpellier, Languedoc-Roussillon, France;
| | | | - Jean Carlier
- CIRAD BIOS, 206941, Montpellier, Languedoc-Roussillon, France;
| | - Adrien Rieux
- CIRAD, 27050, Bios, 7 chemin de l'IRAT, Saint Pierre, Réunion, 97410;
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Vassilieff H, Geering ADW, Choisne N, Teycheney PY, Maumus F. Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes. Biomolecules 2023; 13:1069. [PMID: 37509105 PMCID: PMC10377300 DOI: 10.3390/biom13071069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
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Affiliation(s)
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre de La Réunion, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre de La Réunion, France
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France
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3
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Diouf MB, Guyader S, Nopoly MM, Gaspard O, Filloux D, Candresse T, Marais A, Teycheney PY, Umber M. Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.). Arch Virol 2023; 168:180. [PMID: 37311875 DOI: 10.1007/s00705-023-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France
- CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | | | | | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France
- UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
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4
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Vassilieff H, Haddad S, Jamilloux V, Choisne N, Sharma V, Giraud D, Wan M, Serfraz S, Geering ADW, Teycheney PY, Maumus F. CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mob DNA 2022; 13:31. [PMID: 36463202 PMCID: PMC9719215 DOI: 10.1186/s13100-022-00288-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.
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Affiliation(s)
- Héléna Vassilieff
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Sana Haddad
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.460789.40000 0004 4910 6535Present Address: Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Véronique Jamilloux
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.507621.7Present Address: Université Paris-Saclay, INRAE, PROSE, 92160 Antony, France
| | - Nathalie Choisne
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Vikas Sharma
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.8385.60000 0001 2297 375XPresent Address: Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Delphine Giraud
- UMR AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France
| | - Mariène Wan
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Saad Serfraz
- grid.413016.10000 0004 0607 1563CABB, University of Agriculture Faisalabad, Faisalabad, 38000 Pakistan
| | - Andrew D. W. Geering
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 Australia
| | | | - Florian Maumus
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
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5
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Geering ADW, McTaggart AR, Teycheney PY. Untangling the taxonomy of dahlia mosaic virus. Arch Virol 2022; 167:2325-2329. [PMID: 35969294 PMCID: PMC9556396 DOI: 10.1007/s00705-022-05567-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/04/2022] [Indexed: 11/02/2022]
Abstract
In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare as a pathogen compared to a more recently described but unclassified caulimovirus called dahlia common mosaic virus (DCMV). We have undertaken a new set of analyses to test the hypothesis that DCMV represents a new caulimovirus species whose members infect dahlia, but we ultimately reject this hypothesis. A probable sequencing error was identified in the reference genome sequence of DMV, and consequently, we recommend that an alternative virus isolate be nominated as the exemplar for this species. In accordance with the new binomial nomenclatural system, it is proposed that the virus species be called "Caulimovirus dahliae".
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Affiliation(s)
- Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
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6
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Massé D, Filloux D, Candresse T, Massart S, Marais A, Verdin E, Cassam N, Fernandez E, Roumagnac P, Teycheney PY, Lefeuvre P, Lett JM. Identification of a novel vitivirus from pineapple in Reunion Island. Arch Virol 2022; 167:2355-2357. [PMID: 35857149 DOI: 10.1007/s00705-022-05512-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
We report the complete genome sequence of a novel member of the genus Vitivirus (family Betaflexiviridae, subfamily Trivirinae) infecting pineapple. The complete genome sequence of this virus was obtained from total RNA extracted from pineapple leaf samples collected in Reunion Island, using a combination of high-throughput sequencing technologies. The viral genome is 6,757 nt long, excluding the poly(A) tail, and shares all the hallmarks of vitiviruses. Phylogenetic analysis performed on the replication-associated protein and capsid protein gene sequences unambiguously place this new virus, for which we propose the name "pineapple virus A", in the genus Vitivirus.
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Affiliation(s)
- Delphine Massé
- ANSES, LSV RAPT, 97410, Saint Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgique
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Eric Verdin
- INRAE, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | | | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
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7
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Diouf MB, Gaspard O, Marais A, Filloux D, Gomez RM, Faure C, Roumagnac P, Candresse T, Theil S, Contreras S, Teycheney PY, Umber M. Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp). Arch Virol 2022; 167:2275-2280. [PMID: 35842549 DOI: 10.1007/s00705-022-05535-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Cordyline virus 1 (CoV1) is a velarivirus that has so far only been reported in ornamental Ti plants (Cordyline fruticosa). Using high-throughput sequencing, we identified CoV1 infection in yam accessions from Vanuatu. Using a specific RT-PCR assay, we found that CoV1 is also present and highly prevalent in Dioscorea alata, D. cayenensis, and D. trifida in Guadeloupe. Phylogenetic analysis showed that CoV1 isolates infecting yam in Guadeloupe display a low level of molecular diversity. These data provide insights into the transmission of CoV1 in yam in Guadeloupe.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.,CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sandy Contreras
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.,UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
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8
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Umber M, Pressat G, Fort G, Plaisir Pineau K, Guiougiou C, Lambert F, Farinas B, Pichaut JP, Janzac B, Delos JM, Salmon F, Dubois C, Teycheney PY. Risk Assessment of Infectious Endogenous Banana Streak Viruses in Guadeloupe. Front Plant Sci 2022; 13:951285. [PMID: 35898217 PMCID: PMC9310019 DOI: 10.3389/fpls.2022.951285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Infectious alleles of endogenous banana streak viruses (eBSVs) are present in the genome of all banana interspecific cultivars, including plantains and cooking types. Activation of these infectious eBSV alleles by biotic and abiotic stresses leads to spontaneous infections by cognate viruses and raises concerns about their ability to promote outbreaks of banana streak viruses under field cultivation conditions. We undertook a comprehensive risk assessment study of infectious eBSV alleles of species BSOLV, BSGFV and BSIMV in banana interspecific cultivars in Guadeloupe, a tropical island of the Caribbean where bananas are grown for export and local markets. We carried out a prevalence survey of BSOLV, BSGFV and BSIMV species in a range of cultivars grown in Guadeloupe. Our results suggest that BSOLV and BSGFV infections arise from the activation of infectious eBSVs rather than vector-borne transmission and point to a correlation between altitude and infection rates in interspecific hybrids with AAB genotypes. We studied the dynamics of activation of infectious eBSOLV and eBSGFV alleles by tissue culture and field cultivation in a range of cultivars. We showed that tissue culture and field cultivation trigger distinct activation pathways, resulting in distinct activation patterns. We also showed that activation decreased over time during cell culture and field cultivation and that BSV infections arising from the activation of infectious eBSV alleles cause symptomless infections in the most cultivated plantain in Guadeloupe, French Clair. Overall, our study shows that the risk of BSV outbreaks resulting from the activation of infectious eBSVs in plantain originating from vegetative multiplication is negligible in Guadeloupe.
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Affiliation(s)
- Marie Umber
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Gersende Pressat
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Guillaume Fort
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Kaïssa Plaisir Pineau
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Chantal Guiougiou
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Frédéric Lambert
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Benoît Farinas
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Jean-Philippe Pichaut
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Bérenger Janzac
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Jean-Marie Delos
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Frédéric Salmon
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
| | - Cécile Dubois
- CIRAD, UMR AGAP Institute, Montpellier, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institute, Guadeloupe, France
- UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, Institute Agro, Guadeloupe, France
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9
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Umber M, Filloux D, Svanella-Dumas L, Bonheur L, Acina-Mambole I, Gomez RM, Faure C, Anzala F, Pavis C, Roumagnac P, Marais A, Theil S, Candresse T, Teycheney PY. Host range and molecular variability of the sadwavirus dioscorea mosaic associated virus. Arch Virol 2022; 167:917-922. [PMID: 35107668 DOI: 10.1007/s00705-022-05379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/20/2022] [Indexed: 11/02/2022]
Abstract
Dioscorea mosaic associated virus (DMaV) is a member of the genus Sadwavirus, family Secoviridae, that is associated with mosaic symptoms in Dioscorea rotundata in Brazil. The genome of a DMaV isolate detected in D. trifida in Guadeloupe was sequenced by high-throughput sequencing. Using an RT-PCR-based detection assay, we found that DMaV infects D. alata, D. bulbifera, D. cayenensis-rotundata, D. esculenta, and D. trifida accessions conserved in Guadeloupe and Côte d'Ivoire and displays a very high level of molecular diversity in a relatively small region of the genome targeted by the assay. We also provide evidence that DMaV is also present in D. rotundata in Benin and in D. alata in Nigeria.
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Affiliation(s)
- Marie Umber
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Laurence Svanella-Dumas
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Lydiane Bonheur
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Isabelle Acina-Mambole
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Rose-Marie Gomez
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Fabiola Anzala
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Claudie Pavis
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMY, F-97410, Saint Pierre, La Réunion, France. .,UMR PVBMT, Université de la Réunion, F-97410, Saint Pierre, La Réunion, France.
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10
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Gruel G, Diouf MB, Abadie C, Chilin-Charles Y, Etter EMC, Geffroy M, Herrmann Storck C, Meyer DF, Pagès N, Pressat G, Teycheney PY, Umber M, Vega-Rúa A, Pradel J. Critical Evaluation of Cross-Sectoral Collaborations to Inform the Implementation of the "One Health" Approach in Guadeloupe. Front Public Health 2021; 9:652079. [PMID: 34409004 PMCID: PMC8366749 DOI: 10.3389/fpubh.2021.652079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022] Open
Abstract
In Guadeloupe, a French overseas territory located in the Eastern Caribbean, infectious and non-infectious diseases, loss of biodiversity, natural disasters and global change threaten the health and well-being of animals, plants, and people. Implementing the “One Health” (OH) approach is crucial to reduce the archipelago's vulnerability to these health threats. However, OH remains underdeveloped in Guadeloupe, hampering efficient and effective intersectoral and transdisciplinary collaborations for disease surveillance and control. A multidisciplinary research group of volunteer researchers working in Guadeloupe, with collective expertise in infectious diseases, undertook a study to identify key attributes for OH operationalization by reviewing past and current local collaborative health initiatives and analyzing how much they mobilized the OH framework. The research group developed and applied an operational OH framework to assess critically collaborative initiatives addressing local health issues. Based on a literature review, a set of 13 opinion-based key criteria was defined. The criteria and associated scoring were measured through semi-directed interviews guided by a questionnaire to critically evaluate four initiatives in animal, human, plant, and environmental health research and epidemiological surveillance. Gaps, levers, and prospects were identified that will help health communities in Guadeloupe envision how to implement the OH approach to better address local health challenges. The methodology is simple, generic, and pragmatic and relies on existing resources. It can be transposed and adapted to other contexts to improve effectiveness and efficiency of OH initiatives, based on lessons-learned of local past or current multi-interdisciplinary and intersectoral initiatives.
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Affiliation(s)
- Gaëlle Gruel
- Laboratory for the Study of Microbial Ecosystem Interactions, Institut Pasteur of Guadeloupe, Unit Transmission Reservoir and Pathogens Diversity, Les Abymes, France
| | - Mame Boucar Diouf
- INRAE, UR ASTRO, F-97170, Petit-Bourg, France.,CIRAD, UMR AGAP Institut, F-97130, Capesterre Belle-Eau, France.,AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Catherine Abadie
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Yolande Chilin-Charles
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.,CIRAD, UMR BGPI, F-97130, Capesterre Belle-Eau, France
| | - Eric Marcel Charles Etter
- CIRAD, UMR ASTRE, F-97170, Petit-Bourg, France.,ASTRE, Univ Montpellier, CIRAD INRAE, Montpellier, France
| | - Mariana Geffroy
- CIRAD, UMR ASTRE, F-97170, Petit-Bourg, France.,ASTRE, Univ Montpellier, CIRAD INRAE, Montpellier, France
| | - Cécile Herrmann Storck
- Centre Hospitalier Universitaire CHU de Guadeloupe, Laboratoire de Microbiologie Humaine et Environnementale, Les Abymes, France
| | - Damien F Meyer
- CIRAD, UMR ASTRE, F-97170, Petit-Bourg, France.,ASTRE, Univ Montpellier, CIRAD INRAE, Montpellier, France
| | - Nonito Pagès
- CIRAD, UMR ASTRE, F-97170, Petit-Bourg, France.,ASTRE, Univ Montpellier, CIRAD INRAE, Montpellier, France
| | - Gersende Pressat
- CIRAD, UMR AGAP Institut, F-97130, Capesterre Belle-Eau, France.,AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre Belle-Eau, France.,AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marie Umber
- INRAE, UR ASTRO, F-97170, Petit-Bourg, France
| | - Anubis Vega-Rúa
- Laboratory of Vector Control Research, Institut Pasteur of Guadeloupe, Unit Transmission Reservoir and Pathogens Diversity, Les Abymes, France
| | - Jennifer Pradel
- CIRAD, UMR ASTRE, F-97170, Petit-Bourg, France.,ASTRE, Univ Montpellier, CIRAD INRAE, Montpellier, France
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11
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Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant ( Solanum melongena). Front Plant Sci 2021; 12:683681. [PMID: 34367211 PMCID: PMC8346255 DOI: 10.3389/fpls.2021.683681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/30/2021] [Indexed: 05/20/2023]
Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
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Affiliation(s)
- Saad Serfraz
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- *Correspondence: Pierre-Yves Teycheney,
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12
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Teycheney PY, Geering ADW, Dasgupta I, Hull R, Kreuze JF, Lockhart B, Muller E, Olszewski N, Pappu H, Pooggin MM, Richert-Pöggeler KR, Schoelz JE, Seal S, Stavolone L, Umber M, Report Consortium ICTV. ICTV Virus Taxonomy Profile: Caulimoviridae. J Gen Virol 2020; 101:1025-1026. [PMID: 32940596 PMCID: PMC7660458 DOI: 10.1099/jgv.0.001497] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/04/2020] [Indexed: 11/29/2022] Open
Abstract
Caulimoviridae is a family of non-enveloped reverse-transcribing plant viruses with non-covalently closed circular dsDNA genomes of 7.1-9.8 kbp in the order Ortervirales. They infect a wide range of monocots and dicots. Some viruses cause economically important diseases of tropical and subtropical crops. Transmission occurs through insect vectors (aphids, mealybugs, leafhoppers, lace bugs) and grafting. Activation of infectious endogenous viral elements occurs in Musa balbisiana, Petunia hybrida and Nicotiana edwardsonii. However, most endogenous caulimovirids are not infectious. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caulimoviridae, which is available at ictv.global/report/caulimoviridae.
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Affiliation(s)
- Pierre-Yves Teycheney
- CIRAD, UMR AGAP, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Idranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Roger Hull
- Child Okeford, Blandford Forum, Dorset, UK
| | - Jan F. Kreuze
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Ben Lockhart
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emmanuelle Muller
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Neil Olszewski
- Department of Plant Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hanu Pappu
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | | | | | - James E. Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Chatham, Kent ME4 4TB, UK
| | - Livia Stavolone
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Marie Umber
- INRAE, UR ASTRO, F-97170, Petit-Bourg, Guadeloupe, France
| | - ICTV Report Consortium
- CIRAD, UMR AGAP, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
- Child Okeford, Blandford Forum, Dorset, UK
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- Department of Plant Biology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- INRA, UMR BGPI, F-34398 Montpellier, France
- Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
- Natural Resources Institute, University of Greenwich, Chatham, Kent ME4 4TB, UK
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- INRAE, UR ASTRO, F-97170, Petit-Bourg, Guadeloupe, France
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13
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Umber M, Filloux D, Gélabale S, Gomez RM, Marais A, Gallet S, Gamiette F, Pavis C, Teycheney PY. Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange. Viruses 2020; 12:v12101101. [PMID: 33003342 PMCID: PMC7650539 DOI: 10.3390/v12101101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/25/2023] Open
Abstract
Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.
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Affiliation(s)
- Marie Umber
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
- Correspondence: ; Tel.: +590-590-25-59-29
| | - Denis Filloux
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche—Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France;
- Biologie et Génétique des Interactions Plante-Parasite, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, Montpellier SupAgro, F-34060 Montpellier, France
| | - Suzia Gélabale
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Rose-Marie Gomez
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Armelle Marais
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université de Bordeaux, Unité Mixte de Recherche Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France;
| | - Séverine Gallet
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Franciane Gamiette
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Claudie Pavis
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Pierre-Yves Teycheney
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-97130 Capesterre Belle-Eau, France;
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Institut Agro, F-97130 Capesterre Belle-Eau, France
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14
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Sharma V, Lefeuvre P, Roumagnac P, Filloux D, Teycheney PY, Martin DP, Maumus F. Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants. Virus Evol 2020; 6:veaa071. [PMID: 33391820 PMCID: PMC7758297 DOI: 10.1093/ve/veaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.
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Affiliation(s)
- Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Plant Breeding Division, 78026, Versailles, France.,Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Department of Biological Systems, F-97410 St Pierre, La Réunion, France
| | - Philippe Roumagnac
- CIRAD, BGPI, Department of Biological Systems, 34398 Montpellier CEDEX 5, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Department of Biological Systems, 34398 Montpellier CEDEX 5, France
| | - Denis Filloux
- CIRAD, BGPI, Department of Biological Systems, 34398 Montpellier CEDEX 5, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Department of Biological Systems, 34398 Montpellier CEDEX 5, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP, Department of Biological Systems, F-97130, Capesterre Belle-Eau, Guadeloupe, France.,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Department of Biological Systems, F-97130 Capesterre Belle-Eau, Guadeloupe, France
| | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and molecular Medicine, University of Cape Town, OBSERVATORY 7925 Cape Town, South Africa
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Plant Breeding Division, 78026, Versailles, France
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15
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Marais A, Umber M, Filloux D, Gomez RM, Faure C, Pavis C, Julian C, Roumagnac P, Acina-Mambole I, Bonheur L, Theil S, Contreras S, Candresse T, Teycheney PY. Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection. Arch Virol 2020; 165:2653-2657. [PMID: 32852617 DOI: 10.1007/s00705-020-04787-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/26/2020] [Indexed: 02/05/2023]
Abstract
A novel virus infecting yams (Dioscorea spp.), tentatively named "yam asymptomatic virus 1" (YaV1), was characterized and sequenced from an asymptomatic D. alata plant from Vanuatu. Sequence comparisons and phylogenetic analysis showed that YaV1 is a novel ampelovirus and has the smallest genome among "subgroup 1" members. RT-PCR-based screening of a yam germplasm collection conserved in Guadeloupe showed that YaV1 is prevalent in D. alata, D. bulbifera, D. cayennensis subsp. rotundata, D. esculenta and D. trifida accessions but causes no apparent symptoms. Additional phylogenetic analysis revealed a low variability of YaV1 in Guadeloupe in a limited part of the genome, and suggested the occurrence of plant-to-plant transmission.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit-Bourg, Guadeloupe, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Claudie Pavis
- INRAE, UR ASTRO, 97170, Petit-Bourg, Guadeloupe, France
| | - Charlotte Julian
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Isabelle Acina-Mambole
- CIRAD, UMR AGAP, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, Guadeloupe, France.,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre Belle-Eau, Guadeloupe, France
| | | | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.,INRAE, UMRF, Aurillac, France
| | - Sandy Contreras
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, Guadeloupe, France. .,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre Belle-Eau, Guadeloupe, France.
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16
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Diop SI, Geering ADW, Alfama-Depauw F, Loaec M, Teycheney PY, Maumus F. Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae. Sci Rep 2018; 8:572. [PMID: 29330451 PMCID: PMC5766536 DOI: 10.1038/s41598-017-16399-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/12/2017] [Indexed: 01/24/2023] Open
Abstract
Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.
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Affiliation(s)
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland, 4001, Australia
| | | | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.
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17
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Umber M, Filloux D, Muller E, Laboureau N, Galzi S, Roumagnac P, Iskra-Caruana ML, Pavis C, Teycheney PY, Seal SE. The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species. Mol Plant Pathol 2014; 15:790-801. [PMID: 24605894 PMCID: PMC6638810 DOI: 10.1111/mpp.12137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.
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Affiliation(s)
- Marie Umber
- INRA, UR1321 ASTRO Agrosystèmes tropicaux, F-97170, Petit-Bourg, (Guadeloupe), France
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18
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Côte FX, Galzi S, Folliot M, Lamagnère Y, Teycheney PY, Iskra-Caruana ML. Micropropagation by tissue culture triggers differential expression of infectious endogenous Banana streak virus sequences (eBSV) present in the B genome of natural and synthetic interspecific banana plantains. Mol Plant Pathol 2010; 11:137-44. [PMID: 20078782 PMCID: PMC6640322 DOI: 10.1111/j.1364-3703.2009.00583.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The genome of Musa balbisiana spp. contains several infectious endogenous sequences of Banana streak virus (eBSV). We have shown previously that in vitro micropropagation triggers the activation of infectious eBSOLV (endogenous sequences of Banana streak Obino l'Ewai virus) in the synthetic tetraploid interspecific hybrid FHIA21 (AAAB). In this work, we show that another synthetic tetraploid (AAAB) hybrid and two natural triploid (AAB) plantains are equally prone to the activation of infectious eBSOLV during tissue culture. These results are a strong indication that such activation is a general phenomenon in interspecific Musa cultivars, whether synthetic or natural. We also report the first in-depth study of the correlation between the duration of tissue culture and the level of activation of infectious eBSOLV, and show that specific and common activation patterns exist in these banana plants. We hypothesize that these patterns result from the concomitant activation of infectious eBSOLV and a decrease in the virus titre in neoformed plantlets, resulting from cell multiplication outcompeting virus replication. We provide experimental data supporting this hypothesis. No activation of infectious eBSGFV (endogenous sequences of Banana streak Goldfinger virus) by tissue culture was observed in the two natural AAB plantain cultivars studied here, whereas such activation occurred in the AAAB synthetic hybrid studied. We demonstrate that this differential activation does not result from differences in the structure of eBSGFV, as all banana genomes harbour eaBSGFV-7.
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Affiliation(s)
- François X Côte
- CIRAD-UPR26, TA B-26/PS4, F-34398 Montpellier cedex 5, France.
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19
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Teycheney PY, Tepfer M. Possible roles of endogenous plant viral sequences and transgenes containing viral sequences in both virus resistance and virus emergence. ACTA ACUST UNITED AC 2008. [DOI: 10.1051/ebr:2007045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Teycheney PY, Tepper M. Possible roles of endogenous plant viral sequences and transgenes containing viral sequences in both virus resistance and virus emergence. Environ Biosafety Res 2007; 6:219-21. [PMID: 18409236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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21
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Teycheney PY, Acina I, Lockhart BEL, Candresse T. Detection of Banana mild mosaic virus and Banana virus X by polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR). J Virol Methods 2007; 142:41-9. [PMID: 17280722 DOI: 10.1016/j.jviromet.2007.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 12/22/2006] [Accepted: 01/11/2007] [Indexed: 11/23/2022]
Abstract
Viruses are important constraints to the movement and propagation of plant germplasm, especially for vegetatively propagated crops such as banana and plantain. Their control relies primarily on the use of virus-free plant material, whose production and certification requires sensitive and reliable detection methods. An existing polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR) assay was adapted to the detection of Banana mild mosaic virus (BanMMV) and Banana virus X, two Flexiviridae infecting Musa spp. PDO inosine-containing primers were found to be well suited to the detection of BanMMV, despite its high molecular diversity, but not to that of the highly conserved BVX, for which species-specific primers were designed. Sampling and sample processing steps were optimized in order to avoid nucleic acid purification prior to the reverse transcription step. A polyclonal anti-BanMMV antiserum was raised and successfully used for the immunocapture (IC) of BanMMV viral particles from leaf extracts, leading to the development of a PDO-IC-RT-nested PCR assay. Although the anti-BanMMV antiserum could to some extent recognize BVX viral particles, direct binding (DB) was shown to be a more efficient method for processing BVX-infected samples and a PDO-DB-RT-nested PCR assay was developed for the detection of BVX from leaf extracts.
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Affiliation(s)
- Pierre-Yves Teycheney
- CIRAD, UPR75, Station de Neufchâteau, F-97130 Capesterre Belle-Eau, FWI, Guadeloupe.
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22
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Le Provost G, Iskra-Caruana ML, Acina I, Teycheney PY. Improved detection of episomal Banana streak viruses by multiplex immunocapture PCR. J Virol Methods 2006; 137:7-13. [PMID: 16857272 DOI: 10.1016/j.jviromet.2006.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/17/2006] [Accepted: 05/25/2006] [Indexed: 11/28/2022]
Abstract
Banana streak viruses (BSV) are currently the main viral constraint to Musa germplasm movement, genetic improvement and mass propagation. Therefore, it is necessary to develop and implement BSV detection strategies that are both reliable and sensitive, such as PCR-based techniques. Unfortunately, BSV endogenous pararetrovirus sequences (BSV EPRVs) are present in the genome of Musa balbisiana. They interfere with PCR-based detection of episomal BSV in infected banana and plantain, such as immunocapture PCR. Therefore, a multiplex, immunocapture PCR (M-IC-PCR) was developed for the detection of BSV. Musa sequence tagged microsatellite site (STMS) primers were selected and used in combination with BSV species-specific primers in order to monitor possible contamination by Musa genomic DNA, using multiplex PCR. Furthermore, immunocapture conditions were optimized in order to prevent Musa DNA from interfering with episomal BSV DNA during the PCR step. This improved detection method successfully allowed the accurate, specific and sensitive detection of episomal DNA only from distinct BSV species. Its implementation should benefit PCR-based detection of viruses for which homologous sequences are present in the genome of their hosts, including transgenic plants expressing viral sequences.
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Affiliation(s)
- Grégoire Le Provost
- CIRAD, UMR BGPI, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France
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23
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Teycheney PY, Laboureau N, Iskra-Caruana ML, Candresse T. High genetic variability and evidence for plant-to-plant transfer of Banana mild mosaic virus. J Gen Virol 2006; 86:3179-3187. [PMID: 16227242 DOI: 10.1099/vir.0.81197-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A total of 154 partial nucleotide sequences within the Banana mild mosaic virus (BanMMV) ORF1, which encodes the viral RNA-dependent RNA polymerase (RdRp), was obtained from 68 distinct infected banana accessions originating from various locations worldwide. The 310 nt sequences displayed a high level of variability with a mean pairwise nucleotide sequence divergence level of 20.4 %. This situation resulted essentially from a high rate of synonymous mutations. A similar analysis was performed for a limited selection of 10 banana accessions (30 sequences) on the region comprising approximately the last 310 nt of the BanMMV genome. This region corresponds to the 3' end of ORF5, which encodes the coat protein (234 nt), and to the 3' non-coding region. This analysis confirmed the high level of diversity observed in the RdRp dataset, characterized by a high level of synonymous mutations. Analysis of intra-host diversity indicated the existence of two distinct situations, with some plants containing only closely related sequence variants, whereas others contained widely divergent isolates. Analyses indicated that BanMMV genetic diversity is not structured by the geographical origin of the infected Musa accessions or by their genotype. This situation may be, in part, explained by the exchange of banana germplasm between different parts of the world and also by plant-to-plant transfer of virus isolates, the evidence for which is, for the first time, provided by this study.
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Affiliation(s)
- Pierre-Yves Teycheney
- CIRAD, UPR 75, Station de Neufchâteau, Sainte-Marie, F-97130 Capesterre Belle-Eau, Guadeloupe, French West Indies
| | - Nathalie Laboureau
- CIRAD/UMR BGPI, TA 41/K, Campus International de Baillarguet, F-34398 Montpellier Cedex, France
| | | | - Thierry Candresse
- UMR GD2P, INRA et Université Bordeaux 2, IBVM, Campus INRA de la Grande Ferrade, BP 81, F-33883 Villenave d'Ornon Cedex, France
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24
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Abstract
Potyviruses, such as potato virus Y and tobacco etch virus, as well as cucumber mosaic cucumovirus, interfere with post-transcriptional gene silencing (PTGS). When RedStar-type Petunia hybrida cultivars, whose flowers have alternating white and pigmented sectors, were infected with these viruses, each virus induced a different pattern of restoration of floral anthocyanin pigmentation. Local reversion to coloured phenotypes in the white sectors, which occurred through interference with PTGS of the chalcone synthase A (chs-A) gene, was correlated with locally increased levels of chs-A mRNA and virus concentration. Our results show that virus infection can interfere with PTGS of a native plant gene, and that this can have profound effects on symptom expression.
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Affiliation(s)
| | - Mark Tepfer
- Laboratoire de biologie cellulaire, INRA, F-78026 Versailles cedex, France1
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25
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Berthomé R, Teycheney PY, Renou JP, Okada Y, Tepfer M. Expression of a yeast RNase III gene in transgenic tobacco silences host nitrite reductase genes. Plant Mol Biol 2000; 44:53-60. [PMID: 11094979 DOI: 10.1023/a:1006456603970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
When a gene encoding the Schizosaccharomyces pombe dsRNA-specific RNase III, pac1, was expressed in transgenic tobacco plants, six out of thirteen transformed plants gave progeny among which were individuals displaying a distinctive chlorotic phenotype. These chlorotic plants strongly resemble those transformed with a 35S-Nii (nitrite reductase) transgene, in which both Nii host genes and the 35S-Nii transgene are silenced by co-suppression. RNA blots showed that the host Nii genes were silenced in chlorotic 35S-pac1 plants but not in individuals with a normal green phenotype. Neither the transcript levels of the other cellular genes tested nor the transcription of Nii genes was significantly affected by the expression of pac1. This is the first observation of post-transcriptional silencing of host genes by a transgene with no apparent sequence similarity to the target gene.
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Affiliation(s)
- R Berthomé
- Laboratoire de Biologie Cellulaire, INRA-Versailles, France
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26
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Teycheney PY, Aaziz R, Dinant S, Salánki K, Tourneur C, Balázs E, Jacquemond M, Tepfer M. Synthesis of (-)-strand RNA from the 3' untranslated region of plant viral genomes expressed in transgenic plants upon infection with related viruses. J Gen Virol 2000; 81:1121-6. [PMID: 10725441 DOI: 10.1099/0022-1317-81-4-1121] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When expressed in transgenic tobacco plants, transgene mRNA that includes the 3' untranslated region (3' UTR) of Lettuce mosaic virus served as template for synthesis of complementary (-)-strand RNA following an infection by Tobacco etch virus, Tobacco vein mottle virus or Pepper mottle virus, but not when infected with Cucumber mosaic virus. Deletion of the 3' UTR from the transgene abolished the synthesis of (-)-strand transcripts. Similar results were obtained in transgenic tobacco plants expressing mRNA that includes the RNA3 3' UTR of Cucumber mosaic virus when infected with Tomato aspermy virus. These results show that the viral RNA-dependent RNA polymerase of several potyviruses and Tomato aspermy virus have the ability to recognize heterologous 3' UTRs when included in transgene mRNAs, and to use them as transcription promoters.
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Affiliation(s)
- P Y Teycheney
- INRA, Laboratoire de biologie cellulaire, F-78026 Versailles cedex, France.
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27
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Higgins CM, Cassidy BG, Teycheney PY, Wongkaew S, Dietzgen RG. Sequences of the coat protein gene of five peanut stripe virus (PStV) strains from Thailand and their evolutionary relationship with other bean common mosaic virus sequences. Arch Virol 1998; 143:1655-67. [PMID: 9787652 DOI: 10.1007/s007050050407] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The coat protein gene and part of the 3' non-coding region of five strains of peanut stripe virus (PStV) from Thailand have been cloned and sequenced. Phylogenetic comparisons of these strains, known as T1, T3, T5, T6 and T7, and related sequences showed that these strains are indeed strains of PStV. Further, PStV strains appear to be related to each other according to their geographic origin. That is, the Thai strains are more closely related to each other than they are to strains from the USA or Indonesia, despite the variety of symptoms caused by these strains and the overlap of symptom types between the strains from different locations. Like other PStV strains, PStV-Thai can be considered strains of bean common mosaic virus (BCMV) but can be distinguished from bean-infecting strains of BCMV and blackeye cowpea mosaic virus (B1CMV) through sequence and host range. No evidence was found that PStV-Thai strains, unlike PStV-Ib, are recombinants of PStV and B1CMV, although the T3 strain may be a recombinant of different PStV sequences. Phylogenetic analyses of viruses of the BCMV group suggest that acquisition of the ability to infect peanut may have occurred only once.
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Affiliation(s)
- C M Higgins
- Queensland Department of Primary Industries, Gehrmann Laboratories, University of Queensland, St Lucia, Brisbane, Australia
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28
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Teycheney PY, Dietzgen RG. Cloning and sequence analysis of the coat protein genes of an Australian strain of peanut mottle and an Indonesian 'blotch' strain of peanut stripe potyviruses. Virus Res 1994; 33:199, 201. [PMID: 7975883 DOI: 10.1016/0168-1702(94)90055-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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29
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Teycheney PY, Dietzgen RG. Cloning and sequence analysis of the coat protein genes of an Australian strain of peanut mottle and an Indonesian 'blotch' strain of peanut stripe potyviruses. Virus Res 1994; 31:235-44. [PMID: 7999143 DOI: 10.1016/0168-1702(94)90006-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have analysed the coat protein gene sequences of two potyviruses infecting peanut. The 3' terminal 1247 nucleotides (nt) of an Australian strain of peanut mottle virus (PeMoV-AU) and the 3' terminal 1388 nt of an Indonesian 'blotch' strain of peanut stripe virus (PStV-Ib) were cloned and sequenced. Those regions included the 861 and 864 nt encoding the respective putative coat proteins as well as the 285 and 253 nt, respectively of 3' non-coding sequences. Comparison of the nucleotide sequences of PeMoV-AU and PStV-Ib revealed a sequence similarity of 64.4% for the coat protein gene and 34.6% for the 3' non-coding region. The deduced amino acid sequences of PeMoV-AU and PStV-Ib coat proteins are 66.7% identical. These results provide further evidence that PeMoV and PStV are distinct viruses. Comparisons of the 3' terminal sequences of PeMoV-AU and PStV-Ib with those of the genomic RNA of other strains of PeMoV and PStV and with other potyviruses are discussed.
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Affiliation(s)
- P Y Teycheney
- Department of Primary Industries, Queensland Agricultural Biotechnology Centre, Gehrmann Laboratories, University of Queensland, St. Lucia, Australia
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30
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Abstract
The capsid-encoding gene of plum pox virus (PPV) was fused with the leader sequence of the coat protein mRNA (cp) of tobacco mosaic virus by a novel mutagenesis technique which involves reverse transcription of minus-strand RNA [synthesized by in vitro transcription of a double-stranded (ds) cDNA clone], using an ad hoc synthetic oligodeoxynucleotide as primer. The resulting cDNA was rendered ds and cloned into the plasmid, pBluescribe M13+. Transcription of this chimeric construction produced RNA molecules of 1250 nucleotides in length, which were used as messengers in the in vitro protein-synthesizing systems. The major product of this transcript consists of a 36-kDa polypeptide and was identified as the PPV coat protein (CP) by molecular weight estimation and by immunoprecipitation with a polyclonal antiserum to PPV. Transfer of this cDNA via Agrobacterium tumefaciens into plants was successfully performed. Transgenic Nicotiana plants producing the PPV CP were subsequently obtained.
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Affiliation(s)
- M Ravelonandro
- Station de Pathologie Végétale, INRA, La Grande Ferrade, Villenave d'Ornon, France
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31
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Wetzel T, Tavert G, Teycheney PY, Ravelonandro M, Candresse T, Dunez J. Dot hybridization detection of plum pox virus using 32P-labeled RNA probes representing non-structural viral protein genes. J Virol Methods 1990; 30:161-71. [PMID: 2148174 DOI: 10.1016/0166-0934(90)90017-a] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A cDNA library covering the complete genome of plum pox virus strain D (PPV D) has been obtained, and an endonuclease restriction map derived from it. This map was superposed on the PPV genomic organisation map, established for a nonaphid transmissible strain of PPV (Maiss et al., 1989). This allowed us to select seven probes, corresponding to different regions on the PPV genome. These probes were tested in a dot-blot hybridization assay for the detection of PPV. Probes of various lengths (0.25 to 1.5 kb) were tested and those measuring at least 0.8 kb (4 of the 7 probes selected) proved to be the most sensitive. The detection limit was of about 5 pg of purified virus per assay. Probes representing non-structural viral protein genes were equally sensitive in detecting both serotypes D and M of PPV. The previously described probe pBPPV1 (Varveri et al., 1988), covering the coat protein gene of strain D, was less sensitive, when compared to the above probes, in detecting heterologous strains of PPV. The polyvalence of probes transcribed from non-structural viral protein genes was confirmed by screening isolates of PPV, collected in infected orchards in several Mediterranean countries.
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Affiliation(s)
- T Wetzel
- Station de Pathologie Végétale, Institut National de la Recherche Agronomique, Centre de Bordeaux, Villenave d'Ornon, France
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32
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Affiliation(s)
- P Y Teycheney
- Institut National de la Recherche Agronomique, Station de Pathologie Végétale, Villenave d'Ornon, France
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