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Duroy PO, Seguin J, Ravel S, Rajendran R, Laboureau N, Salmon F, Delos JM, Pooggin M, Iskra-Caruana ML, Chabannes M. Endogenous viral elements are targeted by RNA silencing pathways in banana. THE NEW PHYTOLOGIST 2024. [PMID: 39294885 DOI: 10.1111/nph.20112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/05/2024] [Indexed: 09/21/2024]
Abstract
Endogenous banana streak virus (eBSV) integrants derived from three distinct species, present in Musa balbisiana (B) but not Musa acuminata (A) banana genomes are able to reconstitute functional episomal viruses causing banana streak disease in interspecific triploid AAB banana hybrids but not in the diploid (BB) parent line, which harbours identical eBSV loci. Here, we investigated the regulation of these eBSV. In-depth characterization of siRNAs, transcripts and methylation derived from eBSV using Illumina and bisulfite sequencing were carried out on eBSV-free Musa acuminata AAA plants and BB or AAB banana plants with eBSV. eBSV loci produce low-abundance transcripts covering most of the viral sequence and generate predominantly 24-nt siRNAs. siRNA accumulation is restricted to duplicated and inverted viral sequences present in eBSV. Both siRNA-accumulating and nonaccumulating sequences of eBSV in BB plants are heavily methylated in all three CG, CHG and CHH contexts. Our data suggest that eBSVs are controlled at the epigenetic level in BB diploids. This regulation not only prevents their awakening and systemic infection of the plant but is also probably involved in the inherent resistance of the BB plants to mealybug-transmitted viral infection. These findings are thus of relevance to other plant resources hosting integrated viruses.
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Affiliation(s)
- Pierre-Olivier Duroy
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan Seguin
- Department of Plant Physiology, Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Sébastien Ravel
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Rajeswaran Rajendran
- Department of Plant Physiology, Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Nathalie Laboureau
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Salmon
- CIRAD, UMR AGAP Institut, Capesterre-Belle-Eau, Guadeloupe, F-97130, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, Guadeloupe, France
| | - Jean-Marie Delos
- CIRAD, UMR AGAP Institut, Capesterre-Belle-Eau, Guadeloupe, F-97130, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, Guadeloupe, France
| | - Mikhail Pooggin
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Matthieu Chabannes
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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2
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Tripathi JN, Ntui VO, Tripathi L. Precision genetics tools for genetic improvement of banana. THE PLANT GENOME 2024; 17:e20416. [PMID: 38012108 DOI: 10.1002/tpg2.20416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/22/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023]
Abstract
Banana is an important food security crop for millions of people in the tropics but it faces challenges from diseases and pests. Traditional breeding methods have limitations, prompting the exploration of precision genetic tools like genetic modification and genome editing. Extensive efforts using transgenic approaches have been made to develop improved banana varieties with resistance to banana Xanthomonas wilt, Fusarium wilt, and nematodes. However, these efforts should be extended for other pests, diseases, and abiotic stresses. The commercialization of transgenic crops still faces continuous challenges with regulatory and public acceptance. Genome editing, particularly CRISPR/Cas, offers precise modifications to the banana genome and has been successfully applied in the improvement of banana. Targeting specific genes can contribute to the development of improved banana varieties with enhanced resistance to various biotic and abiotic constraints. This review discusses recent advances in banana improvement achieved through genetic modification and genome editing.
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Affiliation(s)
| | | | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
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3
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Rao X, Chen H, Lu Y, Liu R, Li H. Distribution and Location of BEVs in Different Genotypes of Bananas Reveal the Coevolution of BSVs and Bananas. Int J Mol Sci 2023; 24:17064. [PMID: 38069393 PMCID: PMC10707546 DOI: 10.3390/ijms242317064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Members of the family Caulimoviridae contain abundant endogenous pararetroviral sequences (EPRVs) integrated into the host genome. Banana streak virus (BSV), a member of the genus Badnavirus in this family, has two distinct badnaviral integrated sequences, endogenous BSV (eBSV) and banana endogenous badnavirus sequences (BEVs). BEVs are distributed widely across the genomes of different genotypes of bananas. To clarify the distribution and location of BEVs in different genotypes of bananas and their coevolutionary relationship with bananas and BSVs, BEVs and BSVs were identified in 102 collected banana samples, and a total of 327 BEVs were obtained and categorized into 26 BEVs species with different detection rates. However, the majority of BEVs were found in Clade II, and a few were clustered in Clade I. Additionally, BEVs and BSVs shared five common conserved motifs. However, BEVs had two unique amino acids, methionine and lysine, which differed from BSVs. BEVs were distributed unequally on most of chromosomes and formed hotspots. Interestingly, a colinear relationship of BEVs was found between AA and BB, as well as AA and SS genotypes of bananas. Notably, the chromosome integration time of different BEVs varied. Based on our findings, we propose that the coevolution of bananas and BSVs is driven by BSV Driving Force (BDF), a complex interaction between BSVs, eBSVs, and BEVs. This study provides the first clarification of the relationship between BEVs and the coevolution of BSVs and bananas in China.
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Affiliation(s)
| | | | | | | | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (X.R.); (H.C.); (Y.L.); (R.L.)
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4
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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. FRONTIERS IN PLANT SCIENCE 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] [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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5
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Mertens A, Bawin Y, Vanden Abeele S, Kallow S, Swennen R, Vu DT, Vu TD, Minh HT, Panis B, Vandelook F, Janssens SB. Phylogeography and conservation gaps of Musa balbisiana Colla genetic diversity revealed by microsatellite markers. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2515-2534. [PMID: 36017134 PMCID: PMC9393128 DOI: 10.1007/s10722-022-01389-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10722-022-01389-4.
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Affiliation(s)
- Arne Mertens
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Yves Bawin
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Simon Kallow
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly, UK
| | - Rony Swennen
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
- Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tuong Dang Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ho Thi Minh
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Bart Panis
- Bioversity International, Leuven, Belgium
| | | | - Steven B. Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
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6
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Ricciuti E, Laboureau N, Noumbissié G, Chabannes M, Sukhikh N, Pooggin MM, Iskra-Caruana ML. Extrachromosomal viral DNA produced by transcriptionally active endogenous viral elements in non-infected banana hybrids impedes quantitative PCR diagnostics of banana streak virus infections in banana hybrids. J Gen Virol 2021; 102. [PMID: 34726592 DOI: 10.1099/jgv.0.001670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The main edible and cultivated banana varieties are intra- and interspecific hybrids of the two main Musa species, Musa acuminata and Musa balbisiana, having diploid genomes denoted A and B, respectively. The B genome naturally hosts sequences of banana streak virus (BSV) named endogenous BSV (eBSV). Upon stress, eBSVs are identified as the origin of BSV infection for at least three BSV species, causing banana streak disease. For each of the three species, BSV and eBSV share >99.9 % sequence identity, complicating PCR-based diagnosis of viral infection in the B genome-containing bananas. Here, we designed a quantitative PCR-based method to only quantify episomal BSV particles produced, overcoming the limitation of eBSV also being detected by qPCR by using it as a 'calibrator'. However, our results revealed unexpected variation of eBSV amplification in calibrator plants composed of a clonal population of 53 replicating virus-free banana hybrids with the same AAB genotype. Our in-depth molecular analyses suggest that this calibrator variation is due to the variable abundance of non-encapsidated extrachromosomal viral DNA, likely produced via the transcription of eBSVs, followed by occasional reverse transcription. We also present evidence that accumulation of viral transcripts in AAB plants is downregulated both at post-transcriptional and transcriptional levels by an RNA interference mechanism that keeps the plants free of virus infection. Finally, we recommend that such eBSV amplification variation be taken into account to establish a quantitative viral diagnostic for banana plants with the B genome.
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Affiliation(s)
- Emeline Ricciuti
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Nathalie Laboureau
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Guy Noumbissié
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Matthieu Chabannes
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR AGAP Intitute, F-34398 Montpellier, France.,AGAP Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Natalia Sukhikh
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. Moscow, 119071, Russia
| | - Mikhail M Pooggin
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Marie-Line Iskra-Caruana
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, DGD-RS, F-34398 Montpellier, France
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7
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Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). ANNALS OF BOTANY 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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8
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Chabannes M, Gabriel M, Aksa A, Galzi S, Dufayard J, Iskra‐Caruana M, Muller E. Badnaviruses and banana genomes: a long association sheds light on Musa phylogeny and origin. MOLECULAR PLANT PATHOLOGY 2021; 22:216-230. [PMID: 33231927 PMCID: PMC7814968 DOI: 10.1111/mpp.13019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Badnaviruses are double-stranded DNA pararetroviruses of the family Caulimoviridae. Badnaviral sequences found in banana are distributed over three main clades of the genus Badnavirus and exhibit wide genetic diversity. Interestingly, the nuclear genome of many plants, including banana, is invaded by numerous badnaviral sequences although badnaviruses do not require an integration step to replicate, unlike animal retroviruses. Here, we confirm that banana streak viruses (BSVs) are restricted to clades 1 and 3. We also show that only BSVs from clade 3 encompassing East African viral species are not integrated into Musa genomes, unlike BSVs from clade 1. Finally, we demonstrate that sequences from clade 2 are definitively integrated into Musa genomes with no evidence of episomal counterparts; all are phylogenetically distant from BSVs known to date. Using different molecular approaches, we dissected the coevolution between badnaviral sequences of clade 2 and banana by comparing badnavirus integration patterns across a banana sampling representing major Musa speciation events. Our data suggest that primary viral integrations occurred millions of years ago in banana genomes under different possible scenarios. Endogenous badnaviral sequences can be used as powerful markers to better characterize the Musa phylogeny, narrowing down the likely geographical origin of the Musa ancestor.
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Affiliation(s)
- Matthieu Chabannes
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Marc Gabriel
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Abderrahmane Aksa
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Serge Galzi
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Jean‐François Dufayard
- CIRAD, UMR AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | | | - Emmanuelle Muller
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
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9
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Tripathi L, Ntui VO, Tripathi JN, Kumar PL. Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana. Front Microbiol 2021; 11:609784. [PMID: 33584573 PMCID: PMC7873300 DOI: 10.3389/fmicb.2020.609784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Viral diseases are significant biotic constraints for banana (Musa spp.) production as they affect the yield and limit the international movement of germplasm. Among all the viruses known to infect banana, the banana bunchy top virus and banana streak viruses are widespread and economically damaging. The use of virus-resistant bananas is the most cost-effective option to minimize the negative impacts of viral-diseases on banana production. CRISPR/Cas-based genome editing is emerging as the most powerful tool for developing virus-resistant crop varieties in several crops, including the banana. The availability of a vigorous genetic transformation and regeneration system and a well-annotated whole-genome sequence of banana makes it a compelling candidate for genome editing. A robust CRISPR/Cas9-based genome editing of the banana has recently been established, which can be applied in developing disease-resistant varieties. Recently, the CRISPR system was exploited to detect target gene sequences using Cas9, Cas12, Cas13, and Cas14 enzymes, thereby unveiling the use of this technology for virus diagnosis. This article presents a synopsis of recent advancements and perspectives on the application of CRISPR/Cas-based genome editing for diagnosing and developing resistance against banana viruses and challenges in genome-editing of banana.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | | | - P. Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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10
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Tripathi JN, Ntui VO, Ron M, Muiruri SK, Britt A, Tripathi L. CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. overcomes a major challenge in banana breeding. Commun Biol 2019; 2:46. [PMID: 30729184 PMCID: PMC6355771 DOI: 10.1038/s42003-019-0288-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Presence of the integrated endogenous banana streak virus (eBSV) in the B genome of plantain (AAB) is a major challenge for breeding and dissemination of hybrids. As the eBSV activates into infectious viral particles under stress, the progenitor Musa balbisiana and its derivants, having at least one B genome, cannot be used as parents for crop improvement. Here, we report a strategy to inactivate the eBSV by editing the virus sequences. The regenerated genome-edited events of Gonja Manjaya showed mutations in the targeted sites with the potential to prevent proper transcription or/and translational into functional viral proteins. Seventy-five percent of the edited events remained asymptomatic in comparison to the non-edited control plants under water stress conditions, confirming inactivation of eBSV into infectious viral particles. This study paves the way for the improvement of B genome germplasm and its use in breeding programs to produce hybrids that can be globally disseminated.
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Affiliation(s)
| | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Mily Ron
- Department of Plant Biology, University of California, Davis, CA USA
| | - Samwel K. Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Anne Britt
- Department of Plant Biology, University of California, Davis, CA USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
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