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Journal Article•DOI•

Recombination as a motor of host switches and virus emergence: geminiviruses as case studies.

Pierre Lefeuvre, Enrique Moriones1•
Spanish National Research Council1
01 Feb 2015-Current Opinion in Virology (Curr Opin Virol)-Vol. 10, pp 14-19
TL;DR: In this article, the authors assemble lines of evidences indicating that recombination was crucial in driving host switches and further emergence of geminiviruses, making these viruses such successful plant pathogens.
About: This article is published in Current Opinion in Virology.The article was published on 2015-02-01 and is currently open access. It has received 119 citations till now. The article focuses on the topics: Genetic recombination & Geminiviridae.

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Summary

  • Whereas extensive evidence of recombination suggests that this mechanism might be adaptive in this family, direct demonstration remains scarce.
  • Whereas the vast majority of geminivirus sequences obtained in the last years are from viruses infecting cultivated plants, they most likely emerge from non-cultivated plants (stands for plant pathogens in general [61]).
  • Whereas the networks of genetic exchanges amongst viruses could inform about virus populations that are the most active recombiners, their analyses could reveal key host species, environmental or cultural conditions favouring specific patterns of viral encounter and from where host switch is most likely to originate.
  • Padidam M, Sawyer S, Fauquet CM: Possible emergence of new geminiviruses by frequent recombination.
  • Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S et al.: Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen.
  • Plant Mol Biol 2004, 56:585-599. 21. Lima ATM, Sobrinho RR, González-Aguilera J, Rocha CS, Silva SJC, Xavier CAD, Silva FN, Duffy S, Zerbini FM: Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts.

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Book Chapter•DOI•
Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range

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Lele Zhao1, Karyna Rosario2, Mya Breitbart2, Siobain Duffy1•
Rutgers University1, University of South Florida2
01 Jan 2019-Advances in Virus Research
TL;DR: The explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade is surveyed, similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences are highlighted, and the ecology and evolution of eUKaryoticCRESS DNA viruses are discussed.
Abstract: While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

125 citations

Journal Article•DOI•
Tomato Leaf Curl New Delhi Virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops

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Enrique Moriones1, Shelly Praveen2, Supriya Chakraborty3•
Spanish National Research Council1, Indian Agricultural Research Institute2, Jawaharlal Nehru University3
21 Sep 2017-Viruses
TL;DR: ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus.
Abstract: The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution Important progress has also been made in control strategies to reduce disease damage This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants

95 citations

Cites background from "Recombination as a motor of host sw..."

  • ...Genetic recombination allows parental viruses present in mixed infections to exchange genetic information and derive it to their progeny in a parasexual reproduction manner; this mechanism is a key process in the evolution of many virus families and has been extensively recorded for members of the family Geminiviridae [54]....

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  • ...The tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus species (genus Begomovirus, family Geminiviridae) whose isolates are transmitted in nature by the whitefly Bemisia tabaci (order Hemiptera, family Aleyrodidae) in a circulative and persistent manner [1]....

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Journal Article•DOI•
Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomoviruses.

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Syed Shan-e-Ali Zaidi1, Darren P. Martin2, Imran Amin1, Muhammad Farooq1, Shahid Mansoor1 •
National Institute for Biotechnology and Genetic Engineering1, University of Cape Town2
01 Sep 2017-Molecular Plant Pathology
TL;DR: An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions.
Abstract: ummary Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite-associated begomoviruses with mostly narrow geographical ranges predominate, it is widespread, with a geographical range also including the Far East, Middle East, North Africa and Europe. The success of ToLCNDV probably derives from its broad host range and highly flexible genomic configuration: its DNA-A component is capable of productively interacting with, and trans-replicating, diverse DNA-B components and betasatellites. An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions. Towards this end, we used available ToLCNDV sequences to reconstruct the history of ToLCNDV spread. Taxonomy Family Geminiviridae, Genus Begomovirus. ToLCNDV is a bipartite begomovirus. Following the revised begomovirus taxonomic criteria of 91% and 94% nucleotide identity for species and strain demarcation, respectively, ToLCNDV is a distinct species with two strains: ToLCNDV and ToLCNDV-Spain. Host range The primary cultivated host of ToLCNDV is tomato (Solanum lycopersicum), but the virus is also known to infect 43 other plant species from a range of families, including Cucurbitaceae, Euphorbiaceae, Solanaceae, Malvaceae and Fabaceae. Disease symptoms Typical symptoms of ToLCNDV infection in its various hosts include leaf curling, vein thickening, puckering, purpling/darkening of leaf margins, leaf area reduction, internode shortening and severe stunting.

93 citations

Journal Article•DOI•
Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India.

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R. Vinoth Kumar1, Achuit K. Singh1, Ashish Kumar Singh1, Tribhuwan Yadav2, Tribhuwan Yadav1, Saumik Basu1, Saumik Basu3, Nirbhay Kumar Kushwaha1, Brotati Chattopadhyay1, Supriya Chakraborty1 •
Jawaharlal Nehru University1, Yale University2, University of Nebraska–Lincoln3
01 Oct 2015-Journal of General Virology
TL;DR: Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds, and demonstrates the crucial role of betAsatellites in severe disease development in Capsicum spp.
Abstract: Chilli, which encompasses several species in the genus Capsicum, is widely consumed throughout the world. In the Indian subcontinent, production of chilli is constrained due to chilli leaf curl disease (ChiLCD) caused by begomoviruses. Despite the considerable economic consequences of ChiLCD on chilli cultivation in India, there have been scant studies of the genetic diversity and structure of the begomoviruses that cause this disease. Here we report on a comprehensive survey across major chilli-growing regions in India. Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds. The associated betasatellites neither enhanced the accumulation of the begomovirus components nor reduced the incubation period in Nicotiana benthamiana. The ChiLCD-associated begomoviruses induced mild symptoms on Capsicum spp., but both the level of helper virus that accumulated and the severity of symptoms were increased in the presence of cognate betasatellites. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The betasatellites possess high nucleotide variability, and recombination among them was also evident. The nucleotide substitution rates were determined for the AV1 gene of begomoviruses (2.60 × 10- 3 substitutions site- 1 year- 1) and the βC1 gene of betasatellites [chilli leaf curl betasatellite (ChiLCB), 2.57 × 10- 4 substitution site- 1 year- 1; tomato leaf curl Bangladesh betasatellite (ToLCBDB), 5.22 × 10- 4 substitution site- 1 year- 1]. This study underscores the current understanding of Indian ChiLCD-associated begomoviruses and also demonstrates the crucial role of betasatellites in severe disease development in Capsicum spp.

76 citations

Cites background or result from "Recombination as a motor of host sw..."

  • ...Detection of recombination among ChiLCDassociated begomoviruses and betasatellites Recombination is known to play a major role in the emergence and evolution of geminiviruses (George et al., 2015; Lefeuvre & Moriones, 2015; Padidam et al., 1999)....

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  • ...These results are in line with previous observations of AV1 and AC1 regions as the recombination hotspots (George et al., 2015; Lefeuvre et al., 2007; Lefeuvre & Moriones, 2015)....

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Journal Article•DOI•
Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management.

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Ashish Prasad, Namisha Sharma, Gunaseelen Hari-Gowthem, Mehanathan Muthamilarasan, Manoj Prasad 
01 May 2020-Trends in Plant Science
TL;DR: This review focuses on the impact TYLCV has on worldwide agriculture and the role of recent advances for the authors' understanding ofTYLCV interaction with its host and vector.

67 citations

References
More filters
Journal Article•DOI•
Distribution of the phenotypic effects of random homologous recombination between two virus species.

[...]

Florence Vuillaume1, Gaël Thébaud1, Cica Urbino1, Nadège Forfert1, Martine Granier1, Rémy Froissart2, Rémy Froissart1, Stéphane Blanc1, Michel Peterschmitt1 •
Centre national de la recherche scientifique1, University of Montpellier2
05 May 2011-PLOS Pathogens
TL;DR: Surprisingly, all recombinants were infectious and accumulated at levels comparable or intermediate to that of the parental clones, indicating that, in this experimental system, lethal and/or large deleterious effects of recombination are very rare, in striking contrast to the common view that has emerged from previous studies published on other viruses.
Abstract: Recombination has an evident impact on virus evolution and emergence of new pathotypes, and has generated an immense literature. However, the distribution of phenotypic effects caused by genome-wide random homologous recombination has never been formally investigated. Previous data on the subject have promoted the implicit view that most viral recombinant genomes are likely to be deleterious or lethal if the nucleotide identity of parental sequences is below 90%. We decided to challenge this view by creating a bank of near-random recombinants between two viral species of the genus Begomovirus (Family Geminiviridae) exhibiting 82% nucleotide identity, and by testing infectivity and in planta accumulation of recombinant clones randomly extracted from this bank. The bank was created by DNA-shuffling—a technology initially applied to the random shuffling of individual genes, and here implemented for the first time to shuffle full-length viral genomes. Together with our previously described system allowing the direct cloning of full-length infectious geminivirus genomes, it provided a unique opportunity to generate hundreds of “mosaic” virus genomes, directly testable for infectivity. A subset of 47 randomly chosen recombinants was sequenced, individually inoculated into tomato plants, and compared with the parental viruses. Surprisingly, our results showed that all recombinants were infectious and accumulated at levels comparable or intermediate to that of the parental clones. This indicates that, in our experimental system, despite the fact that the parental genomes differ by nearly 20%, lethal and/or large deleterious effects of recombination are very rare, in striking contrast to the common view that has emerged from previous studies published on other viruses.

20 citations

"Recombination as a motor of host sw..." refers background in this paper

  • ...Interestingly, although natural selection preserves co-evolved intra-genome interaction networks [30], numerous and diverse viable recombinants can be produced during mixed infections [30,57 ] or artificially [58], highlighting the tolerance to disruption of begomoviruses genomes....

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Journal Article•DOI•
Modelling viral evolution and adaptation: challenges and rewards

[...]

Susanna C. Manrubia1•
Spanish National Research Council1
01 Oct 2012-Current Opinion in Virology
TL;DR: Modelling of viral evolution is clearing up the role played by neutral networks of genotypes, by defective and cooperative interactions among viral mutants, or by co-evolution with immune systems, which amounts to unveiling the nature of viral fitness landscapes.

19 citations

"Recombination as a motor of host sw..." refers background in this paper

  • ...The topology of the circuits of genetic exchanges within and between virus communities would determine the probability of viruses to form new genetic combinations and to emerge in a specific spot of the fitness landscape [67]....

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Frequently Asked Questions (1)
Q1. What are the contributions mentioned in the paper "Recombination as a motor of host switches and virus emergence: geminiviruses as case studies" ?

In this paper, the authors assemble lines of evidences indicating that recombination was crucial in driving host switches and further emergence of geminiviruses, making these viruses such successful plant pathogens.