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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

[...]

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.

[...]

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.

[...]

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.

[...]

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•
Cassava mosaic geminiviruses: actual knowledge and perspectives.

[...]

Basavaprabhu L. Patil1, Claude M. Fauquet1•
Donald Danforth Plant Science Center1
01 Sep 2009-Molecular Plant Pathology
TL;DR: The status of recent research findings with regard to the CMD complex is provided, the molecular biology knowledge of CMGs with reference to other geminiviruses is presented, and the mechanisms by which CMGs have exploited nature to their advantage are highlighted.
Abstract: SUMMARY Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is one of the most devastating crop diseases and a major constraint for cassava cultivation. CMD has been reported only from the African continent and Indian subcontinent despite the large-scale cultivation of cassava in Latin America and several South-East Asian countries. Seven CMG species have been reported from Africa and two from the Indian subcontinent and, in addition, several strains have been recognized. Recombination and pseudo-recombination between CMGs give rise not only to different strains, but also to members of novel virus species with increased virulence and a new source of biodiversity, causing severe disease epidemics. CMGs are known to trigger gene silencing in plants and, in order to counteract this natural host defence, geminiviruses have evolved suppressor proteins. Temperature and other environmental factors can affect silencing and suppression, and thus modulate the symptoms. In the case of mixed infections of two or more CMGs, there is a possibility for a synergistic interaction as a result of the presence of differential and combinatorial suppressor proteins. In this article, we provide the status of recent research findings with regard to the CMD complex, present the molecular biology knowledge of CMGs with reference to other geminiviruses, and highlight the mechanisms by which CMGs have exploited nature to their advantage.

240 citations

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

  • ...Some instances of such events have been recorded with, for example, the recent pandemic on cassava in Africa caused by a recombinant virus with an extremely increased severity [54,45], or the emergence of the resistance-breaking recombinant virus named cotton leaf curl Burewala virus (CLCuBuV) that causes devastating damage to cotton production in India and Pakistan [24]....

    [...]

Journal Article•DOI•
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics.

[...]

Muriel Vayssier-Taussat1, Emmanuel Albina, Christine Citti1, Jean-FranÒ«ois Cosson1, Marie-Agnès Jacques1, Marc-Henri Lebrun1, Yves Le Loir1, Mylène Ogliastro1, Marie-Agnès Petit1, Philippe Roumagnac, Thierry Candresse2 •
Institut national de la recherche agronomique1, University of Bordeaux2
05 Mar 2014-Frontiers in Cellular and Infection Microbiology
TL;DR: The contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities is explored and the concept of “pathobiome” and the research questions that this raises are discussed.
Abstract: The concept of pathogenesis has evolved considerably over recent years, and the scenario "a microbe + virulence factors = disease" is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa…). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of "pathobiome" and the research questions that this raises.

240 citations

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

  • ...Several ongoing projects using metagenomics approaches will certainly pave the way to such understanding [62 ,63,64]....

    [...]

Journal Article•DOI•
Direct and Indirect Roles of Viral Suppressors of RNA Silencing in Pathogenesis

[...]

Juan A. Diaz-Pendon1, Shou-Wei Ding1•
University of California, Riverside1
04 Aug 2008-Annual Review of Phytopathology
TL;DR: How the various silencing suppression activities of VSRs may facilitate these distinct steps during plant infection and why they may not play a direct role in eliciting disease symptoms by general impairments of host endogenous small RNA pathways are discussed.
Abstract: Plant and animal viruses overcome host antiviral silencing by encoding diverse viral suppressors of RNA silencing (VSRs). Prior to the identification and characterization of their silencing suppression activities mostly in transgene silencing assays, plant VSRs were known to enhance virus accumulation in the inoculated protoplasts, promote cell-to-cell virus movement in the inoculated leaves, facilitate the phloem-dependent long-distance virus spread, and/or intensify disease symptoms in systemically infected tissues. Here we discuss how the various silencing suppression activities of VSRs may facilitate these distinct steps during plant infection and why VSRs may not play a direct role in eliciting disease symptoms by general impairments of host endogenous small RNA pathways. We also highlight many of the key questions still to be addressed on the role of viral suppression of antiviral silencing in plant infection.

236 citations

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

  • ...However, as for other plant viruses, geminiviruses encode proteins that can suppress gene silencing [15] in a host dependent manner [16 ]....

    [...]

Journal Article•DOI•
The spread of tomato yellow leaf curl virus from the Middle East to the world.

[...]

Pierre Lefeuvre1, Darren P. Martin1, Gordon William Harkins2, Philippe Lemey3, Alistair J. A. Gray1, Sandra Meredith1, Francisco Lakay1, Adérito L. Monjane1, Jean-Michel Lett4, Arvind Varsani1, Arvind Varsani5, Jahangir Heydarnejad6 •
University of Cape Town1, South African National Bioinformatics Institute2, Katholieke Universiteit Leuven3, University of La Réunion4, University of Canterbury5, Shahid Bahonar University of Kerman6
28 Oct 2010-PLOS Pathogens
TL;DR: The results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s and that the global spread only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains.
Abstract: The ongoing global spread of Tomato yellow leaf curl virus (TYLCV; Genus Begomovirus, Family Geminiviridae) represents a serious looming threat to tomato production in all temperate parts of the world. Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future movements of related viruses, determining the consequences of past TYLCV movements could reveal the ecological and economic risks associated with similar viral invasions. Towards this end we applied Bayesian phylogeographic inference and recombination analyses to available TYLCV sequences (including those of 15 new Iranian full TYLCV genomes) and reconstructed a plausible history of TYLCV's diversification and movements throughout the world. In agreement with historical accounts, our results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s (with 95% highest probability density intervals 1905–1972) and that the global spread of TYLCV only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains. Despite the global distribution of TYLCV we found no convincing evidence anywhere other than the Middle East and the Western Mediterranean of epidemiologically relevant TYLCV variants arising through recombination. Although the region around Iran is both the center of present day TYLCV diversity and the site of the most intensive ongoing TYLCV evolution, the evidence indicates that the region is epidemiologically isolated, which suggests that novel TYLCV variants found there are probably not direct global threats. We instead identify the Mediterranean basin as the main launch-pad of global TYLCV movements.

231 citations

Journal Article•DOI•
Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

[...]

Pierre Lefeuvre1, Jean-Michel Lett1, Arvind Varsani2, Arvind Varsani3, Darren P. Martin2 •
University of La Réunion1, University of Cape Town2, University of Canterbury3
15 Mar 2009-Journal of Virology
TL;DR: Combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone, which implies that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.
Abstract: The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.

228 citations

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

  • ...the notorious recombination hot-spot around the origin of replication [10]) when multiple viruses co-infect the same cell [1]....

    [...]

  • ...Recombination patterns in geminiviruses Whereas non-homologous recombination (during which genome regions get rearranged, duplicated, deleted) is mostly apparent above the genus level in the Geminiviridae family, homologous recombination is a widespread phenomenon as almost every geminivirus is the descendent of some inter-species or inter-strain recombinant [10]....

    [...]

  • ...not randomly distributed with conserved recombination hot spots and cold spots [10]....

    [...]

  • ...Current Opinion in Virology 2015, 10:14–19 recombination is available at every level of the diversity spectrum [10]....

    [...]

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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.