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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•
Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination.

[...]

Xueping Zhou1, Yule Liu, L. Calvert, C. Munoz, G W Otim-Nape, David J. Robinson, Bryan D. Harrison •
Scottish Crop Research Institute1
01 Aug 1997-Journal of General Virology
TL;DR: UgV isolates were detected in severely mosaic-affected plants from all 11 widely separated locations sampled, and the probable role of recombination in geminivirus evolution in the short to medium term is discussed.
Abstract: Geminivirus isolates associated with the epidemic of severe cassava mosaic disease in Uganda were studied and compared with virus isolates from the part of Uganda outside the epidemic area, and with African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV). Isolates of a novel type [the Uganda variant (UgV)] were detected in severely affected plants from the epidemic area, whereas those from plants outside the epidemic area were typical of ACMV. The complete nucleotide sequences of DNA-A of UgV (2799 nt) and of a Tanzanian isolate of EACMV (2801 nt) were determined and are extremely similar, except for the coat protein (CP) gene. The CP gene of UgV has three distinct regions: the 5' 219 nt are 99% identical to EACMV (only 79% to ACMV); the following 459 nt are 99% identical to ACMV (75% to EACMV); and the 3' 93 nt are 98% identical to EACMV (76% to ACMV). UgV DNA-A therefore is considered to have arisen by interspecific recombination of EACMV and ACMV. Despite the hybrid nature of their CP, UgV isolates were indistinguishable from ACMV in tests with 20 monoclonal antibodies (MAbs), including seven which reacted with ACMV but not EACMV. The discontinuous epitopes detected by these seven MAbs must involve amino acids which lie in the central part of the CP (residues 74-226) and which differ in ACMV and EACMV. UgV isolates were detected in severely mosaic-affected plants from all 11 widely separated locations sampled. The probable role of recombination in geminivirus evolution in the short to medium term is discussed.

477 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]....

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Journal Article•DOI•
Protein building blocks preserved by recombination.

[...]

Christopher A. Voigt1, Carlos A. Martinez1, Zhen-Gang Wang1, Stephen L. Mayo1, Frances H. Arnold1 •
California Institute of Technology1
01 Jul 2002-Nature Structural & Molecular Biology
TL;DR: A computational algorithm is developed to identify the fragments of proteins, or schemas, that can be recombined without disturbing the integrity of the three-dimensional structure, and results demonstrate a threshold in the amount of schema disruption that the hybrid protein can tolerate.
Abstract: Borrowing concepts from the schema theory of genetic algorithms, we have developed a computational algorithm to identify the fragments of proteins, or schemas, that can be recombined without disturbing the integrity of the three-dimensional structure. When recombination leaves these schemas undisturbed, the hybrid proteins are more likely to be folded and functional. Crossovers found by screening libraries of several randomly shuffled proteins for functional hybrids strongly correlate with those predicted by this approach. Experimental results from the construction of hybrids of two beta-lactamases that share 40% amino acid identity demonstrate a threshold in the amount of schema disruption that the hybrid protein can tolerate. To the extent that introns function to promote recombination within proteins, natural selection would serve to bias their locations to schema boundaries.

376 citations

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

  • ...Whereas the vast majority of recombinant forms, as most mutants, are likely of poorer fitness than the parents [26,31], recombinants bearing favourable combinations [27] might outcompete the parental viruses and become prevalent in the population....

    [...]

Journal Article•DOI•
Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda

[...]

J. S. Pita1, V. N. Fondong1, A. Sangaré, G. W. Otim-Nape2, S. Ogwal2, Claude M. Fauquet1 •
Donald Danforth Plant Science Center1, Agricultural Research Organization, Volcani Center2
01 Mar 2001-Journal of General Virology
TL;DR: Analysis of naturally infected cassava plants showed various assortments of DNA-A and DNA-B of the Ugandan viruses, suggesting the occurrence of natural inter- and intraspecies pseudorecombinations and a pattern of cassava mosaic disease (CMD) more complex than previously reported.
Abstract: The molecular variability of cassava geminiviruses occurring in Uganda was investigated in this study. Infected cassava plants and whiteflies were collected from cassava plantings in different geographical areas of the country and PCR was used for molecular characterization of the viruses. Two complete sequences of DNA-A and -B from African cassava mosaic virus (ACMV), two DNA-A sequences from East African cassava mosaic virus (EACMV), two DNA-B sequences of EACMV and the partial DNA-A nucleotide sequence of a new virus strain isolated in Uganda, EACMV-UG3, are reported here. Analysis of naturally infected cassava plants showed various assortments of DNA-A and DNA-B of the Ugandan viruses, suggesting the occurrence of natural inter- and intraspecies pseudorecombinations and a pattern of cassava mosaic disease (CMD) more complex than previously reported. EACMV-UG2 DNA-A, which contains a recombinant fragment between ACMV and EACMV-UG1 in the coat protein gene that resembles virus from Tanzania, was widespread in the country and always associated with EACMV-UG3 DNA-B, which probably resulted from another natural recombination event. Mixed infections of ACMV-UG and EACMV-UG in cassava and whiteflies were detected in most of the regions where both viruses occurred. These mixed-infected samples always showed extremely severe CMD symptoms, suggesting a synergistic interaction between ACMV-UG and EACMV-UG2. The first demonstration is provided of infectivity of EACMV clones to cassava, proving conclusively that the pseudorecombinant EACMV-UG2 DNA-A+EACMV-UG3 DNA-B is a causal agent of CMD in Uganda.

369 citations

Journal Article•DOI•
Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control.

[...]

Roger A. C. Jones1•
University of Western Australia1
01 May 2009-Virus Research
TL;DR: How rapid expansion in human activity and climate change are likely to impact on plants, vectors and viruses causing increasing instability is described, and the major factors driving virus emergence, evolution and greater epidemic severity at the interface are analysed and explained.

320 citations

Journal Article•DOI•
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

[...]

Chengwei Luo1, Seth T. Walk, David M. Gordon, Michael Feldgarden, James M. Tiedje, Konstantinos T. Konstantinidis •
Georgia Institute of Technology1
26 Apr 2011-Proceedings of the National Academy of Sciences of the United States of America
TL;DR: The genome sequences of nine environmentally adapted strains are reported that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic), but the commensal genomes encode for more functions that are important for fitness in the human gut, and hence do not evolve according to the recently proposed fragmented speciation model.
Abstract: Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.

320 citations

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

  • ...Since recombining viruses obviously have somewhat overlapping geographical distributions, host ranges and tissue tropisms, and patterns of sequence exchange amongst viruses sampled from nature could also be used to retrace the ecological interactions between populations (see [65,66] for a good examples on bacteria)....

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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.