Evolutionary dynamics of Begomoviruses causing Papaya leaf curl disease in India

AbstractThe genus begomovirus represents a group of multipartite viruses that significantly damages many agricultural crops, including papaya and drastically influence the overall production. Understanding the genetic variations, mutations and recombination of the begomovirus population infecting papaya has several important implications in alleviating substantial losses, mainly in developing countries, including India. In an attempt for a bioinformatics driven study of diversity and variability of papaya leaf curl disease in India, a total of thirty-two (32) DNA-A and sixteen (16) betasatellite sequences were retrieved from GenBank. An uneven distribution of evolutionary divergence has been observed across the branch length, which triggered the estimated recombinational event. Interestingly, a maximum of the begomoviruses were found to be intra-species recombinants. Further genetic variability, selection pressure, and substitution rate acting on the population were estimated and found to be high enough to support the evolution of geminiviruses. Genetic divergence composition in all begomovirus datasets revealed predominance of nucleotide diversity driven by mutation. The analysis indicates that even though a significant fraction of the genetic variations might be due to recombination but, it was constantly lower than the mutation rate. Thus, the diversification of the begomovirus population is principally impelled by mutational dynamics.

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Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan

Microbiology ◽

10.1099/0022-1317-81-7-1839 ◽

2000 ◽

Vol 81 (7) ◽

pp. 1839-1849 ◽

Cited By ~ 81

Author(s):

Ana I. Sanz ◽

Aurora Fraile ◽

Fernando García-Arenal ◽

Xueping Zhou ◽

David J. Robinson ◽

...

Keyword(s):

Indian Subcontinent ◽

Multiple Infection ◽

Pcr Analysis ◽

Cotton Leaf ◽

Evolutionary Divergence ◽

Cotton Leaf Curl Virus ◽

Geographical Regions ◽

Leaf Curl Virus ◽

Leaf Curl Disease ◽

Leaf Curl

Begomoviruses occur in many plant species in Pakistan and are associated with an epidemic of cotton leaf curl disease that has developed since 1985. PCR analysis with primer pairs specific for each of four already sequenced types of DNA-A of cotton leaf curl virus (CLCuV-PK types a, 26, 72b and 804a), or for okra yellow vein mosaic virus (OYVMV), indicated that many individual naturally infected plants of cotton and other malvaceous species contained two or three begomovirus sequences. Similarly, sequence differences among overlapping fragments of begomovirus DNA-A, amplified from individual naturally infected plants, indicated much multiple infection in malvaceous and non-malvaceous species. Some cotton plants contained DNA-A sequences typical of begomoviruses from non-malvaceous species, and some non-malvaceous plants contained sequences typical of CLCuV-PK. Some DNA-A sequences were chimaeric; they each included elements typical of different types of CLCuV-PK, or of different malvaceous and/or non-malvaceous begomoviruses. Often an apparent recombination site occurred at the origin of replication. No complete CLCuV-PK DNA-A sequence was found in malvaceous or non-malvaceous species collected in Pakistan outside the area of the cotton leaf curl epidemic but chimaeric sequences, including a part that was typical of CLCuV-PK DNA-A, did occur there. We suggest that recombination among such pre-existing sequences was crucial for the emergence of CLCuV-PK. Recombination, following multiple infection, could also explain the network of relationships among many of the begomoviruses found in the Indian subcontinent, and their evolutionary divergence, as a group, from begomoviruses causing similar diseases in other geographical regions.

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Characterization of circular DNA molecules from cotton plants with leaf curl disease

Pakistan Journal of Botany ◽

10.30848/pjb2019-1(29) ◽

2018 ◽

Vol 51 (1) ◽

Author(s):

Sohail Akhtar ◽

Muhammad Nouman Tahir ◽

Imran Amin ◽

Rana Binyamin ◽

Shahid Mansoor

Keyword(s):

Dna Molecules ◽

Circular Dna ◽

Cotton Plants ◽

Leaf Curl Disease ◽

Leaf Curl

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Transmission, characterization and occurrence of recombination in Indian strain of squash leaf curl China virus associated with yellow mosaic and leaf curl disease of Summer squash

3 Biotech ◽

10.1007/s13205-021-02821-9 ◽

2021 ◽

Vol 11 (6) ◽

Author(s):

V. Venkataravanappa ◽

C. N. Lakshminarayana Reddy ◽

M. Nandan ◽

Shridhar Hiremath ◽

K. V. Ashwathappa ◽

...

Keyword(s):

Indian Strain ◽

Summer Squash ◽

Leaf Curl Disease ◽

Leaf Curl

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Potato apical leaf curl disease: current status and perspectives on a disease caused by tomato leaf curl New Delhi virus

Journal of Plant Diseases and Protection ◽

10.1007/s41348-021-00463-w ◽

2021 ◽

Author(s):

Ravinder Kumar ◽

Rahul Kumar Tiwari ◽

Arjunan Jeevalatha ◽

Sundaresha Siddappa ◽

Mohd. Abas Shah ◽

...

Keyword(s):

Tomato Leaf ◽

Current Status ◽

New Delhi ◽

Apical Leaf ◽

Tomato Leaf Curl ◽

Leaf Curl Disease ◽

Leaf Curl

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Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Virology Journal ◽

10.1186/s12985-020-01466-z ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Edith Khamonya Avedi ◽

Adedapo Olutola Adediji ◽

Dora Chao Kilalo ◽

Florence Mmogi Olubayo ◽

Isaac Macharia ◽

...

Keyword(s):

Genetic Diversity ◽

Selection Pressure ◽

Management Strategies ◽

Purifying Selection ◽

Tomato Leaf ◽

Amino Acid Sequences ◽

Virus Population ◽

Tomato Production ◽

Tomato Leaf Curl ◽

Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

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Characterization of novel French bean leaf curl virus and betasatellite associated with leaf curl disease of French bean (Phaseolus vulgaris L.)

Journal of General Plant Pathology ◽

10.1007/s10327-020-00979-3 ◽

2021 ◽

Author(s):

V. Venkataravanappa ◽

Priti Sonavane ◽

C. N. Lakshminarayana Reddy ◽

M. Krishna Reddy

Keyword(s):

Phaseolus Vulgaris ◽

French Bean ◽

Phaseolus Vulgaris L ◽

Leaf Curl Virus ◽

Leaf Curl Disease ◽

Leaf Curl

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Implication of the Whitefly Protein Vps Twenty Associated 1 (Vta1) in the Transmission of Cotton Leaf Curl Multan Virus

Microorganisms ◽

10.3390/microorganisms9020304 ◽

2021 ◽

Vol 9 (2) ◽

pp. 304

Author(s):

Yao Chi ◽

Li-Long Pan ◽

Shu-Sheng Liu ◽

Shahid Mansoor ◽

Xiao-Wei Wang

Keyword(s):

Coat Protein ◽

Molecular Mechanisms ◽

Cotton Leaf ◽

Yeast Two Hybrid ◽

Yeast Two Hybrid System ◽

Vacuolar Protein ◽

Leaf Curl Disease ◽

Two Hybrid ◽

Asia Ii 1 ◽

Leaf Curl

Cotton leaf curl Multan virus (CLCuMuV) is one of the major casual agents of cotton leaf curl disease. Previous studies show that two indigenous whitefly species of the Bemisia tabaci complex, Asia II 1 and Asia II 7, are able to transmit CLCuMuV, but the molecular mechanisms underlying the transmission are poorly known. In this study, we attempted to identify the whitefly proteins involved in CLCuMuV transmission. First, using a yeast two-hybrid system, we identified 54 candidate proteins of Asia II 1 that putatively can interact with the coat protein of CLCuMuV. Second, we examined interactions between the CLCuMuV coat protein and several whitefly proteins, including vacuolar protein sorting-associated protein (Vps) twenty associated 1 (Vta1). Third, using RNA interference, we found that Vta1 positively regulated CLCuMuV acquisition and transmission by the Asia II 1 whitefly. In addition, we showed that the interaction between the CLCuMuV coat protein and Vta1 from the whitefly Middle East-Asia Minor (MEAM1), a poor vector of CLCuMuV, was much weaker than that between Asia II 1 Vta1 and the CLCuMuV coat protein. Silencing of Vta1 in MEAM1 did not affect the quantity of CLCuMuV acquired by the whitefly. Taken together, our results suggest that Vta1 may play an important role in the transmission of CLCuMuV by the whitefly.

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