Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus

Mishra, Megha; Verma, Rakesh Kumar; Pandey, V. N.; Srivastava, Aarshi; Sharma, Pradeep; Gaur, Rajarshi Kumar; Ali, Akhtar

doi:10.3390/pathogens11050529

Cited by 7 publications

(12 citation statements)

References 49 publications

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“…These findings underscore the substantial sequence divergence and the higher frequency of unique mutations within the PeLCV population, emphasizing their roles in the emergence of PeLCV. Our results corroborated a study on chili leaf curl virus (ChiLCV) that highlighted similar diversity patterns [57]. Notably, papaya leaf curl virus (PaLCuV) exhibited low sequence divergence but a high frequency of unique mutations [58].…”

Section: Discussionsupporting

confidence: 89%

Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Iqbal,

Shafiq,

Sattar

et al. 2023

Viruses

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Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10−3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined.

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Section: Discussionsupporting

confidence: 89%

Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Iqbal,

Shafiq,

Sattar

et al. 2023

Viruses

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“…For monopartite begomoviruses, betasatellite mostly causes the onset of characteristic symptoms signs (Gnanasekaran et al, 2019; Li et al, 2018). ChiLCV is one of the most destructive begomoviruses, significantly reducing yields in chilli farming around the globe (Mishra et al, 2022; Pandey et al, 2022). Numerous plants are susceptible to ChiLCV infection, including hibiscus, tomato, papaya, eggplant, and chilli (Malathi et al, 2017; Mishra et al, 2022; Srivastava et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…ChiLCV is one of the most destructive begomoviruses, significantly reducing yields in chilli farming around the globe (Mishra et al, 2022; Pandey et al, 2022). Numerous plants are susceptible to ChiLCV infection, including hibiscus, tomato, papaya, eggplant, and chilli (Malathi et al, 2017; Mishra et al, 2022; Srivastava et al, 2022). Similarly, phytoplasmas induce approximately 300 distinct plant diseases, including both wild and cultivated species of plants of various families, inflicting substantial harm to the economy globally (Kumari et al, 2019; Rao et al, 2011; Hoshi et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

“…The cultivars of chilli are susceptible to a wide array of pathogens and diseases. Among the important biotic factors that limit the productivity of chilli crops in various regions of the globe are begomoviruses and phytoplasma (Pandey et al, 2022; Mishra et al, 2022; Lavanya and Arun, 2021; Pandey et al, 2021; Mishra et al, 2020; Kumari et al, 2019, Ganefianti et al, 2017)‥ In the chilli plant, infection of begomovirus has been described in distinct states of India and was revealed to cause severe yielding loss (Khan and Khan, 2017). Symptoms of varying severity were observed in plants, ranging from vein yellowing of leaves, mosaic, mottling, stunting, curling, flower abortion, distortion, and small-unvendible fruits reported in Rojas et al, 2018 study.…”

Section: Introductionmentioning

confidence: 99%

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Perilous coexistence:Chilli Leaf Curl VirusandCandidatus Phytoplasma trifoliiinfectingCapsicum annuum, India

Pandey

Srivastava

Mall

et al. 2022

Preprint

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Molecular computing was used to investigate the possible causal agents of chilli crop samples showing mixed symptoms of yellow leaf curl and little leaf type diseases in the Uttar Pradesh province, India. Total genomic DNA was extracted from twenty-five samples and amplified by PCR using a universal primer pair for begomovirus and phytoplasma. Mixed infection samples show positive amplified products for begomovirus (DNA-A and betasatellite) and phytoplasma (16S rRNA and Sec A). The identified begomovirus from chilli samples was identified as a strain isolate of the previously described Chilli Leaf Curl Virus (94.2% nucleotide sequence identity), which is known to infect Solanum lycopersicon, in Oman, whereas the 16S rRNA was identified from the source Candidatus Phytoplasma trifolii (99.04% nucleotide sequence identity), which is known to infect Helichrysum flowering plants in India. Subsequently, molecular computing research based on phylogenetic interweaves, putative recombination, amino acid selection, and genetic diversity were investigated, revealing divergent evolutionary patterns with significant variation and recombination events. The majority of the sequence variations observed in begomovirus and phytoplasma were caused via inter- and intra-specific recombination. These findings could be the first in silico combined infection analysis of ChiLCV and Ca.P.trifolii in a chilli crop in India, revealing the potential adaption and evolution of begomovirus and phytoplasma to a new geographic range and crop. Keywords: Chilli Leaf Curl Virus, Candidatus Phytoplasma trifolii, molecular computing, Genetic variation

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“…CMBs are transmitted by whiteflies in the Bemisia tabaci cryptic species complex in a persistent, non-propagative manner (Mugerwa et al, 2012 ). Begomoviruses have high rates of mutation and recombination, leading to intra-host diversity and the emergence of novel species of begomoviruses (Duffy and Holmes, 2008 , 2009 ; Crespo-Bellido et al, 2021 ; Mishra et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Cassava begomovirus species diversity changes during plant vegetative cycles

Dye,

Muga,

Mwangi

et al. 2023

Front. Microbiol.

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Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.

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Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus

Cited by 7 publications

References 49 publications

Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Perilous coexistence:Chilli Leaf Curl VirusandCandidatus Phytoplasma trifoliiinfectingCapsicum annuum, India

Cassava begomovirus species diversity changes during plant vegetative cycles

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