Chilli leaf curl disease populations in India are highly recombinant, and rapidly segregated

Pandey, V. N.; Srivastava, Aarshi; Mishra, Megha; Gaur, Rajeeva

doi:10.1007/s13205-022-03139-w

Cited by 9 publications

(7 citation statements)

References 36 publications

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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%

“…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

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Pandey

Srivastava

Mall

et al. 2022

Preprint

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“…Recently, Pandey et al ( 2022 ) ascertained the genetic diversity of ChiLCD based on 121 reference genome sequences of DNA-A, DNA-B, and α and β-satellites. Moreover, transitional and transversional bias was recorded highest in C4 and REn genes.…”

Section: Genome Organizationmentioning

confidence: 99%

“…A total of 987 mutations were also detected in the Rep gene which was the maximum among all ORFs. Based genetic mutations and recombination events evidenced that the ChiLCD rapidly adapted to new environments and led its evolution along with the satellite molecules that help in expanding the virus-host range and diversity in Indian subcontinents (Kumar et al, 2015 ; Pandey et al, 2022 ). Natural mixed infections of a bipartite and monopartite might have facilitated their emergence in new hosts, severity, and recombination.…”

Section: Genome Organizationmentioning

confidence: 99%

An Overview of Chili Leaf Curl Disease: Molecular Mechanisms, Impact, Challenges, and Disease Management Strategies in Indian Subcontinent

et al. 2022

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Leaf curl disease in a chili plant is caused mainly by Chili leaf curl virus (ChiLCV) (Family: Geminiviridae, Genus: Begomovirus). ChiLCV shows a widespread occurrence in most of the chili (Capsicum spp.) growing regions. ChiLCV has a limited host range and infects tomatoes (Solanum lycopersicum), potatoes (S. tuberosum), and amaranth (Amaranthus tricolor). The virus genome is a monopartite circular single-stranded DNA molecule of 2.7 kb and associated with α and β-satellites of 1.3 and 1.4 kb, respectively. The virus genome is encapsulated in distinct twinned icosahedral particles of around 18–30 nm in size and transmitted by Bemisia tabaci (Family: Aleyrodidae, Order: Hemiptera). Recently, bipartite begomovirus has been found to be associated with leaf curl disease. The leaf curl disease has a widespread distribution in the major equatorial regions viz., Australia, Asia, Africa, Europe, and America. Besides the PCR, qPCR, and LAMP-based detection systems, recently, localized surface-plasmon-resonance (LPSR) based optical platform is used for ChiLCV detection in a 20–40 μl of sample volume using aluminum nanoparticles. Management of ChiLCV is more challenging due to the vector-borne nature of the virus, therefore integrated disease management strategies need to be followed to contain the spread and heavy crop loss. CRISPR/Cas-mediated virus resistance has gained importance in disease management of DNA and RNA viruses due to certain advantages over the conventional approaches. Therefore, CRISPR/Cas system-mediated resistance needs to be explored in chili against ChiLCV.

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“…Similarly, the sequences of β-satellites were retrieved from the NCBI GenBank and constructed phylogenetic analyses and revealed the distinct 12 clades (Figure 4B). Recently, Pandey et al (2022) ascertained the genetic diversity of ChiLCD based on 121 reference genome sequences of DNA-A, DNA-B, and α and β-satellites. Moreover, transitional and transversional bias was recorded highest in C4 and REn genes.…”

Section: Genetic Diversity and Recombinationmentioning

confidence: 99%

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Chilli leaf curl disease populations in India are highly recombinant, and rapidly segregated

Cited by 9 publications

References 36 publications

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

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

An Overview of Chili Leaf Curl Disease: Molecular Mechanisms, Impact, Challenges, and Disease Management Strategies in Indian Subcontinent

Data_Sheet_1.docx

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