Biocomputational Recombination, Evolution, and Distribution Patterns Analysis of Begomovirus Beta-satellites in Chilli Crop Affected by Leaf Curl Disease in Pakistan: Distribution Patterns Analysis of Begomovirus Beta-satellites in Chilli Leaf Curl Disease

Muhammad Atif; Uzma Bashir; Muhammad Tariq Manzoor; Qandeel Ishfaq; Madiha Zahoor

doi:10.54393/fbt.v6i1.223

Authors

Muhammad Atif Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
Uzma Bashir Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
Muhammad Tariq Manzoor Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
Qandeel Ishfaq Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
Madiha Zahoor Department of Plant Pathology, University of the Punjab, Lahore, Pakistan

DOI:

https://doi.org/10.54393/fbt.v6i1.223

Keywords:

Betasatellites, Diversity, Geminiviridae, Recombination, Transmission

Abstract

Geminiviridae is one of the largest families of single-stranded DNA (ssDNA) plant viruses. Among 15 genera, begomoviruses are the most important, comprising more than 464 species. Vegetable crops are primary hosts of begomoviruses, and whiteflies are insect vectors that persistently transmit them. Beta-satellites are subviral particles and are actively associated with leaf curl diseases of solanaceous crops caused by begomoviruses. Objectives: To classify begomoviruses beta-satellites into species and variants and to check the recombination in isolated molecules. Methods: 59 full-length sequences of Chilli leaf curl beta-satellite were downloaded from the National Center for Biotechnology Information and were analyzed using different bioinformatics tools such as MEGA, SDT, and RDP. Our phylogenetic analysis suggested that chilli leaf curl beta-satellites associated with chilli crops having accession number OQ076340, isolated from Pakistan, appear at the bottom of the phylogenetic tree. Results: The current study recombination tests (BootScan, SiScan, Chimaera, MaxChi, RDP, GENCONV, and 3Seq) showed recombination in 21 satellite molecules, 11 sequences missing their major and minor parents, and 27 sequences found to be unique. Conclusions: Betasatellites show huge diversity in nature. Recombination with other viruses helps betasatellites produce a more complex structure and greater diversity. This complex nature makes them difficult to control.

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