Begomoviruses associated with yellow leaf curl disease of Hot Pepper in Thailand

Name: Amisa Laprom

keyword: Yellow Leaf Curl

MeSH: Plant viruses -- 278933

Classification :.LCCS: QR351

; PepYLCV, Begomovirus, Full Genome, NGS

MeSH: Plant viruses -- Genetics -- 230086

MeSH: Begomovirus -- 278934

MeSH: Yellow Leaf Curl -- 278935

MeSH: Plant diseases -- 278936

LCSH: Plant viruses -- 278933

LCSH: Plant viruses -- Genetics -- 230086

LCSH: Begomovirus -- 278934

LCSH: Yellow Leaf Curl -- 278935

LCSH: Plant diseases -- 278936

Abstract: Pepper (Capsicum annuum L.) is an economically vegetable crop in Thailand. In recent years, a yellow leaf curl disease caused by whitefly-transmitted begomovirus has emerged as an important threat to the production of pepper crop. In this study, the incidence of begomoviruses infecting pepper was investigated in 3 major production areas of Thailand (central, northern and northeastern regions). A total of 2,149 samples were tested for the presence of the following viruses: Cucumber mosaic virus (CMV), Chilli veinal mottle virus (ChiVMV), Tomato necrotic ringspot virus (TNRV), Tobacco mosaic virus (TMV), Potato virus Y (PVY), Tomato spotted wilt virus (TSWV), and begomoviruses, using an enzyme-linked immunosorbent assay (ELISA). The polymerase chain reaction (PCR) was then undertaken to confirm the presence of begomoviruses. In total, 796 samples were tested positive for the begomovirus infection, accounting for 37% from collected samples. The full-length genome of the begomoviruses were then amplified from six diseased Capsicum samples using rolling circles amplification (RCA). The circular DNAs obtained were cloned and sequenced for species identification. Based on the sequence analysis, these begomoviruses were found to be a member of a bipartite species, closely related to the Pepper yellow leaf curl Thailand virus (PepYLCTHV) and Eggplant golden mosaic virus (EGMV). The viral genomes of the begomoviruses in symptomatic pepper leaves and a viruliferous whitefly body from a field in Chiang Dao district, Chiang Mai province, were characterized using a metagenomics approach. The viral DNA was enriched using RCA and sequenced using HiSeq Illumina next-generation sequencing (NGS) to generate the full-length DNA-A and DNA-B components. The analysis of the assembled genomes and pairwise identity revealed that the component A shared the highest nucleotide identity (99.3%) with the PepYLCTHV DNA-A isolate SNS-CM5 (KT322142). For the DNA-B, the sequence homology was highest (96%) to the PepYLCTHV isolate WF-SPN-Pep2015 (NC040186) and TMK-KR8 (KX885225). Based on the same workflow analysis, the begomovirus bipartite genome of a viruliferous whitefly body was found to be closely related to the PepYLCTHV isolate KKN601 (MW715819), KKN603 (MW715821) and KKN604 (MW715822) for the DNA-A, and to the isolate WF-SPN-Pep2015 for the DNA-B. Phylogenetic tree of whole-genome sequences revealed the cluster of PepYLCTHV from this study and many locations in Thailand, separating groups from the other begomovirus species causes disease in Capsicum. This study provides valuable information for further epidemiological study related to the begomovirus’s diversity and distribution. In addition, the findings of this project could help to develop strategies to monitor the virus infection, and to develop the means for disease management.

Mae Fah Luang University. Learning Resources and Educational Media Center

Address: CHIANG RAI

Email: library@mfu.ac.th

Name: Ekachai Chukeatirote

Role: Advisor

Created: 2021

Modified: 2022-03-04

Issued: 2022-03-04

วิทยานิพนธ์/Thesis

application/pdf

CallNumber: QR351 A517b 2021

eng

DegreeName: Doctor of Philosophy

Level: Doctoral Degree

Descipline: Biosciences

Grantor: Mae Fah Luang University

©copyrights Mae Fah Luang University

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