Deep sequencing reveals genetic identity of pepper yellow leaf curl Thailand virus from pepper and whiteflies from Chiang Mai, Thailand

Abstract

Importance of the work: The production of pepper (Capsicum spp.) in Thailand is affected
greatly by viral diseases, particularly those caused by begomoviruses. Transmitted by the
whitefly Bemisia tabaci (Gennadius, 1889), these viruses cause severe symptoms, including
yellow leaf curl and considerable yield losses. Understanding the diversity and distribution
of begomoviruses is essential for developing effective disease management strategies.
Objectives: To identify and characterize begomoviruses associated with yellow leaf curl
disease in pepper plants from Chiang Dao District, Chiang Mai Province, Thailand and to
assess their genetic relationships to known isolates in Thailand.
Materials and Methods: Symptomatic pepper leaves and viruliferous whiteflies were
collected from the field. Viral DNA was extracted, enriched using rolling circle amplification
and analyzed using Illumina HiSeq next-generation sequencing. De novo genome assembly
and sequence comparisons were conducted to identify Begomovirus components and to
assess genetic variation.
Results: Components (two full-length DNA-A and one DNA-B) were recovered from both
plant and whitefly samples. The DNA-A sequences showed 98.0–99.3% identity to Pepper
yellow leaf curl Thailand virus (PepYLCTHV) isolate SNS-CM5, while DNA-B shared
96.0% identity with isolates WF-SPN-Pep2015 and TMK-KR8. Minor sequence variation
was observed in AC1 and AC4 genes. Phylogenetic analysis confirmed that the Chiang Dao
isolates formed a distinct clade within the PepYLCTHV group.
Main finding: PepYLCTHV is the predominant Begomovirus associated with yellow
leaf curl disease in pepper in northern Thailand and the Chiang Dao isolates represent
a genetically consistent but regionally distinct cluster, emphasizing the need for localized
surveillance in viral disease management.