Complete genomes of begomovirus associated with pepper yellow leaf curl disease in the Northeastern Thailand

Abstract

This research aims to study the complete genome of Pepper yellow leaf curl virus (PepYLCV) to support the development of accurate diagnosis and will benefit for the disease resistance breeding program afterward.  Pepper symptoms associated with yellow leaf curl disease were collected in 2018 harboring 5 provinces including Chaiyaphum, Nakhon Ratchasima, Buriram, Surin and Sisaket. Total DNA of the samples from Buriram province (BRM103) was extracted and its genome was amplified by rolling circle amplification (RCA). Then single digestion was performed using HindIII for DNA-A and SphI for DNA-B. Analysis of the nucleotide sequences showed that the DNA-A contained 2,742 nucleotides which comprised of 6 open reading frame (ORFs); AV1, AV2, AC1, AC2, AC3 and AC4 while the DNA-B contained 2,731 nucleotides and comprised of 2 ORFs; BC1 and BV1. Comparison of the nucleotide sequences obtained in this study with the GenBank database showed close relationship to Pepper yellow leaf curl Thailand virus (PepYLCTHV) isolate KON-KG5 segment DNA-A (accession no. KT322141) at 98.58 % and PepYLCTHV isolate KON-KG5B segment DNA-B (accession no. KX885224) at 97.44 %, respectively. The begomovirus in this study was designated Pepper yellow leaf curl Thailand virus (PepYLCTHV) isolate BRM103 and the sequences were submitted in the GenBank database (accession no. MK946436 and MK946435). Analysis of the genetic relationship among 6 reported isolates of begomoviruses associated with pepper yellow leaf curl disease in Thailand based on DNA-A, using pairwise sequence comparison program, showed that five reported isolates are the same species and four out of those are the same strain.