Molecular analysis of Cotton leaf curl virus-Sudan reveals an evolutionary history of recombination

Virus Genes. 2002 Jun;24(3):249-56. doi: 10.1023/a:1015380600089.

Abstract

Monopartite begomoviral DNAs (2761 bp) were cloned and sequenced from field cotton, okra, and Sida alba, from Gezira, and field okra from Shambat. Comparison of the four apparent full-length begomoviral DNAs revealed 99.3-99.5% shared nucleotide (nt) identity, indicating that they are the same viral species, hereafter, referred to as Cotton leaf curl virus-Sudan (CLCuV-SD). Host range studies revealed that the field okra isolate of CLCuV-SD was whitefly-transmissible from okra to okra, M. parviflora, and hollyhock, but not to cotton. In contrast, the cotton isolate of CLCuV-SD infected cotton and hollyhock, but not okra. The genome of CLCuV-SD encodes six open reading frames (ORFs), and was most closely related to other monopartite begomoviruses of the Eastern Hemisphere. CLCuV-SD shared highest nucleotide sequence identity (95.5%) with Okra enation virus (OkEV), but was distantly related (approximately 74% nt sequence identity) to begomoviruses isolated from cotton in Pakistan. While extensive genomic regions of CLCuV-SD and OkEV are highly conserved (approximately 99% nt identity), nt sequence identity of the V1 ORF encoding the coat protein was uncharacteristically low (87.9%), suggesting a history of recombination. An analysis conducted with Sawyer's GENECONV program support the recombination hypothesis, indicating that the V1 ORF and a small segment of the intergenic region of CLCuV-SD and OkEV were derived from other begomoviruses. As a BLAST analysis failed to identify a prospective extant source of either V1 ORF, the parental viruses serving as CP donors remain undiscovered or are extinct.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Evolution, Molecular*
  • Geminiviridae / classification
  • Geminiviridae / genetics*
  • Geminiviridae / isolation & purification
  • Geminiviridae / physiology
  • Genome, Viral
  • Gossypium / virology*
  • Phylogeny
  • Recombination, Genetic*