Characterization of DNA beta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A

Eighteen samples of begomoviruses isolated from tobacco, tomato and weed species in Yunnan, China were found to be associated with DNA beta molecules, for which the complete nucleotide sequences were found to contain 1333-1355 nt. The 18 DNA beta molecules identified consist of three main types, each associated with a different begomovirus species: 72-99% nucleotide identity was found within one type, but only 39-57% identity was found between types. All the DNA beta molecules reported here and elsewhere contain a 115 nt conserved region that has 93-100% identity with a consensus sequence, and have a common ORF encoding 118 amino acids on the complementary strand (designated C1). Co-agroinoculation of the DNA-A component of Tomato yellow leaf curl China virus tobacco isolate Y10, with its associated DNA beta (Y10 beta ), shows this DNA beta to be involved in symptom induction in tobacco and tomato. The in-frame ATG mutation of C1 of Y10 beta caused much milder symptoms as compared with wild Y10 beta , indicating a functional role for this ORF. Pairwise nucleotide sequence identity comparisons of DNA beta molecules and their cognate viral DNA-A molecules indicate that DNA beta molecules have co-evolved with their cognate helper viruses. Recombination between DNA beta molecules is documented and a DNA beta species concept is proposed and discussed.