| Geminiviruses occur in world and have caused significant yield losses to many crops. In China, the genomic structure and variation of geminiviruses were not studied in any detail. In an attempt to study the genomic variation and evolution of geminiviruses in China, many geminiviruses samples were collected from different parts of Yunnan.144 samples of geminiviruses were isolated from tobacco, tomato and squash in Yunnan province. On the base of the reactions with a set of monoclonal antibodies in triple antibody sandwich ELISA (TAS-ELISA), the complete nucleotide sequence of 15 isolates were determined. Analysis of full-length DNA-A showed there are four types of geminiviruses, among them three are distinct Begomovirus species, for which the names Tobacco leaf curl Yunnna virus (TbLCYNV), Tobacco curly shoot virus (TbCSV) and Squash leaf curl Yunnan virus (SLCYV) were proposed, one belongs to Tomato yellow leaf curl China Virus (TYLCCNV). SLCYV is considered to have arisen by recombination among viruses related to Tomato yellow leaf curl Thailand virus, Pepper leaf curl Bangladesh virus and another unidentified begomovirus. The genomic variation of DNA-A of TYLCCNV isolates exsited on AC1-AC4 regions.Defective DNA molecule of the TbCSV-Y2 had been identified in infected tobacco plants. The sequence analysis showed it was about half the size of the TbCSV DNA-A, and was derived from TbCSV DNA-A by large deletion. The defective DNA contained the intergenic region , AV2, AC4 ORFs and part of the AC1 (Rep), AV1(CP) ORFs, and also contained novel open reading frames. The immunotrapping tests showed the defective DNA was associated with geminate particles, suggesting it could be encapsidated in virus particles. It was transmitted, along with full-length TbCSV DNA-A, between tobacco plants by grafting and by whitefly (Bemisia tabaci).Novel satellite DNA molecules-DNA were identified in association with TbCSV, TYLCCNV and Malvastrum yellow vein virus (MYVV). Analysis of DNA molecules revealed that it is approximately half the size of the genomic DNA-A, and has little sequence homology to either DNA-A or DNA-B ofbegomoviruses, except for the conserved TAATATTAC loop sequence. DNAp molecules contain a 115 nucleotides conserved region and an A-rich region with the length of about 230 nucleotides and have a common ORF encoding 118 amino acids on the complementary strand (designated C1). The immunotrapping PCR and whitefly transmission tests showed DNA P molecule could be encapsidated in virus particle and transmitted by Bemisia tabaci. On the bases of analysis of 18 DNA molecules associated with begomoviruses in China, it was found these DNAp molecules identified consist of three main types and are associated with three Chinese begomovirus species (TbCSV, TYLCCNV and MYVV). 72-99% nucleotide identity was found within TYLCCNV ,83-98% nucleotide identity was found within TbCSV , 52~57%nucleotide identity was found between TYLCCNV and TbCSV , 39~42% nucleotide identity was found between TYLCCNV , TbCSV and MYVV . We demonstrated that C1 ORF has the same degree of variability as DNAP molecule. There is a high correlation between the variability of the DNAP molecules and their cognate DNA-A components, suggesting DNAP molecules co-evolved with their virus genome. We propose that DNAp sequence identity could be used as a taxonomic criterion for species demarcation of DNAP molecules.Nanovirus-like DNA components, referred to as DNA1, were found in association with TbLCYNV, TbCSV or TYLCCNV. DNA1 is a novel circular single-stranded DNA molecule, which is approximately half the size of helper begomovirus but shares no homology with helper viruses. DNA1 contains nano virus-conserved nonanucleotide TAGTATTAC and a stem-loop structure similar to geminiviruses. DNA1 encodes a protein about 36~37kDa in virion-sense DNA which resembles a replication-associated protein of nanoviruses.Mixed infection were tested with primers specific for DNA-A or DNA of TbCSV, TbLCYNV and TYLCCNV. The results showed that mixe...
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