Genetic Structure Of Tobacco Vein-banding Mosaic Virus Turnip Mosaic Virus And Potato Virus Y

Tobacco vein banding mosaic virus (TVBMV), Turnip mosaic virus (TuMV) and Potato virus Y (PVY) belong to the genus Potyvirus, the family Potyviridae. TVBMV and PVY infect plants of the family Solanaceae and TuMV infects the family Cruciferae in nature and they cause great economic losses to crop production. The genetic structures of TVBMV, TuMV and PVY were analyzed in this study.TVBMV is one of the most economically important viruses infecting tobacco in China. In this paper, we determined the HC-Pro, P3, 6K1 and CP gene sequences of 40 TVBMV isolates collected from different tobacco-growing areas in China and compared them with those sequences available to study its genetic diversity and population structure. TVBMV isolates could be divided into two (6K1 and CP) or three (P3 and HC-Pro) groups, depending on which gene was analyzed. The populations from most part of China showed high genetic identities and had frequent gene flow. The population from Yunnan, a southern western province of China, formed a separate group and had frequent gene flow within this region. However, the gene flow between TVBMV isolates from Yunnan and other parts of China was infrequent. TVBMV genes were under strong negative selection, but the pressures were different for different genes. Recombination was common in the evolution of TVBMV isolates. Our data also suggested that the most recent outbreak of TVBMV in China was not due to the emergence of new TVBMV subtype(s).The 3′- terminal genome of 56 TuMV isolates were determined and analyzed with other Chinese and Japanese isolates available in the GenBank to understand the genetic structure of this virus. Twelve of 105 isolates were clear recombination. Isolates from Radish in China formed three groups: Asian-BR, basal-BR and world B. Group basal-BR consisted of 50.5% isolates and were divided into three subpopulations. Subpopulations I and II were genetical identical with Janpanese subpopulations but subpopulation III was not, while subpopulation IV only existed in Japan. Isolates in the group basal-BR from Tai′an and Weifang were new emergent and in a state of expansion. All populations and subpopulations were under negative pression. Gene flow between Tai′an and Weifang was frequent.Genetic variability of PVY isolates infecting potato has been characterized, but little is known about genetic diversity of PVY isolates infecting tobacco crops. In this study, PVY isolates were collected from major tobacco-growing areas in China and single-lesion isolates produced by serial inoculation on Chenopodium amaranticolor. Twenty-two of 25 isolates caused systemic veinal necrosis symptoms and three isolates caused mosaic in tobacco. Nineteen of 25 isolates were detected by PVYO CP specific antibodies. Serological and phylogenetic analyses showed that, among the 25 isolates, three isolates belonged to group O, two isolates belonged to group N, two isolates belonged to group NTN, sixteen isolates belonged to group N-Wi and two isolates belonged to group N-HcO. Isolates Feixian8 and Mengyin60 contained a PVYN-like coat protein (CP) and PVYO-like helper componentproteinase (HC-Pro) but caused systemic veinal necrosis symptoms in tobacco, and hence designated as PVYN-HcO recombination. Seven amino acids in HC-Pro and six amino acids in CP were under positive selection. Selection pressures differed between the subpopulations of PVY distinguished by phylogenetic analysis of HC-Pro and CP sequences. When PVY isolates from potato were included, no host-specific clustering of the PVY isolates was observed in phylogenetic and nucleotide diversity analyses. Potato virus X (PVX) is one of the most common plant viruses that cause great economic losses to solanaceous plants. The complete genome of PVX-1985 is 6 435 nucleotides (nt) exinclude Poly (A) and contains five open reading frames (ORFs). ORF1 encodes a protein of 166 kDa that functions as RNA-dependent RNA polymerase (RdRp). The overlapping ORFs 2, 3 and 4 encode triple gene block proteins (TGBp) of 25, 12 and 8 kDa, respectively. ORF 5 encodes the 25 kDa coat protein (CP). The phylogenetic trees of the full genomic sequences and the CP gene demonstrated that PVX isolates were clustered into two groups: Eurasia and America, and PVX-1985 fell within the group Eurasia. All the open reading frames of PVX were under negative (or purifying) selection, but the central region of RdRp was under positive or diversifying selection.