Abstract
BackgroundDestructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide. Recently, TSWV was reported to infect different hosts in China. It is of value to clone TSWV isolates from different hosts and examine diversity and evolution among different TSWV isolates in China as well as worldwide.MethodsRT-PCR was used to clone the full-length genome (L, M and S segments) of three new isolates of TSWV that infected different hosts (tobacco, red pepper and green pepper) in China. Identity of nucleotide and amino acid sequences among TSWV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates.ResultsWhole-genome sequences of three new TSWV isolates in China were determined. Together with other available isolates, 29 RNA L, 62 RNA M and 66 RNA S of TSWV isolates were analyzed for molecular diversity, phylogenetic and recombination events. This analysis revealed that the entire TSWV genome, especially the M and S RNAs, had major variations in genomic size that mainly involve the A-U rich intergenic region (IGR). Phylogenetic analyses on TSWV isolates worldwide revealed evidence for frequent reassortments in the evolution of tripartite negative-sense RNA genome. Significant numbers of recombination events with apparent 5′ regional preference were detected among TSWV isolates worldwide. Moreover, TSWV isolates with similar recombination events usually had closer relationships in phylogenetic trees.ConclusionsAll five Chinese TSWV isolates including three TSWV isolates of this study and previously reported two isolates can be divided into two groups with different origins based on molecular diversity and phylogenetic analysis. During their evolution, both reassortment and recombination played roles. These results suggest that recombination could be an important mechanism in the evolution of multipartite RNA viruses, even negative-sense RNA viruses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-015-0457-3) contains supplementary material, which is available to authorized users.
Highlights
Destructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide
RNA L of YNta, YNrp and YNgp were identical lengths (8913 nts), while the genomic sizes of RNAs M and S varied slightly due to size variation in the intergenic region (IGR) (Additional file 1: Table S1)
Based on molecular diversity on 29 RNA L, 62 RNA M and 66 RNA S of TSWV, it is suggested that the entire TSWV genome, especially the M and S RNAs, have undergone extreme variations in genomic size that mainly involve the A-U rich intergenic region (IGR)
Summary
Destructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide. TSWV was reported to infect different hosts in China. TSWV is mainly transmitted in a persistent manner by several species of thrips, especially the western flower thrip Frankliniella occidentalis, which may contribute to the worldwide spread of TSWV as well as to tomato spotted wilt disease [14, 18, 19]. TSWV infectes many important economic plants including tomato and potato, and causes serious damage including ringspot, black streak and tip dieback [20,21,22]. M plus-sense [M(+)RNA] encodes a nonstructural protein (NSm) responsible for cell-to-cell movement and its complementary minus-strand [M(−)RNA] encodes a Gn-Gc glycoprotein [25]. S(+)RNA encodes a second nonstructural protein (NSs) involved in the suppression of gene silencing and S(−)RNA encodes the nucleocapsid (N) protein [26]
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