Population genetic diversity analysis of tobacco mosaic virus on tobacco in Yunnan based on the CP gene sequences
This study investigated the population genetic diversity of tobacco mosaic virus(TMV)on tobacco in Yunnan province.Specific primers targeting the TMV coat protein(CP)gene were used to detect suspected samples with mosaic symptoms from various tobacco-growing regions in Yunnan.A total of 138 TMV CP gene sequences were obtained through cloning,sequencing,and BLAST with NCBI database.These sequences were then analyzed for consistency,systematic development,mismatch distribution,genetic variation,and population diversity.Variation analysis showed that TMV CP gene contained 122 mutation sites,accounting for 25.42%out of the total mutation sites.The nucleotide substitution was the only type of mutation,with a nucleic acid diversity of 0.018 and a haplotype diversity of 0.970.Consistency comparison results revealed that the identities of nucleotide and amino acid sequences of the 138 TMV CP gene were 96%to 100%.Recombination analysis did not detect any recombination signals.A phylogenetic analysis was conducted on the CP genes of TMV isolates from Yunnan tobacco,tobacco from other regions on NCBI,and other hosts in Yunnan.The results showed that all TMV isolates could be divided into four groups in evolution.All 138 isolates obtained in this experiment were distributed in group 1,2,and 3,with only the isolates from Zhaotong region tending to cluster,indicating that the adaptive evolution of TMV isolates from Yunnan tobacco was driven by geographical adaptability and basically independent on host adaptability.Mismatch distribution analysis indicated that TMV populations from Yunnan tobacco exhibit multimodal distribution,suggesting that they have not undergone any group expansion events recently.The genetic differentiation analysis between populations indicate that it is easy for genetic drift to occur between tobacco TMV populations in Zhaotong and Qujing and other TMV populations,leading to genetic differentiation in the populations,However,the genetic drift may be resisted by gene flow among other TMV populations.This study is the first report on the genetic variation of TMV populations in various tobacco-growing regions of Yunnan.The findings provide important references for disease resistance breeding and the development of more effective control strategies against TMV.