Sequencing and phylogenetic characterization of a novel Polerovirus from Nicotiana tabacum
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Sequencing and phylogenetic characterization of a novel Polerovirus from Nicotiana tabacum Yingjie Liu1,2 · Yonghao Dong1 · Xi Chen1 · Yun Zang1 · Jinyan Liu1 · Guangwei Ren1 · Pengjun Xu1 Received: 20 December 2019 / Accepted: 11 July 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract In this study, we reported the complete genome of a novel Polerovirus, named Tobacco yellow virus (TYV), which can be transmitted by Myzus persicae. TYV had a single-stranded RNA genome of 5735 nucleotides in length and contained six putative open reading frames (ORFs). Phylogenetic analysis with whole genome nucleotide sequences and amino acid sequences deduced from the conserved domain of the RNA-dependent RNA polymerase, clustered TYV with Potato leafroll virus from the genus Polerovirus with high bootstrap values. However, TYV clustered with Brassica yellow virus using amino acid sequences deduced from the conserved domain of the coat protein. Taken together with the identities between ORFs in TYV and related ORFs in species from Polerovirus, our results strongly suggested TYV is a novel species of the genus Polerovirus. Keywords Tobacco · Myzus persicae · Tobacco yellow virus · Genome · Phylogenetic characterization Abbreviations aa Amino acid nt Nucleotide RACE Rapid amplification of cDNA ends RT-PCR Reverse transcription polymerase chain reaction UTRs Untranslated regions ORFs Open reading frames pI Isoelectric point RdRP RNA-dependent RNA polymerase Rh RNA helicase Edited by Seung-Kook Choi. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-020-01782-0) contains supplementary material, which is available to authorized users. * Guangwei Ren [email protected] * Pengjun Xu [email protected] 1
Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2
Plant viruses cause serious losses to agricultural crop production throughout the world, and there have been no effective approaches to control them if the plant is infected with phytopathogenic viruses. As more than 75% of the 697 virus species recognized by the International Committee on Taxonomy of Viruses (ICTV) were transmitted by insects, vector control is frequently used for plant virus management [1, 2]. Hemipteran families are considered as the most economically important insect vectors, e.g., Aphididae (aphids) transmit 197 plant viruses [1]. Since the insect vectors transmit virus species by different mechanisms, the previous detection of definite plant viruses and the identification of novel plant viruses in crop or insect vectors are crucial to develop control measures. Recently, with the development of high-throughput RNA sequencing (RNA-seq) and metagenomics, many microorganisms (e.g., viruses) in some insect and plant species have been di
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