Abstract
In September 2017, Phellodendron amurense Rupr. plants showing yellow ringspots on leaves were observed in Liaoning, China. Flexuous filamentous particles (~1000 × 13 nm) were observed in the sap prepared from symptomatic leaves. A virus was detected in the symptomatic leaves by sequencing small RNAs and assembling the genome sequence. The complete genomic RNA was found to be 10,457 nucleotides in length excluding the poly(A) tail and to have the closest phylogenetic relationship to rose yellow mosaic virus (RoYMV), the sole member of newly established genus Roymovirus in the family Potyviridae. The coat protein gene (CP) of this virus shares 49.2% nucleotide and 55.1% amino acid sequence identity with that of RoYMV. These results suggest that this virus, which was named “phellodendron yellow ringspot-associated virus” (PYRaV) is a new member of the genus Roymovirus.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Yan ZF, Zhang BG, Zhang Z, Junlin, Yu JL (2006) Genetic diversity in wild populations of Phellodendron amurense, a rare and endangered medicinal plant, detected by AFLP. Biodivers Sci 14(6):488–497
Yang HS, Li FH, Wang CB, Qi XL, Luo ZW, Li XP, Zhang WD (2016) ISSR analysis on genetic diversity in natural populations of rare and endangered species Phellodendron amurense. J Northeast Agric Univ 47(06):26–32
Fu JJ, Yang CX, Han T, Liao YM, Li L, Li MX, Sun W, Wang S (2017) Identification and sequence analysis of Zucchini yellow mosaic virus in Liaoning. Fujian Agric For Univ (Nat Sci Ed) 46(5):488–494
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:5–9
Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6(4):471–487
Wen RH, Hajimorad MR (2010) Mutational analysis of the putative pipo of soybean mosaic virus suggests disruption of PIPO protein impedes movement. Virology 400:1–7
Marchler-Bauer A, Bo Y, Han LY, He J, Lanczycki CJ, Lu SN, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang ZX, Yamashita RA, Zhang D, Zheng CJ, Geer LY, Bryant SH (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45(Database issue):D200–D203
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577
Janssen D, Martín G, Velasco L, Gómez P, Segundo E, Ruiz L, Cuadrado IM (2005) Absence of a coding region for the helper component-proteinase in the genome of cucumber vein yellowing virus, a whitefly-transmitted member of the Potyviridae. Arch Virol 150(7):1439–1447
Valli AA, Gallo A, Rodamilans B, López-Moya JJ, García JA (2018) The HCPro from the Potyviridae family: an enviable multitasking helper component that every virus would like to have. Mol Plant Pathol 19(3):744–763
Mollov D, Lockhart B, Zlesak D (2013) Complete nucleotide sequence of rose yellow mosaic virus, a novel member of the family Potyviridae. Arch Virol 158(9):1917–1923
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2014) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol 32:268–274
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522
King AM, Adams MJ, Lefkowitz EJ (2012) Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Elsevier, Amsterdam
Acknowledgments
This work was financially supported by the Natural Science Foundation of Liaoning Province (20180550863, 2015020806), the General Project of Liaoning Provincial Department of Education (L2015362), and the Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016). We would like to express our special appreciation to Dr. Fangluan Gao and Zhenguo Du from Fujian Agriculture and Forestry University for help in the phylogenetic tree construction and useful discussion, respectively.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no competing interests.
Ethical approval
This article does not contain any experiments involving humans or animals performed by any of the authors.
Additional information
Handling Editor: Ioannis E. Tzanetakis.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Han, T., Hou, Q., Cheng, X. et al. Complete genome sequence of a novel member of the family Potyviridae isolated from Phellodendron amurense Rupr. in Liaoning, China. Arch Virol 164, 1705–1709 (2019). https://doi.org/10.1007/s00705-019-04210-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-019-04210-3