Complete genome sequence analysis of a novel coguvirus isolated from Paris polyphylla var. yunnanensis.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
Jul 2021
Jul 2021
Historique:
received:
04
02
2021
accepted:
21
03
2021
pubmed:
5
5
2021
medline:
22
6
2021
entrez:
4
5
2021
Statut:
ppublish
Résumé
A novel negative-stranded (ns) RNA virus tentatively named "Yunnan paris negative-stranded virus" (YPNSV), was isolated from Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. YPNSV has a bipartite genome that consists of a negative-stranded (ns) RNA1 encoding the viral RNA-dependent RNA polymerase (RdRp, p251), an ambisense RNA2 coding for the putative movement protein (MP, p46) and nucleocapsid protein (NP, p39), with the two open reading frames separated by a long intergenic region that is rich in A and U. Sequence comparisons showed that the RdRp, MP, and NP of YPNSV are most similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4%, and 60.9% amino acid sequence identity, respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP showed that YPNSV clustered in a clade with coguviruses and that its closest known relative is WCLaV-2. Based on the above results, YPNSV should be regarded as a new member of genus Coguvirus, family Phenuiviridae.
Identifiants
pubmed: 33944994
doi: 10.1007/s00705-021-05087-x
pii: 10.1007/s00705-021-05087-x
doi:
Substances chimiques
RNA, Viral
0
Viral Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2045-2050Subventions
Organisme : the National Natural Science Foundation of China
ID : 81860774
Références
Li B, Ruotti V, Stewart RM et al (2009) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493–500
doi: 10.1093/bioinformatics/btp692
Chase MW, Christenhusz M, Fay M et al (2016) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants:APG IV. Bot J Linn Soc 181:1–20
doi: 10.1111/boj.12385
Qin XJ, Ni W, Chen CX et al (2018) Seeing the light: shifting from wild rhizomes to extraction of active ingredients from above-ground parts of Paris polyphylla var. yunnanensis. J Ethnopharmacol 224:134–139
doi: 10.1016/j.jep.2018.05.028
Huang Y, Zhou N, Yang M et al (2019) Comparative study of the population genetics of wild and cultivated populations of Paris polyphylla var. yunnanensis based on amplified fragment length polymorphism markers. Ecol Evol 9:10707–10722
doi: 10.1002/ece3.5589
Dong JH, Ding M, Fang Q et al (2007) Molecular identification of a Potexvirus isolate infecting Parispolyphylla var. Yunnanensis and analysis of 3’terminal sequence. Acta Phytopathol Sin 37(3):237–241
Lan P, Zhao J, Zhou Y et al (2018) Complete genome sequence of Paris mosaic necrosis virus, a distinct member of the genus Potyvirus. Arch Virol 163(3):78
doi: 10.1007/s00705-017-3649-x
Chen L, Anane RF, Wang Z et al (2020) Whole-genome sequence analysis of paris virus 1: a novel member of the genus Potyvirus infecting Paris polyphylla var. yunnanensis. Arch Virol 165:985–988
doi: 10.1007/s00705-020-04560-3
Wen GS, Yang LY, Anane RF, Chen ZL et al (2019) First report of Pepper mild mottle virus in Pairs polyphylla var Yunnanensis in China. Plant Dis 103:3289
doi: 10.1094/PDIS-03-19-0445-PDN
Cao MJ, Zhang S, Li M et al (2019) Discovery of four novel viruses associated with flower yellowing disease of green Sichuan pepper (Zanthoxylum armatum) by virome analysis. Viruses 11:696
doi: 10.3390/v11080696
Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modelling, prediction and analysis. Nat Protoc 10:845–858
doi: 10.1038/nprot.2015.053
Navarro B, Minutolo M, De Stradis A et al (2018) The first phlebo-like virus infecting plants: a case study on the adaptation of negative-stranded RNA viruses to new hosts. Mol Plant Pathol 19:1075–1089
doi: 10.1111/mpp.12587
Xin M, Cao M, Liu W et al (2017) Two negative-strand RNA viruses identified in watermelon represent a novel clade in the order Bunyavirales. Front Microbiol 8:1514
doi: 10.3389/fmicb.2017.01514
van Poelwijk F, Prins M, Goldbach R (1997) Completion of the impatiens necrotic spot virus genome sequence and genetic comparison of the L proteins within the family Bunyaviridae. J Gen Virol 78:543–546
doi: 10.1099/0022-1317-78-3-543
Kormelink R, Garcia ML, Goodin M et al (2011) Negative-strand RNA viruses: the plant-infecting counterparts. Virus Res 162:184–202
doi: 10.1016/j.virusres.2011.09.028
Bruenn JA (2003) A structural and primary sequence comparison of the viral RNA dependent RNA polymerases. Nucleic Acids Res 31:1821–1829
doi: 10.1093/nar/gkg277
Elbeaino T, Digiaro M, Alabdullah A et al (2009) A multipartite single-stranded negative-sense RNA virus is the putative agent of fig mosaic disease. J Gen Virol 90:1281–1288
doi: 10.1099/vir.0.008649-0
Reguera J, Weber F, Cusack S (2010) Bunyaviridas RNA polymerases (L-Protein) have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription. PLOS Pathog 6:1–14
doi: 10.1371/journal.ppat.1001101
Navarro B, Zicca S, Minutolo M et al (2018) A negative-stranded RNA virus infecting citrus trees: the second member of a new genus within the order bunyavirales. Virology 9:1–11
Diaz-Lara A, Navarro B, Di Serio F et al (2019) Two novel negative-sense RNA viruses infecting grapevine are members of a newly proposed genus within the family Phenuiviridae. Viruses 11:685
doi: 10.3390/v11080685
Kuhn JH, Adkins S, Alioto D et al (2020) taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 165:3023–3072
doi: 10.1007/s00705-020-04731-2