Complete sequence and genome characterization of a new potexvirus isolated from Chaenostoma cordatum.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
Oct 2022
Oct 2022
Historique:
received:
16
03
2022
accepted:
20
05
2022
pubmed:
8
7
2022
medline:
27
8
2022
entrez:
7
7
2022
Statut:
ppublish
Résumé
Leaves from the ornamental plant Chaenostoma cordatum (Thunb.) Benth. expressing virus-like symptoms were collected for pathogen testing. A virus with features consistent with those of members of the genus Potexvirus was identified by high-throughput sequencing. The genome sequence was confirmed and completed using RT-PCR, cloning, rapid amplification of cDNA ends kits, and Sanger sequencing, revealing a complete viral genome of 6,071 nucleotides, excluding the poly-A tail. Phylogenetic analysis of the RNA-dependent RNA polymerase sequence from the viral genome indicated that its closest relative is Plantago asiatica mosaic virus. Further analysis of the nucleotide and amino acid sequences revealed that it had diverged enough from other potexviruses to be considered a member of a new species.
Identifiants
pubmed: 35796833
doi: 10.1007/s00705-022-05520-9
pii: 10.1007/s00705-022-05520-9
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2089-2092Informations de copyright
© 2022. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
Références
Kornhall P, Bremer B (2004) New circumscription of the tribe Limoselleae (Scrophulariaceae) that includes the taxa of the tribe Manuleeae. Bot J Linn Soc 146:453–467
doi: 10.1111/j.1095-8339.2004.00341.x
USDA, Floriculture crops 2019 summary. 2020, Agricultural Statistics Board, Washington D.C.
Maroon-Lango C et al (2006) Molecular and biological characterization of a novel ilarvirus in bacopa. Phytopathology 96(6):S73
Hammond J, Kim I-H, Lim H-S (2017) Alternanthera mosaic virus - an alternative “model” potexvirus of broad relevance. Agricult Sci Res 44(2):145–180
Walker PJ et al (2020) Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses. Arc Virol 165(11):2737–2748
doi: 10.1007/s00705-020-04752-x
Ryu, K.H., E.G. Song, and J.S. Hong, Potexviruses (Alphaflexiviridae), in Encyclopedia of Virology D. Bamford and M. Zuckerman, Editors. 2021, Academic Press. p. 623-630.
Miglino R et al (2011) Molecular characterization of allium virus X, a new potexvirus in the family Alphaflexiviridae, infecting ornamental allium. Arc Virol 156(11):2113–2115
doi: 10.1007/s00705-011-1109-6
Chen J et al (2005) The complete sequence of the genomic RNA of an isolate of Lily virus X (genus Potexvirus). Arc Virol 150(4):825–832
doi: 10.1007/s00705-004-0441-5
Lu S et al (2019) CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 48(D1):D265–D268
doi: 10.1093/nar/gkz991
Li YI et al (2001) The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity. J Virol 75(24):12114–12120
doi: 10.1128/JVI.75.24.12114-12120.2001
Kamer G, Argos P (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12(18):7269–7282
doi: 10.1093/nar/12.18.7269
Wong SM et al (1997) Cymbidium mosaic potexvirus RNA: complete nucleotide sequence and phylogenetic analysis. Arc Virol 142(2):383–391
doi: 10.1007/s007050050084
Fuji S et al (2005) Complete nucleotide sequence of the new potexvirus “Alstroemeria virus X. Arc Virol 150(11):2377–2385
doi: 10.1007/s00705-005-0574-1
Dolja VV et al (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184(1):79–86
doi: 10.1016/0042-6822(91)90823-T
Lozano I et al (2017) Resolution of cassava-infecting alphaflexiviruses: Molecular and biological characterization of a novel group of potexviruses lacking the TGB3 gene. Virus Res 241:53–61
doi: 10.1016/j.virusres.2017.03.019
Lezzhov AA et al (2015) Translation of the shallot virus X TGB3 gene depends on non-AUG initiation and leaky scanning. J Gen Virol 96(10):3159–3164
doi: 10.1099/jgv.0.000248
Kim KH, Hemenway C (1997) Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation. Virology 232(1):187–197
doi: 10.1006/viro.1997.8565
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 38(7):3022–3027
doi: 10.1093/molbev/msab120