Complete genome sequence of a novel marafivirus infecting pearl millet in Burkina Faso.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
Jan 2022
Jan 2022
Historique:
received:
15
07
2021
accepted:
21
08
2021
pubmed:
27
10
2021
medline:
18
1
2022
entrez:
26
10
2021
Statut:
ppublish
Résumé
Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food that is widely cultivated in sub-Saharan Africa. In August 2018, a survey was conducted in the main producing regions of Burkina Faso, and leaf samples were analyzed using virion-associated nucleic acid (VANA)-based metagenomic approach and Illumina sequencing. A new virus, tentatively named "Pennisetum glaucum marafivirus" (PGMV), was detected, and its complete nucleotide sequence of 6364 nucleotides was determined. The sequence contains a large open reading frame (ORF) encoding a polyprotein of 224.2 kDa with five domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), typical of marafiviruses. Additionally, a characteristic conserved marafibox domain was detected in the genome. The nucleotide sequence of the complete PGMV genome shares 68.5% identity with that of sorghum bicolor marafivirus, and its coat protein shares 58.5% identity with that of oat blue dwarf virus. Phylogenetic analysis confirmed that the pearl millet virus is unambiguously grouped with members of the genus Marafivirus in the family Tymoviridae. This is the first report on the occurrence of a marafivirus in pearl millet.
Identifiants
pubmed: 34697658
doi: 10.1007/s00705-021-05262-0
pii: 10.1007/s00705-021-05262-0
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
245-248Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
Références
Fauquet C, Thouvenel JC (1987) Maladies virales des plantes en Côte d'Ivoire = Plant viral diseases in the Ivory Coast. ORSTOM, Paris, Initiations—Documentations Techniques No 46, p 344 (ISBN 2-7099-0846-8)
Wilson JP (1999) Pearl millet diseases: a compilation of Information on the Known Pathogens of Pearl Millet Pennisetum glaucum (L.) R. Br. U.S. Department of Agriculture, Agricultural Research Service, Agriculture Handbook No 176
François S, Filloux D, Fernandez E et al (2018) Viral metagenomics approaches for high-resolution screening of multiplexed arthropod and plant viral communities. Methods Mol Biol 1746:77–95. https://doi.org/10.1007/978-1-4939-7683-6_7
doi: 10.1007/978-1-4939-7683-6_7
pubmed: 29492888
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Palanga E, Martin DP, Galzi S et al (2017) Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso. Arch Virol 162:2149–2152. https://doi.org/10.1007/s00705-017-3327-z
doi: 10.1007/s00705-017-3327-z
pubmed: 28337544
Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277. https://doi.org/10.1371/journal.pone.0108277
doi: 10.1371/journal.pone.0108277
pubmed: 25259891
pmcid: 25259891
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
doi: 10.1093/nar/gkh340
pubmed: 15034147
pmcid: 390337
Guindon S, Dufayard JF, Lefort V et al (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 59:307–321. https://doi.org/10.1093/sysbio/syq010
doi: 10.1093/sysbio/syq010
pubmed: 20525638
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
doi: 10.1093/molbev/msy096
pubmed: 29722887
pmcid: 5967553
Dreher TW, Edwards MC, Gibbs AJ, Haenni A-L, Hammond RW Jupin I, Koenig R, Sabanadzovic S, Martelli GP (2012) Family Tymoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy. Ninth Report of the International committee on Taxonomy of Viruses. Elsevier Academic Press, Oxford, pp 944–952. https://doi.org/10.1016/B978-0-12-384684-6.00136-1
Edwards MC, Weiland JJ (2014) Coat protein expression strategy of oat blue dwarf virus. Virology 450–451:290–296. https://doi.org/10.1016/j.virol.2013.12.018
doi: 10.1016/j.virol.2013.12.018
pubmed: 24503092
Maccheroni W, Alegria MC, Greggio CC et al (2005) Identification and genomic characterization of a new virus (Tymoviridae family) associated with citrus sudden death disease. J Virol 79:3028–3037. https://doi.org/10.1128/jvi.79.5.3028-3037.2005
doi: 10.1128/jvi.79.5.3028-3037.2005
pubmed: 15709023
pmcid: 548464
Hammond RW, Ramirez P (2001) Molecular characterization of the genome of Maize rayado fino virus, the type member of the genus Marafivirus. Virology 282:338–347. https://doi.org/10.1006/viro.2001.0859
doi: 10.1006/viro.2001.0859
pubmed: 11289816
Boukari W, Mollov D, Wei C et al (2021) Screening for sugarcane yellow leaf virus in sorghum in Florida revealed its occurrence in mixed infections with sugarcane mosaic virus and a new marafivirus. Crop Prot 139:105373. https://doi.org/10.1016/j.cropro.2020.105373
doi: 10.1016/j.cropro.2020.105373