Abstract
The discovery and full-genome sequences of two isolates of a fourth capulavirus species are reported. The viruses were discovered during a viral metagenomics survey of uncultivated Plantago lanceolata plants in the Åland archipelago of south western Finland. The newly discovered viruses apparently produce no symptoms in P. lanceolata. They have a genome organization that is very similar to that of the three known capulavirus species and additionally share between 62.9 and 67.1% genome-wide sequence identity with the isolates of these species. It is therefore proposed that these viruses be assigned to a new capulavirus species named “Plantago lanceolata latent virus”.
References
Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55:539–552
Bernardo P, Golden M, Akram M, Naimuddin Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P (2013) Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 177:35–45
Bernardo P, Muhire B, Francois S, Deshoux M, Hartnady P, Farkas K, Kraberger S, Filloux D, Fernandez E, Galzi S, Ferdinand R, Granier M, Marais A, Monge Blasco P, Candresse T, Escriu F, Varsani A, Harkins GW, Martin DP, Roumagnac P (2016) Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Virology 493:142–153
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
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
Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9–16
Huang XQ, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877
Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage phi 29 DNA polymerase. J Virol Methods 116:209–211
Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1–7
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet 17(1):10
Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424
Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277
Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727
Roumagnac P, Granier M, Bernardo P, Deshoux M, Ferdinand R, Galzi S, Fernandez E, Julian C, Abt I, Filloux D, Mesleard F, Varsani A, Blanc S, Martin DP, Peterschmitt M (2015) Alfalfa leaf curl virus: an aphid-transmitted geminivirus. J Virol 89:9683–9688
Shepherd DN, Martin DP, Lefeuvre P, Monjane AL, Owor BE, Rybicki EP, Varsani A (2008) A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods 149:97–102
Simmonds P, Adams MJ, Benko M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AMQ, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM (2017) Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol 15(3):161–168
Varsani A, Martin DP, Navas-Castillo J, Moriones E, Hernandez-Zepeda C, Idris A, Murilo Zerbini F, Brown JK (2014) Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Arch Virol 159:1873–1882
Varsani A, Navas-Castillo J, Moriones E, Hernandez-Zepeda C, Idris A, Brown JK, Murilo Zerbini F, Martin DP (2014) Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol 159:2193–2203
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Acknowledgements
This work was supported by INRA, Département Santé des Plantes et Environnement (grant AAP SPE 2015) awarded to PR. DPM and AV are supported by the National Research Foundation of South Africa. PR is supported by EU grant FP7-PEOPLE-2013-IOF (N° PIOF-GA-2013-622571).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
This study was funded by INRA, Département Santé des Plantes et Environnement (grant AAP SPE 2015) awarded to PR.
Conflict of interest
Author DPM and AV have received research grants from the National Research Foundation of South Africa. Author PR has received an EU grant FP7-PEOPLE-2013-IOF (N° PIOF-GA-2013-622571). Author DPM, AV and PR declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
GenBank Accession #: KT214389, KT214390.
Electronic supplementary material
Below is the link to the electronic supplementary material.
705_2017_3298_MOESM2_ESM.pdf
Supplementary Figure 2: Pairwise amino acid sequence identity matrix of capulavirus replication-associated proteins. (PDF 707 kb)
Rights and permissions
About this article
Cite this article
Susi, H., Laine, AL., Filloux, D. et al. Genome sequences of a capulavirus infecting Plantago lanceolata in the Åland archipelago of Finland. Arch Virol 162, 2041–2045 (2017). https://doi.org/10.1007/s00705-017-3298-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-017-3298-0