Abstract
Two complete nucleotide sequences of an alphasatellite isolated from a cassava plant with mosaic disease symptoms in Madagascar are described and analyzed. While the helper begomovirus was identified as an isolate of East African cassava mosaic Kenya virus (EACMKV), its associated alphasatellite was most closely related (80 % nucleotide sequence identity) to cotton leaf curl Gezira alphasatellite. These satellite molecules have typical features of alphasatellites, with a single gene in the virion sense, an A-rich region and a stem-loop structure. According to the proposed species demarcation threshold of alphasatellites (83 % nucleotide identity), they are isolates of a new species for which we propose the name “Cassava mosaic alphasatellite”.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Briddon RW, Bull SE, Amin I, Mansoor S, Bedford ID, Rishi N, Siwatch SS, Zafar Y, Abdel-Salam AM, Markham PG (2004) Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus–DNA β complexes. Virology 324:462–474
Cui X, Tao X, Xie Y, Fauquet CM, Zhou X (2004) A DNAβ associated with tomato yellow leaf curl China virus is required for symptom induction. J Virology 78:13966–13974
Gorbalenya AE, Koonin EV, Wolf YI (1990) A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148
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
Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK (2011) An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol 92:706–717
Katul L, Maiss E, Morozov SY, Vetten HJ (1997) Analysis of six DNA components of the faba bean necrotic yellows virus genome and their structural affinity to related plant virus genomes. Virology 233:247–259
Koonin EV, Ilyina TV (1992) Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins. J Gen Virol 73:2763
Laufs J, Schumacher S, Geisler N, Jupin I, Gronenborn B (1995) Identification of the nicking tyrosine of geminivirus Rep protein. FEBS Lett 377:258–262
Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262
Mubin M, Briddon RW, Mansoor S (2009) Complete nucleotide sequence of Chili leaf curl virus and its associated satellites naturally infecting potato in Pakistan. Arch Virol 154:365–368
Nawaz-ul-Rehman MS, Briddon RW, Fauquet CM (2012) A melting pot of old world begomoviruses and their satellites infecting a collection of Gossypium species in Pakistan. PLoS One 7:e40050
Paprotka T, Metzler V, Jeske H (2010) The first DNA 1-like α satellites in association with New World begomoviruses in natural infections. Virology 404:148–157
Patil BL, Fauquet CM (2010) Differential interaction between cassava mosaic geminiviruses and geminivirus satellites. J Gen Virol 91:1871
Romay G, Chirinos D, Geraud-Pouey F, Desbiez C (2010) Association of an atypical alphasatellite with a bipartite New World begomovirus. Arch Virol 155:1843–1847
Saunders K, Stanley J (1999) A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses. Virology 264:142–152
Tiendrébéogo F, Lefeuvre P, Hoareau M, Villemot J, Konaté G, Traoré AS, Barro N, Traoré VS, Reynaud B, Traoré O, Lett JM (2010) Molecular diversity of Cotton leaf curl Gezira virus isolates and their satellite DNAs associated with okra leaf curl disease in Burkina Faso. Virol J 7:48
Wu PJ, Zhou XP (2005) Interaction between a nanovirus-like component and the Tobacco curly shoot virus/satellite complex. Acta Biochim Biophys Sin 37:25–31
Acknowledgements
This study was funded by the European Union (FEDER), the Région Réunion and CIRAD. MH is a recipient of a PhD fellowship for Regional Cooperation from the Conseil Régional de La Réunion. The authors wish to thank Nathalie Becker and anonymous reviewers for their comments, critical reviewing, and revising the English version of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
705_2013_1664_MOESM1_ESM.docx
Supplementary material 1 Nucleotide sequence annotation of cassava mosaic alphasatellite and the corresponding amino acid sequence of the Rep gene. The nucleotide sequences begin after the nick site (↓) within the conserved nonanucleotide sequence TAGTATT↓AC (bold font) located in the stem-loop structure (highlighted in red). The TATA box (nucleotides 1453-1460, highlighted in blue) is located at the 5’ of the stem-loop, and the polyadenylation signal (nucleotides 990-995, highlight in green) is located at the 3’ of the Rep gene (highlighted in yellow). The predicted Rep amino acid sequence contains the tyrosine residue (amino acid 90, in bold) and the NTP-binding motif GGEGKS (amino acids 188-193, highlighted in purple) (DOCX 16 kb)
705_2013_1664_MOESM2_ESM.xlsx
Supplementary material 2 Description of cassava samples from the north of Madagascar (Diana region) in which cassava mosaic alphasatellite was detected by PCR (XLSX 10 kb)
705_2013_1664_MOESM3_ESM.xlsx
Supplementary material 3 Names, acronyms and GenBank/EMBL/DDBJ accession numbers of alphasatellites used in this study (XLSX 17 kb)
Rights and permissions
About this article
Cite this article
Harimalala, M., De Bruyn, A., Hoareau, M. et al. Molecular characterization of a new alphasatellite associated with a cassava mosaic geminivirus in Madagascar. Arch Virol 158, 1829–1832 (2013). https://doi.org/10.1007/s00705-013-1664-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-013-1664-0