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Archives of Virology

, Volume 162, Issue 3, pp 849–855 | Cite as

Comparative analysis of common regions found in babuviruses and alphasatellite molecules

  • Daisy Stainton
  • Darren P. Martin
  • David A. Collings
  • Arvind VarsaniEmail author
Brief Report

Abstract

Viruses in the genus Babuvirus have multi-component ssDNA genomes and often associate with alphasatellite molecules containing two common motifs, a common-region stem-loop (CR-SL) involved in initiation of rolling-circle replication and a common-region major (CR-M) motif involved in secondary-strand synthesis. We compared known babuvirus genome components and alphasatellite CR-SL and CR-M sequences, defining five divergent CR-SL sequence classes. We identified iterated sequence elements in babuvirus genome components that have particularly conserved sequences and spatial arrangements between known babuviruses.

Keywords

Genome Component Faba Bean Necrotic Yellow Virus Subterranean Clover Stunt Virus Milk Vetch Dwarf Virus Coconut Foliar Decay 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was supported by the Marsden Fund Council from Government funding, administered by the Royal Society of New Zealand (Grant UOC0903 to AV).

Compliance with ethical standards

There are no conflicts of interest; the research did not involve human participants or animals. The data used for these analyses are publicly available in GenBank.

Supplementary material

705_2016_3168_MOESM1_ESM.doc (633 kb)
Sup. Table 1: Accession numbers of the sequences used in the CR-M and CR-SL datasets for the BBTV, ABTV and CBDV isolates. Except for a small number of CBDV sequences, CR-M and CR-SL were analysed from all isolates (DOC 633 kb)
705_2016_3168_MOESM2_ESM.doc (138 kb)
Sup. Table 2: Alphasatellite accession numbers for sequences used in CR-M and CR-SL analyses, and their allocated datasets (DOC 138 kb)
705_2016_3168_MOESM3_ESM.docx (14 kb)
Sup. Table 3: Percentage pairwise identities of the iteron sequences, R, F1 and F2 identified using the sequence demarcation tool SDT v 1.2 (DOCX 13 kb)
705_2016_3168_MOESM4_ESM.pdf (200 kb)
Sup. Fig. 1 Illustration of the genomes of babuviruses depicting the location of the open reading frames, the common regions (CR-SL and CR-M), the nonanucleotide motif, and the iterons (F1, F2 and R) (PDF 200 kb)
705_2016_3168_MOESM5_ESM.pdf (1.2 mb)
Sup. Fig. 2 CR-M sequences of canonical babuvirus genome components. Sequences of members of each species were aligned separately. The letter heights indicate the relative proportions of nucleotides at each site, while the letter widths reflect the number of gaps at that site across all the isolates in the alignment (narrower implying more gaps) (PDF 1269 kb)

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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  1. 1.School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
  2. 2.Department of Clinical Laboratory SciencesUniversity of Cape TownCape TownSouth Africa
  3. 3.School of Environmental and Life SciencesUniversity of NewcastleCallaghanAustralia
  4. 4.The Biodesign Center for Fundamental and Applied Microbiomics, and School of Life SciencesArizona State UniversityTempeUSA

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