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Virus Genes

, Volume 42, Issue 2, pp 171–177 | Cite as

Characterization of indels in poxvirus genomes

  • Danielle Coulson
  • Chris UptonEmail author
Article

Abstract

By comparing sets of variola virus (VARV) genomes and sets of vaccinia virus (VACV) genomes, it was found that the insertion and deletion of small pieces of DNA (3–25 nucleotides) were common events among these poxviruses. Insertion events were characterized by the creation of tandem direct repeats, whereas the deletion events generally took place between two direct repeats that were separated by a few nucleotides. A number of the VARV and VACV indels clearly did not fit the expected phylogenetic tree patterns. Some of these were found to be the result of coincident events, but others, in VACV, suggest recombination among the VACV genomes. Such recombination would make the construction of phylogenetic trees problematic. The growth of VACV under artificial conditions and at high multiplicities does not select against these deletions.

Keywords

Variola virus Vaccinia virus Poxvirus Genomics Indel Recombination Insertion Deletion 

Notes

Acknowledgments

This work was funded by a Canadian NSERC Discovery grant. We would like to thank all the University of Victoria Co-op students that have contributed to the Virology.ca Bioinformatics Resource.

Supplementary material

11262_2010_560_MOESM1_ESM.doc (71 kb)
Supplementary material 1 (DOC 71 kb)
11262_2010_560_MOESM2_ESM.doc (240 kb)
Supplementary material 2 (DOC 240 kb)
11262_2010_560_MOESM3_ESM.txt (3.6 mb)
Alignment of VARV genomes, generated by MAFFT, in Base-By-Base format—Supplementary material 3 (TXT 27 kb)
11262_2010_560_MOESM4_ESM.txt (6.3 mb)
Alignment of VACV genomes, generated by MAFFT, in Base-By-Base format—Supplementary material 4 (TXT 69 kb)
11262_2010_560_MOESM5_ESM.doc (70 kb)
Supplementary material 5 (DOC 69 kb)

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaCanada

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