Heterogeneity in codon usages of sobemovirus genes.

Journal Article (Journal Article)

When conventional phylogenetic trees were built using 14 genome sequences of 9 sobemoviruses, two main lineages were apparent: monocot-infecting viruses and dicot-infecting viruses. To investigate whether members of the genus Sobemovirus originated from monocot hosts or from dicot hosts, we constructed relationship trees based on Relative Synonymous Codon Usage (RSCU) of the viruses. The RSCU relationship trees grouped the monocot-infecting and dicot-infecting viruses even better than the genome phylogenetic trees. The RSCU approach also enabled direct comparisons among viral and host species. When host species were added into the RSCU tree, the viral species clustered with the monocot hosts, indicating codon usage homologies to monocots. The stability of the RSCU tree was improved when RSCU values were calculated for individual viral open reading frames (ORFs). Most interestingly, the codon usages of the viral ORF-2 that encodes the replicase showed affinity to that of the plants whereas codon usages of the other viral ORFs were not relevant to the host species. All ORF-2s from 3 monocot viruses and 4 out of 6 dicot viruses had greater RSCU affinities to sequences of ORFs in monocot than to dicot hosts, possibly indicating that ORF-2, and therefore the replicase module of sobemovirus has a monocot origin.

Full Text

Duke Authors

Cited Authors

  • Zhou, H; Wang, H; Huang, LF; Naylor, M; Clifford, P

Published Date

  • August 2005

Published In

Volume / Issue

  • 150 / 8

Start / End Page

  • 1591 - 1605

PubMed ID

  • 15834656

Electronic International Standard Serial Number (EISSN)

  • 1432-8798

International Standard Serial Number (ISSN)

  • 0304-8608

Digital Object Identifier (DOI)

  • 10.1007/s00705-005-0510-4


  • eng