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Antonie van Leeuwenhoek

, Volume 107, Issue 2, pp 467–485 | Cite as

A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives

  • Sohail Naushad
  • Mobolaji Adeolu
  • Shirley Wong
  • Misbah Sohail
  • Herbert E. Schellhorn
  • Radhey S. Gupta
Original Paper

Abstract

The current taxonomy of the order Xanthomonadales is highly problematic and no comprehensive phylogenomic studies have been completed that include the most divergent members within the order. In this work, we have completed a phylogenomic analysis of a wide range of genomes, five of which were sequenced for the first time for this work, representing the vast majority of the diversity within the order Xanthomonadales. Using comparative genomic techniques, we have identified a large number of conserved signature inserts/deletions (CSIs) that are specifically found in different groups of related organisms, at different taxonomic levels, within the order. Our phylogenetic analyses do not support a monophyletic grouping of the members of the order Xanthomonadales and no CSIs were identified which are uniquely shared by all sequenced species within this order. However, our work has identified 10 CSIs which are specific to all members of the family Xanthomonadaceae and an additional 10 and 11 CSIs that are specific to one of two phylogenetically well-defined clades within the family Xanthomonadaceae. On the basis of the identified CSIs and the results of phylogenomic analyses, we propose a new taxonomic framework for the order Xanthomonadales. In this proposal, the families Algiphilaceae and Solimonadaceae (Nevskiaceae), which do not branch with the other members of the order Xanthomonadales, are transferred into the order Nevskiales ord. nov. The remaining members of the order Xanthomonadales are divided into two families: the family Xanthomonadaceae, containing the genus Xanthomonas and its closest relatives, and a new family, Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Additionally, we have also emended descriptions of the order Lysobacterales, the family Lysobacteraceae, and the family Nevskiaceae to indicate that they are earlier synonyms of the order Xanthomonadales, the family Xanthomonadaceae, and the family Solimonadaceae, respectively.

Keywords

Xanthomonadales Lysobacterales Lysobacteraceae Rhodanobacteraceae Nevskiales Nevskiaceae Salinisphaeraceae Phylogenetic trees Conserved signature indels Molecular signatures 

Notes

Acknowledgments

We thank Professor Iain Sutcliffe for valuable comments and suggestions for improvement of this manuscript. This work was supported by a research grant from the Natural Science and Engineering Research Council of Canada to RSG.

Supplementary material

10482_2014_344_MOESM1_ESM.pdf (347 kb)
Supplementary material 1 (PDF 346 kb)

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Sohail Naushad
    • 1
  • Mobolaji Adeolu
    • 1
  • Shirley Wong
    • 2
  • Misbah Sohail
    • 1
  • Herbert E. Schellhorn
    • 2
  • Radhey S. Gupta
    • 1
  1. 1.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada
  2. 2.Department of BiologyMcMaster UniversityHamiltonCanada

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