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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

Antonie van Leeuwenhoek volume 107, pages 467–485 (2015)Cite this article

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.

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Notes

  1. The genus Steroidobacter does not branch monophyletically with the other members of the family Nevskiaceae in 16S rRNA gene based phylogenies. However, Steroidobacter is clearly distinct from the order Xanthomonadales and family Xanthomonadaceae in which it was previously placed. Its placement within the family Nevskiaceae is tentative until more detailed phylogenetic analysis can be completed for this genus.

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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.

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  1. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada

    Sohail Naushad, Mobolaji Adeolu, Misbah Sohail & Radhey S. Gupta

  2. Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada

    Shirley Wong & Herbert E. Schellhorn

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  1. Sohail Naushad
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Correspondence to Radhey S. Gupta.

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Naushad, S., Adeolu, M., Wong, S. et al. 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. Antonie van Leeuwenhoek 107, 467–485 (2015). https://doi.org/10.1007/s10482-014-0344-8

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