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Antonie van Leeuwenhoek

, Volume 112, Issue 4, pp 561–588 | Cite as

A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera

  • Radhey S. GuptaEmail author
  • Jeen Son
  • Aharon Oren
Original Paper
  • 168 Downloads

Abstract

The “Spiroplasma cluster” is a taxonomically heterogeneous assemblage within the phylum Tenericutes encompassing different Entomoplasmatales species as well as the genus Mycoplasma, type genus of the order Mycoplasmatales. Within this cluster, the family Entomoplasmataceae contains two non-cohesive genera Entomoplasma and Mesoplasma with their members exhibiting extensive polyphyletic branching; additionally, the genus Mycoplasma is also embedded within this family. Genome sequences are now available for all 19 Entomoplasmataceae species with validly published names, as well as 6 of the 7 species from the genus Mycoplasma. With the aim of developing a reliable phylogenetic and taxonomic framework for the family Entomoplasmataceae, exhaustive phylogenetic and comparative genomic studies were carried out on these genome sequences. Phylogenetic trees were constructed based on concatenated sequences of 121 core proteins for this cluster, 67 conserved proteins shared with the phylum Firmicutes, 40 ribosomal proteins, three major subunits of RNA polymerase (RpoA, B and C) by different means and also for the 16S rRNA gene sequences. The interspecies relationships as well as different species groups observed in these trees were identical and robustly resolved. In all of these trees, members of the genera Mesoplasma and Entomoplasma formed three and two distinct clades, respectively, which were interspersed among the members of the other genus. The observed species groupings in the phylogenetic trees are independently strongly supported by our identification of 103 novel molecular markers or synapomorphies in the forms of conserved signature indels and conserved signature proteins, which are uniquely shared by the members of different observed species clades. To account for the different observed species clades, we are proposing a division of the genus Mesoplasma into an emended genus Mesoplasma and two new genera Tullyiplasma gen. nov. and Edwardiiplasma gen. nov. Likewise, to recognize the distinct species groupings of Entomoplasma, we are proposing its division into an emended genus Entomoplasma and a new genus Williamsoniiplasma gen. nov. Lastly, to rectify the long-existing taxonomic anomaly caused by the presence of genus Mycoplasma (order Mycoplasmatales) within the Entomoplasmatales, we are proposing an emendation of the family Mycoplasmataceae to include both Entomoplasmataceae plus Mycoplasma species and an emendation of the order Mycoplasmatales, which now comprises of the emended family Mycoplasmataceae and the family Spiroplasmataceae. The taxonomic reclassifications proposed here accurately reflect the species relationships within this group of Tenericutes and they should lead to a better understanding of their biological and pathogenic characteristics.

Keywords

Tenericutes Mollicutes Orders Mycoplasmatales and Entomoplasmatales Spiroplasma cluster Family Entomoplasmataceae Phylogeny Taxonomy Conserved signature indels and proteins Phylogenomic studies Comparative genomics Molecular signatures 

Notes

Acknowledgements

We thank Rahul Sharma, Bijendra Khadka and Joseph Manalo for their assistance in the identification and formatting of some of the described CSIs and CSPs. This work was supported by Research Grant number 249924 from the Natural Science and Engineering Research Council of Canada awarded to Radhey S. Gupta.

Authors’ contributions

RSG was responsible for planning and supervision of the entire project, obtaining funding for this project, and carrying out phylogenomic and other comparative genomic analyses leading to identification of CSIs. RSG was also responsible for the writing and finalizing of the manuscript and presented data. JS was responsible for analysis and organization of the comparative genomic data on identification of described molecular signatures, under the direction of RSG. AO was responsible for ensuring that the taxonomical proposals made here are in accordance with the rules the Prokaryotic Code and contributed in the writing of etymology and protologues for the names of various newly proposed taxa and new name combinations. He also contributed significantly towards the editing and improvement of the finalized manuscript.

Conflict of interest

All of the authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (PDF 8417 kb)

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© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada
  2. 2.Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael

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