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Antonie van Leeuwenhoek

, Volume 110, Issue 10, pp 1287–1309 | Cite as

Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

  • Marike Palmer
  • Emma T. Steenkamp
  • Martin P. A. Coetzee
  • Wai-Yin Chan
  • Elritha van Zyl
  • Pieter De Maayer
  • Teresa A. Coutinho
  • Jochen Blom
  • Theo H. M. Smits
  • Brion Duffy
  • Stephanus N. VenterEmail author
Original Paper

Abstract

Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.

Keywords

Phylogenetics Non-phylogenetic signal MLSA Core genome Enterobacteriaceae 

Notes

Acknowledgements

We would like to acknowledge the Centre for Bioinformatics and Computational Biology, University of Pretoria, for the use of the facility and server access. For genome sequencing, we want to acknowledge the Ion Torrent Sequencing Facility at the University of Pretoria and Markus Oggenfuss and Jürg E. Frey for sequencing at Agroscope (Wädenswil, Switzerland). We would also like to acknowledge the Genome Research Institute (GRI) as well as the Centre of Excellence in Tree Health Biotechnology (CTHB) at the University of Pretoria for additional funding. THMS and BD acknowledge the funding by the Swiss Federal Office of Agriculture ACHILLES project (BLW/FOAG Project ACHILLES) as part of the Agroscope Research Programme ProfiCrops and the Department of Life Sciences and Facility Management of ZHAW.

Supplementary material

10482_2017_852_MOESM1_ESM.pdf (3.4 mb)
(pdf 3456 kb)
10482_2017_852_MOESM2_ESM.pdf (229 kb)
(pdf 230 kb)

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Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  • Marike Palmer
    • 1
  • Emma T. Steenkamp
    • 1
  • Martin P. A. Coetzee
    • 2
  • Wai-Yin Chan
    • 1
  • Elritha van Zyl
    • 1
  • Pieter De Maayer
    • 3
  • Teresa A. Coutinho
    • 1
  • Jochen Blom
    • 4
  • Theo H. M. Smits
    • 5
  • Brion Duffy
    • 5
  • Stephanus N. Venter
    • 1
    Email author
  1. 1.Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
  2. 2.Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI),University of PretoriaPretoriaSouth Africa
  3. 3.School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
  4. 4.Computational Genomics, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
  5. 5.Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource SciencesZürich University of Applied Sciences (ZHAW)WädenswilSwitzerland

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