title: Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella.
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.
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
authors.forename: Marike
authors.initials: M
authors.lastname: Palmer
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
authors.forename: Emma T
authors.initials: ET
authors.lastname: Steenkamp
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI),, University of Pretoria, Pretoria, South Africa.
authors.forename: Martin P A
authors.initials: MPA
authors.lastname: Coetzee
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
authors.forename: Wai-Yin
authors.initials: WY
authors.lastname: Chan
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
authors.forename: Elritha
authors.initials: E
authors.lastname: van Zyl
authors.affiliation: School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Pieter
authors.initials: P
authors.lastname: De Maayer
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
authors.forename: Teresa A
authors.initials: TA
authors.lastname: Coutinho
authors.affiliation: Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.
authors.forename: Theo H M
authors.initials: THM
authors.lastname: Smits
authors.affiliation: Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.
authors.forename: Brion
authors.initials: B
authors.lastname: Duffy
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. fanus.venter@up.ac.za.
authors.forename: Stephanus N
authors.initials: SN
authors.lastname: Venter
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D030541:Databases, Genetic; D004755:Enterobacteriaceae / Q000145:classification* / Q000235:genetics; D004885:Erwinia / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D020636:Pantoea / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D004269:DNA, Bacterial
keywords: Core genome; Enterobacteriaceae; MLSA; Non-phylogenetic signal; Phylogenetics