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

Show simple item record Palmer, Marike Steenkamp, Emma Theodora Coetzee, Martin Petrus Albertus Chan, Wai Yin Van Zyl, Elritha De Maayer, Pieter Coutinho, Teresa A. Blom, Jochen Smits, Theo H. M. Duffy, Brion Venter, S.N. (Stephanus Nicolaas) 2017-04-07T10:07:18Z 2017-10
dc.description.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. en_ZA
dc.description.department Genetics en_ZA
dc.description.department Microbiology and Plant Pathology en_ZA
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI)
dc.description.embargo 2018-10-31
dc.description.librarian hb2017 en_ZA
dc.description.sponsorship 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. en_ZA
dc.description.uri en_ZA
dc.identifier.citation Palmer, M., Steenkamp, E.T., Coetzee, M.P.A. et al. Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella', Antonie van Leeuwenhoek (2017) 110: 1287-1309. en_ZA
dc.identifier.issn 0003-6072 (print)
dc.identifier.issn 1572-9699 (online)
dc.identifier.other 10.1007/s10482-017-0852-4
dc.language.iso en en_ZA
dc.publisher Springer en_ZA
dc.rights © Springer International Publishing Switzerland 2017. The original publication is available at : en_ZA
dc.subject Core genome en_ZA
dc.subject Enterobacteriaceae en_ZA
dc.subject Non-phylogenetic signal en_ZA
dc.subject Phylogenetics en_ZA
dc.subject Multi-locus sequence analysis (MLSA) en_ZA
dc.subject Ribosomal MLSA (rMLSA) en_ZA
dc.title Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella en_ZA
dc.type Postprint Article en_ZA

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