Phylogenomic resolution of the bacterial genus Em

Authors: Marike Palmer Emma T Steenkamp Martin P A Coetzee WaiYin Chan Elritha van Zyl Pieter De Maayer Teresa A Coutinho Jochen Blom Theo H M Smits Brion Duffy Stephanus N Venter

Publish Date: 2017/03/02

Volume: 110, Issue: 10, Pages: 1287-1309

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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 multilocus 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 1039gene 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 longbranch attraction The robust and wellsupported 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 bacteriaWe 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

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