title: Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data.
abstract: The genera Erwinia and Pantoea contain species that are devastating plant pathogens, non-pathogen epiphytes, and opportunistic human pathogens. However, some controversies persist in the taxonomic classification of these two closely related genera. The phylogenomic analysis of these two genera was investigated via a comprehensive analysis of 25 Erwinia genomes and 23 Pantoea genomes. Single-copy orthologs could be extracted from the Erwinia/Pantoea core-genome to reconstruct the Erwinia/Pantoea phylogeny. This tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome; strains from the same species showed ANI values ≥96% and isDDH values >70%. These data confirm that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of Erwinia/Pantoea, e.g. Pantoea agglomerans 299R was not clustered into a single group with other P. agglomerans strains, and the ANI values and isDDH values between them were <91% and around 43.8%, respectively. These data indicate P. agglomerans 299R should not be classified into the P. agglomerans species. In addition, another strain (Pantoea sp. At_9b) was identified that may represent a novel Pantoea species. We also evaluated the performance of six commonly used housekeeping genes (atpD, carA, gyrB, infB, recA, and rpoB) in phylogenetic inference. A single gene was not enough to obtain a reliable species tree, and it was necessary to use the multilocus sequence analysis of the six marker genes to recover the Erwinia/Pantoea phylogeny.
authors: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA. yuchengzhang@ufl.edu.
authors: Yucheng
authors: Y
authors: Zhang
authors: Department of Nematology and Entomology, University of Florida, Gainesville, FL, 32611, USA.
authors: Sai
authors: S
authors: Qiu
mesh_terms: D004885:Erwinia / Q000145:classification* / Q000235:genetics*; D005798:Genes, Bacterial; D020043:Genes, Essential; D059646:Genome Size; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058885:Multilocus Sequence Typing; D016366:Open Reading Frames; D020636:Pantoea / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny
keywords: ANI; Erwinia; Pantoea; Phylogenomics; Systematics; isDDH