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. 2023 Nov 9:14:1254999.
doi: 10.3389/fmicb.2023.1254999. eCollection 2023.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

Katherine C Crosby #  1 , Mariah Rojas #  1 , Parul Sharma  1   2 , Marcela A Johnson  1   2 , Reza Mazloom  3 , Brian H Kvitko  4 , Theo H M Smits  5 , Stephanus N Venter  6 , Teresa A Coutinho  6   7 , Lenwood S Heath  3 , Marike Palmer  8   9 , Boris A Vinatzer  1
Affiliations

Genomic delineation and description of species and within-species lineages in the genus Pantoea

Katherine C Crosby et al. Front Microbiol. .

Abstract

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Keywords: Pantoea; core genome; genomics; pangenome analysis; reverse ecology; taxonomy.

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Conflict of interest statement

Life Identification Number and LIN are registered trademarks of this Genomic Life Inc. LSH and BAV report in accordance with Virginia Tech policies and procedures and their ethical obligation as researchers, that they have a financial interest in this Genomic Life Inc. that may be affected by the publication of this manuscript. They have disclosed those interests fully to Virginia Tech, and they have in place an approved plan for managing any potential conflicts arising from this relationship. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
ML phylogeny of 437 representative genomes of the genus Pantoea based on the alignment of 2,509 core genes and rooted with Mixta calida DSM 22759T (outgroup not shown). Species names (or GTDB species cluster identifiers for yet-unnamed species) as well as isolation sources are provided in the legend. Species newly named under the SeqCode are indicated with “sp. nov.” following the species epithet. The nomenclatural type for the genus, P. agglomerans DSM 3493T, is indicated with an arrow. Strain names were suppressed but are included in the same tree shown in Supplementary Figure 1, which also highlights type strains or type sequences, respectively, and includes within-species lineage information. Strain isolation sources from the NCBI BioSample database and other strain metadata are provided in Supplementary Table 1, which also includes the 122 genomes omitted from the tree because of high similarity to the genomes that were included.
See this image and copyright information in PMC

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