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

Crosby, Katherine C.; Rojas, Mariah; Sharma, Parul; Johnson, Marcela A.; Mazloom, Reza; Kvitko, Brian H.; Smits, Theo H. M.; Venter, Stephanus N.; Coutinho, Teresa A.; Heath, Lenwood S.; Palmer, Marike; Vinatzer, Boris A.

doi:10.3389/fmicb.2023.1254999

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-29150

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	Genomic delineation and description of species and within-species lineages in the genus Pantoea
Authors:	Crosby, Katherine C. Rojas, Mariah Sharma, Parul Johnson, Marcela A. Mazloom, Reza Kvitko, Brian H. Smits, Theo H. M. Venter, Stephanus N. Coutinho, Teresa A. Heath, Lenwood S. Palmer, Marike Vinatzer, Boris A.
et. al:	No
DOI:	10.3389/fmicb.2023.1254999 10.21256/zhaw-29150
Published in:	Frontiers in Microbiology
Volume(Issue):	14
Issue:	1254999
Issue Date:	2023
Publisher / Ed. Institution:	Frontiers Research Foundation
ISSN:	1664-302X
Language:	English
Subjects:	Pantoea; Taxonomy; Genomics; Reverse ecology; Core genome; Pangenome analysis
Subject (DDC):	572: Biochemistry 579: Microbiology
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 di􀀀erences, 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.
URI:	https://digitalcollection.zhaw.ch/handle/11475/29150
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Natural Resource Sciences (IUNR)
Published as part of the ZHAW project:	Genomik und Transkriptomik von Erwinia und Pantoea
Appears in collections:	Publikationen Life Sciences und Facility Management

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Crosby, K. C., Rojas, M., Sharma, P., Johnson, M. A., Mazloom, R., Kvitko, B. H., Smits, T. H. M., Venter, S. N., Coutinho, T. A., Heath, L. S., Palmer, M., & Vinatzer, B. A. (2023). Genomic delineation and description of species and within-species lineages in the genus Pantoea. Frontiers in Microbiology, 14(1254999). https://doi.org/10.3389/fmicb.2023.1254999

Crosby, K.C. et al. (2023) ‘Genomic delineation and description of species and within-species lineages in the genus Pantoea’, Frontiers in Microbiology, 14(1254999). Available at: https://doi.org/10.3389/fmicb.2023.1254999.

K. C. Crosby et al., “Genomic delineation and description of species and within-species lineages in the genus Pantoea,” Frontiers in Microbiology, vol. 14, no. 1254999, 2023, doi: 10.3389/fmicb.2023.1254999.

CROSBY, Katherine C., Mariah ROJAS, Parul SHARMA, Marcela A. JOHNSON, Reza MAZLOOM, Brian H. KVITKO, Theo H. M. SMITS, Stephanus N. VENTER, Teresa A. COUTINHO, Lenwood S. HEATH, Marike PALMER und Boris A. VINATZER, 2023. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Frontiers in Microbiology. 2023. Bd. 14, Nr. 1254999. DOI 10.3389/fmicb.2023.1254999

Crosby, Katherine C., Mariah Rojas, Parul Sharma, Marcela A. Johnson, Reza Mazloom, Brian H. Kvitko, Theo H. M. Smits, et al. 2023. “Genomic Delineation and Description of Species and Within-Species Lineages in the Genus Pantoea.” Frontiers in Microbiology 14 (1254999). https://doi.org/10.3389/fmicb.2023.1254999.

Crosby, Katherine C., et al. “Genomic Delineation and Description of Species and Within-Species Lineages in the Genus Pantoea.” Frontiers in Microbiology, vol. 14, no. 1254999, 2023, https://doi.org/10.3389/fmicb.2023.1254999.