Pan-genome of Novel &lt;em&gt;Pantoea stewartii&lt;/em&gt; subsp. &lt;em&gt;indologenes&lt;/em&gt; Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Agarwal, Gaurav; Gitaitis, R. D.; Dutta, Bhabesh

doi:10.20944/preprints202107.0400.v1

Cited by 3 publications

(1 citation statement)

References 52 publications

(68 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…P. stewartii subsp. indologenes was originally described as a pathogen of leaf spot on pearl millet (Pennisetum glaucum) and foxtail millet (Setaria italica) (Mergaert et al, 1993) but, since then, it has been found to cause disease on several additional plant species, including onion (Allium cepa) (Agarwal et al, 2021b;Koirala et al, 2021). P. stewartii subsp.…”

Section: Ecology Lifestyle and Biotechnological Usesmentioning

confidence: 99%

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

Crosby,

Rojas,

Sharma

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

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.

show abstract

Section: Ecology Lifestyle and Biotechnological Usesmentioning

confidence: 99%

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

Crosby,

Rojas,

Sharma

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

Aggarwal

Singh

Choudhary

et al. 2022

Genes

View full text Add to dashboard Cite

Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.

show abstract

Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Phyllosphere Reveals Genes Involved in Plant Growth Promotion

et al. 2023

View full text Add to dashboard Cite

The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain. Comparative genomics revealed that this strain belongs to the indologenes subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated P. stewartii subsp. indologenes strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.

show abstract

Pan-genome of Novel <em>Pantoea stewartii</em> subsp. <em>indologenes</em> Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Cited by 3 publications

References 52 publications

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

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

Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Phyllosphere Reveals Genes Involved in Plant Growth Promotion

Contact Info

Product

Resources

About