The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions
Open accessAbstract
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
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Siguier, P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj014 · Cited by 2,767
Metabolism of 1-Aminocyclopropane-1-carboxylic Acid
Honma, M., & Shimomura, T. (1978) · Agricultural and Biological Chemistry · doi:10.1080/00021369.1978.10863261 · Cited by 695
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Pieterse, C. M. J., Zamioudis, C., Berendsen, R. L., Weller, D. M., Van Wees, S. C. M., & Bakker, P. A. H. M. (2014) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-082712-102340 · Cited by 3,272
Self-citationPlant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates
Oteino, N., Lally, R. D., Kiwanuka, S., Lloyd, A., Ryan, D., Germaine, K. J., & Dowling, D. N. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00745 · Cited by 787
Dimkić, I., Janakiev, T., Petrović, M., Degrassi, G., & Fira, D. (2022) · Physiological and Molecular Plant Pathology · doi:10.1016/j.pmpp.2021.101754 · Cited by 448
Biodiversity of Refrigerated Raw Milk Microbiota and Their Enzymatic Spoilage Potential
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Metadata
- Authors
- Loper, J. E., Hassan, K. A., Mavrodi, D. V., Davis, E. W., Lim, C. K., Shaffer, B. T., Elbourne, L. D. H., Stockwell, V. O., Hartney, S. L., Breakwell, K., Henkels, M. D., Tetu, S. G., Rangel, L. I., Kidarsa, T. A., Wilson, N. L., van de Mortel, J. E., Song, C., Blumhagen, R., Radune, D., Hostetler, J. B., Brinkac, L. M., Durkin, A. S., Kluepfel, D. A., Wechter, W. P., Anderson, A. J., Kim, Y. C., Pierson, L. S., Pierson, E. A., Lindow, S. E., Kobayashi, D. Y., Raaijmakers, J. M., Weller, D. M., Thomashow, L. S., Allen, A. E., & Paulsen, I. T.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-07-05
- Volume
- 8
- Issue
- 7
- Pages
- e1002784
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2055455922
- Cited by
- 642
- References
- 3
- FWCI
- 61.19
- Type
- journal article
- Language
- en
- Open access
- gold
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- The paper
- Loper, J. E., Hassan, K. A., Mavrodi, D. V., Davis, E. W., Lim, C. K., Shaffer, B. T., Elbourne, L. D. H., Stockwell, V. O., Hartney, S. L., Breakwell, K., Henkels, M. D., Tetu, S. G., Rangel, L. I., Kidarsa, T. A., Wilson, N. L., van de Mortel, J. E., Song, C., Blumhagen, R., Radune, D., . . . Paulsen, I. T. (2012). Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1002784
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
