The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis
Open accessAbstract
Yersinia pestis , the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis . Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis -specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis . In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis . Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis . These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
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Cites
Massive gene decay in the leprosy bacillus.
Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honoré, N., Garnier, T., Churcher, C., Harris, D., et al. (2001) · Nature · doi:10.1038/35059006 · Cited by 1,777
Escherichia coli and Salmonella.
Neidhart, F. C. (1996) · Cited by 1,577
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
Parkhill, J., Dougan, G., James, K. D., Thomson, N. R., Pickard, D., Wain, J., Churcher, C., Mungall, K. L., Bentley, S. D., Holden, M. T. G., et al. (2001) · Nature · doi:10.1038/35101607 · Cited by 1,271
Genome sequence of Yersinia pestis, the causative agent of plague
Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T. G., Prentice, M. B., Sebaihia, M., James, K. D., Churcher, C., Mungall, K. L., et al. (2001) · Nature · doi:10.1038/35097083 · Cited by 1,243
Yersinia pestis , the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis
Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A., & Carniel, E. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.14043 · Cited by 1,126
Assembly and Function of Type III Secretory Systems
Cornelis, G. R., & Van Gijsegem, F. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.735 · Cited by 782
The glyoxylate cycle is required for fungal virulence
Lorenz, M. C., & Fink, G. R. (2001) · Nature · doi:10.1038/35083594 · Cited by 745
Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., Hauser, L., Hooper, A., Klotz, M., Norton, J., et al. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.9.2759-2773.2003 · Cited by 550
Self-citationGenome Sequence of Yersinia pestis KIM
Deng, W., Burland, V., Plunkett, G., Boutin, A., Mayhew, G. F., Liss, P., Perna, N. T., Rose, D. J., Mau, B., Zhou, S., et al. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4601-4611.2002 · Cited by 540
Self-citationHepatic pathology in relatives of patients with hæmochromatosis
Scheuer, P. J., Williams, R., & Muir, A. R. (1962) · The Journal of Pathology and Bacteriology · doi:10.1002/path.1700840107 · Cited by 431
Cited by
A draft genome of Yersinia pestis from victims of the Black Death
Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., McPhee, J. B., DeWitte, S. N., Meyer, M., Schmedes, S., et al. (2011) · Nature · doi:10.1038/nature10549 · Cited by 619
YERSINIA OUTER PROTEINS: Role in Modulation of Host Cell Signaling Responses and Pathogenesis
Viboud, G. I., & Bliska, J. B. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.030804.121320 · Cited by 600
González Barrios, A. F., Zuo, R., Hashimoto, Y., Yang, L., Bentley, W. E., & Wood, T. K. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.1.305-316.2006 · Cited by 549
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., Feldkamp, M., Kusecek, B., Vogler, A. J., Li, Y., et al. (2010) · Nature Genetics · doi:10.1038/ng.705 · Cited by 498
Self-citationYersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis
Wagner, D. M., Klunk, J., Harbeck, M., Devault, A., Waglechner, N., Sahl, J. W., Enk, J., Birdsell, D. N., Kuch, M., Lumibao, C., et al. (2014) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(13)70323-2 · Cited by 404
Metadata
- Authors
- Chain, P. S. G., Carniel, E., Larimer, F. W., Lamerdin, J., Stoutland, P. O., Regala, W. M., Georgescu, A. M., Vergez, L. M., Land, M. L., Motin, V. L., Brubaker, R. R., Fowler, J., Hinnebusch, J., Marceau, M., Medigue, C., Simonet, M., Chenal-Francisque, V., Souza, B., Dacheux, D., Elliott, J. M., Derbise, A., Hauser, L. J., & Garcia, E.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2004-09-09
- Volume
- 101
- Issue
- 38
- Pages
- 13826-13831
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2015316514
- Cited by
- 666
- References
- 34
- FWCI
- 28.29
- Type
- journal article
- Language
- en
- Open access
- green
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- Chain, P. S. G., Carniel, E., Larimer, F. W., Lamerdin, J., Stoutland, P. O., Regala, W. M., Georgescu, A. M., Vergez, L. M., Land, M. L., Motin, V. L., Brubaker, R. R., Fowler, J., Hinnebusch, J., Marceau, M., Medigue, C., Simonet, M., Chenal-Francisque, V., Souza, B., Dacheux, D., . . . Garcia, E. (2004). Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0404012101
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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.
