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      Yersinia Pestis in Enzootic Plague Foci in China

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          Abstract

          Plague, which is caused by Yersinia pestis ( Y. pestis), is a typical enzootic disease that is cycled among rodent reservoirs by flea vectors. Nineteen distinct plague foci have been characterized in China. Y. pestis strains from these foci exhibit considerable genetic variation because of gene acquisition, loss, and inactivation, which promote its microevolution and the expansion of various endemic plague foci. Available evidence suggests that Y. pestis microevolution likely results from complex interactions among the environment, hosts, vectors, and Y. pestis.

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          Horizontal gene transfer, genome innovation and evolution.

          To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets of prokaryotic genomes in which most homologous genes show extremely low sequence divergence, gene content can vary enormously, implying that those genes that are variably present or absent are frequently horizontally transferred. Traditionally, successful horizontal gene transfer was assumed to provide a selective advantage to either the host or the gene itself, but could horizontally transferred genes be neutral or nearly neutral? We suggest that for many prokaryotes, the boundaries between species are fuzzy, and therefore the principles of population genetics must be broadened so that they can be applied to higher taxonomic categories.
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            Genome sequence of Yersinia pestis, the causative agent of plague.

            The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.
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              Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.

              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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                Author and article information

                Contributors
                Journal
                Infectious Diseases and Translational Medicine
                Infect. Dis. Transl. Med.
                Infect. Dis. Transl. Med.
                International Biological and Medical Journals Publishing House Co., Limited (Room E16, 3/f, Yongda Commercial Building, No.97, Bonham Stand (Sheung Wan), HongKong )
                2411-2917
                20 November 2016
                20 November 2016
                : 2
                : 3
                : 100-108
                Affiliations
                From Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China
                From Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China
                From Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China
                From Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China
                Author notes
                Correspondence to: Zhizhen Qi, Email: qzz7777@ 123456163.com .

                †: These authors contributed equally to this work.

                Article
                10.11979/idtm.201603004
                ec29e3d1-2a1d-4214-9ef7-4f1f70d4aff6

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                Page count
                Figures: 3, Tables: 2, References: 65, Pages: 9
                Product
                Categories
                Review

                Medicine,Infectious disease & Microbiology
                Adaptive microevolution,Enzootic plague foci,Yersinia pestis

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