Genome sequence of Yersinia pestis, the causative agent of plague

By Julian Parkhill, B. Wren, N. Thomson, R. Titball, M. Holden, M. Prentice, M. Sebaihia, K. James, C. Churcher, K. Mungall and 25 more. Nature, 2001

1,229 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/4c25639a25e7a900bc1eeff83b87470c28bc46c7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Pharmacology

Citations in the corpus

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria (2003, background): “anthracis enhancin is also found in the genome of Yersinia pestis , which survives in both mammals and insect”
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (2015, neutral): “pestis (Parkhill et al., 2001), although the murine toxin (yMT) gene itself was not covered by any reads.”
The COG database: an updated version includes eukaryotes (2003, background): “The second case in point that we consider here is a search for COGs, which are represented in the causative agent of plague, Yersinia pestis [52], but not in other Proteobacteria (the taxon to which Y.”
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica (2003, background): “Such ISE expansions have previously been seen in rarely recombining organisms whose effective population size was greatly reduced by an evolutionary bottlenec”
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences (2003, neutral): “0.132 5615 6 397 126 [96] Buchnera aphidicola (Ap) 0.133 618 640000 [97] Methanococcus jannaschii 0.14 1738 1734000 [98] Mesorhizobium loti b 0.142 6752 7036071 [99] Yersina pestis 0.142 3908 4653728 [100] Xanthomonas axonopodis 0.144 2710 5175554 [101] Haemophilus influenzae Rd 0.15 4553 4524893 [1”
Domain Architectures of σ54-Dependent Transcriptional Activators (2003, background): “However, Y. pestis CO92 encodes an additional EBP, YPO0712 (also annotated as FleQ) (46).”
The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity (2019, methodology): “Prior to mapping reads to the Y. pestis reference genome (CO92) (2001), a pseudogenome was created in which all nucleotides were masked to ensure that only nucleotides”
Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria (2005, neutral): “…et al. 2001), 15 8 (Jin et al. 2002), 16 (Wei et al. 2003), 17 (Heidelberg et al. 2002), 18 (McClelland et al. 9 2001), 19 (Deng et al. 2003), 20 (Parkhill et al. 2001a), 21 (Heidelberg et al. 2000), 22 10 (Makino et al. 2003), 23 (Kim et al. 2003), 24 (Akman et al. 2002), 25 (da Silva et al.…”
Molecular basis of bacterial resistance to chloramphenicol and florfenicol. (2004, background): “…of ﬂorfenicol resistance genes were also detected in whole genome sequences of C. tetani strain E88 [90], B. melitensis [22], Yersinia pestis [167], F. nucleatum subsp. nucleatum [168], Legionella pneumo-phila [169], Heliobacillus mobilis [170], and the photo-synthetic green-sulfur bacterium…”
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. (2005, background): “pestis CO92 (Parkhill et al., 2001), biovar Orientalis, and of strain KIM (Deng et al.”