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Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E - Cell (2015)

Bottom Line: How and when it originated remains contentious.We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague.Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.

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Identification of Virulence Genes(A) Gene coverage heatmap of 55 virulence genes (rows) in 140 Y. pestis strains (columns). Sample ordering is based on hierarchical clustering (not shown) of the gene coverage distributions. RISE505 and RISE509 are marked with a red asterisk. Coloring goes from 0% gene coverage (white) to 100% gene coverage (blue).(B) Depth of coverage of high quality reads mapping across pMT1. Outer ring is mappability (gray), genes (RNA: black, transposon: purple, positive strand: blue, negative strand: red) and then the RISE samples ordered after direct AMS dating. Sample ordering are RISE509, RISE511, RISE00, RISE386, RISE139, RISE505 and RISE397. See also Figure S6, Tables S2, S6, and S7. AMS: Accelerator Mass Spectrometry.
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fig5: Identification of Virulence Genes(A) Gene coverage heatmap of 55 virulence genes (rows) in 140 Y. pestis strains (columns). Sample ordering is based on hierarchical clustering (not shown) of the gene coverage distributions. RISE505 and RISE509 are marked with a red asterisk. Coloring goes from 0% gene coverage (white) to 100% gene coverage (blue).(B) Depth of coverage of high quality reads mapping across pMT1. Outer ring is mappability (gray), genes (RNA: black, transposon: purple, positive strand: blue, negative strand: red) and then the RISE samples ordered after direct AMS dating. Sample ordering are RISE509, RISE511, RISE00, RISE386, RISE139, RISE505 and RISE397. See also Figure S6, Tables S2, S6, and S7. AMS: Accelerator Mass Spectrometry.

Mentions: For the high-depth ancient Y. pestis genomes, we investigated the presence of 55 genes that have been associated with the virulence of Y. pestis (Figure 5A, Table S6). We found all virulence genes to be present, except the Yersinia murine toxin (ymt) gene that is located at 74.4–76.2 kb on the pMT1 plasmid (Figure 2C, arrow 1). The ymt gene encodes a phospholipase D that protects Y. pestis inside the flea gut, thus enabling this enteric bacteria to use an arthropod as vector; it further allows for higher titers of Y. pestis and higher transmission rates (Hinnebusch, 2005, Hinnebusch et al., 2002). When investigating all seven samples for the presence of ymt, we identified a 19 kb region (59–78 kb, Figure 2C arrow 2–3, Figure 5B) to be missing except in the youngest sample (RISE397, 951 cal BC) (Figure 5B, Table S7). We find this region to be present in all other published Y. pestis strains (modern and ancient), except three strains (5761, 945, and CA88) that are lacking the pMT1 plasmid completely.


Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E - Cell (2015)

Identification of Virulence Genes(A) Gene coverage heatmap of 55 virulence genes (rows) in 140 Y. pestis strains (columns). Sample ordering is based on hierarchical clustering (not shown) of the gene coverage distributions. RISE505 and RISE509 are marked with a red asterisk. Coloring goes from 0% gene coverage (white) to 100% gene coverage (blue).(B) Depth of coverage of high quality reads mapping across pMT1. Outer ring is mappability (gray), genes (RNA: black, transposon: purple, positive strand: blue, negative strand: red) and then the RISE samples ordered after direct AMS dating. Sample ordering are RISE509, RISE511, RISE00, RISE386, RISE139, RISE505 and RISE397. See also Figure S6, Tables S2, S6, and S7. AMS: Accelerator Mass Spectrometry.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4644222&req=5

fig5: Identification of Virulence Genes(A) Gene coverage heatmap of 55 virulence genes (rows) in 140 Y. pestis strains (columns). Sample ordering is based on hierarchical clustering (not shown) of the gene coverage distributions. RISE505 and RISE509 are marked with a red asterisk. Coloring goes from 0% gene coverage (white) to 100% gene coverage (blue).(B) Depth of coverage of high quality reads mapping across pMT1. Outer ring is mappability (gray), genes (RNA: black, transposon: purple, positive strand: blue, negative strand: red) and then the RISE samples ordered after direct AMS dating. Sample ordering are RISE509, RISE511, RISE00, RISE386, RISE139, RISE505 and RISE397. See also Figure S6, Tables S2, S6, and S7. AMS: Accelerator Mass Spectrometry.
Mentions: For the high-depth ancient Y. pestis genomes, we investigated the presence of 55 genes that have been associated with the virulence of Y. pestis (Figure 5A, Table S6). We found all virulence genes to be present, except the Yersinia murine toxin (ymt) gene that is located at 74.4–76.2 kb on the pMT1 plasmid (Figure 2C, arrow 1). The ymt gene encodes a phospholipase D that protects Y. pestis inside the flea gut, thus enabling this enteric bacteria to use an arthropod as vector; it further allows for higher titers of Y. pestis and higher transmission rates (Hinnebusch, 2005, Hinnebusch et al., 2002). When investigating all seven samples for the presence of ymt, we identified a 19 kb region (59–78 kb, Figure 2C arrow 2–3, Figure 5B) to be missing except in the youngest sample (RISE397, 951 cal BC) (Figure 5B, Table S7). We find this region to be present in all other published Y. pestis strains (modern and ancient), except three strains (5761, 945, and CA88) that are lacking the pMT1 plasmid completely.

Bottom Line: How and when it originated remains contentious.We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague.Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.

Show MeSH
Related in: MedlinePlus