Nine Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. Altaica Strains Isolated from the Altai Mountain Natural Plague Focus (No. 36) in Russia

Abstract

We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica strains isolated from the Altai Mountain plague focus (no. 36), which represent the 0.PE4 phylogroup circulating in populations of Mongolian pika (Ochotona pallasi).

Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete

“…SNP calling, SNP evaluation and phylogenetic analysis of Y. pestis Variance calling was performed with MultiVCFAnalyzer v0.0.87 71 using the vcf-file from the merged libraries of HGC009 together with ten published ancient LNBA plague genomes 10,11,13 as well as 22 ancient 6,7,9,93,94,95 and 226 modern Y. pestis genomes. [96][97][98][99][100][101][102][103] Y. pseudotuberculosis IP32953 was added as an outgroup. Only positions which were covered at least three times with a minimum quality score of 30 were called.…”

Ancient pathogen genomics as an emerging tool for infectious disease research

“…Early evolution: plague in prehistory. The time of divergence between Y. pestis and Y. pseudotuberculosis has been difficult to determine given the wide temporal interval produced by recent molecular dating attempts 92,130,[169][170][171][172][173][187][188][189][190][191][192][193][194][195][196][197][198][199]200 , are shown as grey circles within their geographical country or region of isolation, and the size of each circle is proportional to the number of strains sequenced from each location (number indicated when more than one genome is shown). The areas highlighted in brown are regions that contain active plague foci as determined by contemporary or historical data.…”

Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia

“…SNPs were called on the chromosomal Y. pestis mapped reads using the UnifiedGenotyper in GATK (DePristo et al, 2011). GLZ001 and GLZ002 were analyzed alongside a dataset of modern Y. pestis genomes (n = 233) (Cui et al, 2013;Eroshenko et al, 2017;Kislichkina et al, 2015Kislichkina et al, , 2018aKislichkina et al, , 2018bKutyrev et al, 2018;Morelli et al, 2010;Zhgenti et al, 2015) (as listed in (Keller et al, 2019)). In addition, we included previously published historical Y. pestis genomes with R 10-fold coverage (Bos et al, 2011(Bos et al, , 2016Feldman et al, 2016;Keller et al, 2019;Namouchi et al, 2018;Spyrou et al, 2016Spyrou et al, , 2019, and all previously published Late Neolithic and Bronze Age genomes with R 3-fold coverage (Andrades Valtueñ a et al, 2017;Rasmussen et al, 2015b;Spyrou et al, 2018) Article SNPs were called using the 'EMIT_ALL_SITES' option in GATK, which generated a call for every position in the chromosomal reference genome (CO92).…”