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Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

Kathryn E. Holt, Yik Y. Teo, Heng Li, Satheesh Nair, Gordon Dougan, John Wain, Julian Parkhill
2009 Computer applications in the biosciences : CABIOS  
Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using highthroughput short-read sequencing.  ...  The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool.  ...  expected and estimated allele frequencies and (iv) the proportion (among the 403 SNPs with reliable frequency estimates) of loci for which estimated and expected allele frequencies differed by ≥1 strain  ... 
doi:10.1093/bioinformatics/btp344 pmid:19497932 pmcid:PMC2722999 fatcat:fcp2ylesnnfjloevbnhiimmfkq

Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus [article]

Yujun Cui, Xianwei Yang, Xavier Didelot, Chenyi Guo, Dongfang Li, Yanfeng Yan, Yiquan Zhang, Yanting Yuan, Huanming Yang, Jian Wang, Jun Wang, Yajun Song, Dongsheng Zhou, Daniel Falush (+1 others)
2014 arXiv   pre-print
We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways.  ...  However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf.  ...  Acknowledgements We thank Hin-chung Wong and Biao Kan for providing the strains of VP, and we thank  ... 
arXiv:1406.7750v2 fatcat:hqmsst4wu5hpbjp7537mi3xyga

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

Lon M. Chubiz, Ming-Chun Lee, Nigel F. Delaney, Christopher J. Marx, Jürg Bähler
2012 PLoS ONE  
Our data reveal largescale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.  ...  Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements.  ...  Acknowledgments We would like to thank Christian Daly, Jiangwen Zhang and Claire Reardon for their technical assistance in Illumina sequencing.  ... 
doi:10.1371/journal.pone.0047959 pmid:23118913 pmcid:PMC3485326 fatcat:darlikzikfflbkoa3f3tdfc43a

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

Yujun Cui, Xianwei Yang, Xavier Didelot, Chenyi Guo, Dongfang Li, Yanfeng Yan, Yiquan Zhang, Yanting Yuan, Huanming Yang, Jian Wang, Jun Wang, Yajun Song (+3 others)
2015 Molecular biology and evolution  
We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways.  ...  However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf.  ...  This work was supported by the National Key Program for Infectious Diseases of China (grant numbers 2012ZX10004215, 2013ZX10004216, and 2013ZX10004221-002) and International Science & Technology Cooperation  ... 
doi:10.1093/molbev/msv009 pmid:25605790 fatcat:cywuddqvjjfcbgref45opwh5cu

Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli

J. E. Barrick, R. E. Lenski
2009 Cold Spring Harbor Symposia on Quantitative Biology  
With 50-fold genome coverage, we were able to catch beneficial mutations as they swept to fixation, discover contending beneficial alleles that were eliminated by clonal interference, and detect other  ...  By sequencing mixed-population samples, we have identified single-nucleotide polymorphisms (SNPs) present at various points in the history of an Escherichia coli population that has evolved for almost  ...  ACKNOWLEDGMENTS We thank many individuals for maintaining and studying the long-term evolution experiment over the years; Titus Brown, Michael Desai, Jonathon Dushoff, Philip Johnson,  ... 
doi:10.1101/sqb.2009.74.018 pmid:19776167 pmcid:PMC2890043 fatcat:766sl5qe45c7vhsxrpw2xokz5y

Signatures of Natural Selection and Ecological Differentiation in Microbial Genomes [chapter]

B. Jesse Shapiro
2013 Advances in Experimental Medicine and Biology  
This chapter explores how the evolutionary forces of recombination and selection act to shape microbial genome sequences, leaving signatures that can be detected using comparative genomics and population-genetic  ...  Making sense of this vast diversity is a daunting task, but one that can be approached systematically by analyzing microbial genome sequences.  ...  In the clonal scenario, the gene's tree and the cell's tree are identical, so DNA sequence data from any (or every) gene in the genome can be used to infer, using a model of sequence evolution, the correct  ... 
doi:10.1007/978-94-007-7347-9_17 pmid:24277308 fatcat:xvwhoog4unhsfcs5w4w6lpremy

Microarray-based resequencing of multiple Bacillus anthracis isolates

Michael E Zwick, Farrell Mcafee, David J Cutler, Timothy D Read, Jacques Ravel, Gregory R Bowman, Darrell R Galloway, Alfred Mateczun
2004 Genome Biology  
Sequence quality was shown to be very high by replication (discrepancy rate of 7.4 x 10(-7)) and by comparison to independently generated shotgun sequence (discrepancy rate < 2.5 x 10(-6)).  ...  Population genomics studies of microbial pathogens using rapid resequencing technologies such as resequencing arrays are critical for recognizing newly emerging or genetically engineered strains.  ...  The authors would like to thank Peter Turnbull for aid in B. anthracis strain selection, Michael Chute for B. anthracis genomic DNA isolation and David Rasko for comments on the manuscript.  ... 
doi:10.1186/gb-2004-6-1-r10 pmid:15642093 pmcid:PMC549062 fatcat:m52g6hxd3jbwlkkoasyiz7foty

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

Sarah G. Earle, Chieh-Hsi Wu, Jane Charlesworth, Nicole Stoesser, N. Claire Gordon, Timothy M. Walker, Chris C. A. Spencer, Zamin Iqbal, David A. Clifton, Katie L. Hopkins, Neil Woodford, E. Grace Smith (+7 others)
2016 Nature Microbiology  
Charlesworth and B. Charlesworth for comments on the manuscript, X. Zhou and M. Stephens for helping adapt their software, S. Niemann for assisting with tuberculosis isolates and X.  ...  In these cases, absence of the wild-type allele was found to confer resistance, with power gained by pooling over the alternative mutant alleles.  ...  These sequences were then imputed again using ClonalFrameML and Beagle. Accuracy was summarized per site as a function of the frequency of Ns per site and the minor allele frequency.  ... 
doi:10.1038/nmicrobiol.2016.41 pmid:27572646 pmcid:PMC5049680 fatcat:ozqhy5xpu5cj5dxurg7vbiodfu

A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting

Charlotte L Nelson, Kimberly Pelak, Mihai V Podgoreanu, Sun Hee Ahn, William K Scott, Andrew S Allen, Lindsay G Cowell, Thomas H Rude, Yurong Zhang, Amy Tong, Felicia Ruffin, Batu K Sharma-Kuinkel (+1 others)
2014 BMC Infectious Diseases  
controls), testing 542,410 SNPs and adjusting for age (by decade), sex, and 6 significant principal components from our EIGENSTRAT analysis.  ...  Additionally, we evaluated the joint effect of the host and pathogen genomes in association with severity of SAB infection via logistic regression, including an interaction of host SNP with bacterial genotype  ...  The minimum RR detectable over a range of possible minor allele frequencies is shown in the Figure 1 .  ... 
doi:10.1186/1471-2334-14-83 pmid:24524581 pmcid:PMC3928605 fatcat:ga34dt2dmjgzlemaxq3kwrgmti

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

Tanya Golubchik, Elizabeth M. Batty, Ruth R. Miller, Helen Farr, Bernadette C. Young, Hanna Larner-Svensson, Rowena Fung, Heather Godwin, Kyle Knox, Antonina Votintseva, Richard G. Everitt, Teresa Street (+9 others)
2013 PLoS ONE  
Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution  ...  Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both  ...  Sarah Walker and Peter Donnelly for their advice. Author Contributions  ... 
doi:10.1371/journal.pone.0061319 pmid:23658690 pmcid:PMC3641031 fatcat:fhhkbgvnqrcq3kxcatqwrkvvsq

How clonal are bacteria over time? [article]

B. Jesse Shapiro
2016 bioRxiv   pre-print
Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static.  ...  Clonality -- defined here as the balance between vertical and horizontal inheritance -- is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool.  ...  I am grateful to Rex Malmstrom, Yan Boucher, and Salvador Almagro-  ... 
doi:10.1101/036780 fatcat:demzvh7ksbcnzcxs7j5vw2mjga

Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation

Marie Nancy Séraphin, Anders Norman, Erik Michael Rasmussen, Alexandra M. Gerace, Calin B. Chiribau, Marie-Claire Rowlinson, Troels Lillebaek, Michael Lauzardo
2019 EBioMedicine  
We used deep sequencing to track minority allele frequencies (<50·0% abundance) during transmission and standard treatment.  ...  By tracking the frequency of these heterogeneous alleles over the two-month therapy, we observed distinct signatures of drift and negative selection, but limited evidence for de novo mutations, even under  ...  Kristiansen from the Statens Serum Institut for technical assistance with DNA isolation and sequencing. We thank Dr.  ... 
doi:10.1016/j.ebiom.2019.08.010 pmid:31420303 pmcid:PMC6796532 fatcat:adr6uemo5ffrhiftm7fusy36ry

Identifying lineage effects when controlling for population structure improves power in bacterial association studies [article]

Sarah G Earle, Chieh-Hsi Wu, Jane Charlesworth, Nicole Stoesser, N Claire Gordon, Timothy M Walker, Chris C A Spencer, Zamin Iqbal, David A Clifton, Katie L Hopkins, Neil Woodford, E Grace Smith (+7 others)
2016 arXiv   pre-print
We demonstrate its ability to detect genes and genetic variants underlying resistance to 17 antimicrobials in 3144 isolates from four taxonomically diverse clonal and recombining bacteria: Mycobacterium  ...  Hence our method pinpoints locus-specific effects where possible, and boosts power by detecting lineage-level differences when fine-mapping is intractable.  ...  Acknowledgements We would like to thank Jean-Baptiste Veyrieras, Deborah Charlesworth and Brian Charlesworth for comments on the manuscript, Xiang Zhou and Matthew Stephens for helping adapt their software  ... 
arXiv:1510.06863v3 fatcat:hj2rxe2whrcxjlnnynz6jogstm

Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone ofCampylobacter jejuni

Zuowei Wu, Balamurugan Periaswamy, Orhan Sahin, Michael Yaeger, Paul Plummer, Weiwei Zhai, Zhangqi Shen, Lei Dai, Swaine L. Chen, Qijing Zhang
2016 Proceedings of the National Academy of Sciences of the United States of America  
Infections due to clonal expansion of highly virulent bacterial strains are clear and present threats to human and animal health.  ...  Here, we developed a strategy, termed "directed genome evolution," by using hybridization between abortifacient and nonabortifacient strains followed by selection in an animal disease model and whole-genome  ...  Inclusion of CA12 in the analysis would falsely increase the overall diversity of a clonally expanding population without an apparent increase in haplotype frequency.  ... 
doi:10.1073/pnas.1605869113 pmid:27601641 pmcid:PMC5035848 fatcat:3byd265dyvgkddyxo5pzlstqpu

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

Alexander Crits-Christoph, Matthew R Olm, Spencer Diamond, Keith Bouma-Gregson, Jillian F Banfield
2020 The ISME Journal  
sequence from a cell in each population.  ...  Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species.  ...  Suttle for establishing the field site's grassland plots and maintaining experimental precipitation regimes and for the aerial photograph in Fig. 1  ... 
doi:10.1038/s41396-020-0655-x pmid:32327732 pmcid:PMC7305173 fatcat:gkrhbln3izc65l3yow475psr34
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