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A New Method to Reconstruct Recombination Events at a Genomic Scale

Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit, Chris P. Ponting
2010 PLoS Computational Biology  
We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker  ...  A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations.  ...  Finally, we thank the anonymous reviewers of PLoS Computational Biology, specially the second one for his comments and suggestions which helped to improve the present manuscript. The  ... 
doi:10.1371/journal.pcbi.1001010 pmid:21124860 pmcid:PMC2991245 fatcat:gwq5ztufnrdajneptagsqczjtu

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Xavier Didelot, Daniel J. Wilson, Andreas Prlic
2015 PLoS Computational Biology  
Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample.  ...  Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction.  ...  in the reconstructed scale.  ... 
doi:10.1371/journal.pcbi.1004041 pmid:25675341 pmcid:PMC4326465 fatcat:yqff2pqijvbkdklq236zihekry

On the Ability to Reconstruct Ancestral Genomes from Mycobacterium Genus [chapter]

Christophe Guyeux, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot, Michel Salomon
2017 Lecture Notes in Computer Science  
Since most dramatic genomic changes are caused by genome rearrangements (gene duplications, gain/loss events), it becomes crucial to understand their mechanisms and reconstruct ancestors of the given genomes  ...  Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap.  ...  And such putative correlations may be learnt by deep learning algorithms, leading to a new way to predict epidemic risks. Fig. 1 . 1 Various genome rearrangement events.  ... 
doi:10.1007/978-3-319-56148-6_57 fatcat:mck23qiwe5fhda74n4unhgpnpq

Deep phylogenetic analysis of Orthocoronavirinae genomes traces the origin, evolution and transmission route of 2019 novel coronavirus [article]

Amresh Kumar Sharma, Anup Som
2020 bioRxiv   pre-print
events led to the evolution of new 2019-nCoV strain and/or could be determinant of its pathogenicity.  ...  To achieve the aims we conducted a large-scale deep phylogenetic analysis on the 162 complete Orthocoronavirinae genomes consisting of four genera namely Alphacoronavirus, Betacoronavirus, Deltacoronavirus  ...  Thanks to Dr. Rachana Banerjee for several useful discussions. We thank Mr. Arindam Ghosh for editorial supports.  ... 
doi:10.1101/2020.05.12.091199 fatcat:tpt4iaplmjbrvku52lolnwonm4

Identification of meiotic recombination through gamete genome reconstruction using whole genome linked-reads [article]

Peng Xu, Zechen Chong
2018 bioRxiv   pre-print
However, direct identification of MR events for individuals is still challenging due to the difficulty in resolving the haplotypes of homologous chromosomes and reconstructing the gamete genome.  ...  Meiotic recombination (MR), which transmits exchanged genetic materials between homologous chromosomes to offspring, plays a crucial role in shaping genomic diversity in eukaryotic organisms.  ...  MRLR can narrow down MR breakpoint length to a more precise scale (7kb vs 24kb). 385 We also discovered new MR events that were missed in Strand-seq results 386 (Supplemental Table S6 ).  ... 
doi:10.1101/363341 fatcat:33gytj4qqbew5ebbmcv2rbeuci

Reconstructing past changes in locus-specific recombination rates

Murray P Cox, Barbara R Holland, Matthew C Wilkins, Jan Schmid
2013 BMC Genetics  
More usefully, we describe a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point.  ...  Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time.  ...  This research was supported by the Australian Research Council through a Future Fellowship (FT100100031) to BRH, and by the Royal Society of New Zealand through a Marsden Grant (MAU0603) to JS and BRH,  ... 
doi:10.1186/1471-2156-14-11 pmid:23442125 pmcid:PMC3605148 fatcat:bxg2l3kbbfd4zc7a5g5dpnrgcq

Inference of Ancestral Recombination Graphs through Topological Data Analysis

Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán, Sergei L. Kosakovsky Pond
2016 PLoS Computational Biology  
histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations.  ...  Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination.  ...  We also indicate the number of recombination events detected at each genomic interval, as well as some of the orthologous genes present at regions where recombination events are detected.  ... 
doi:10.1371/journal.pcbi.1005071 pmid:27532298 pmcid:PMC4988722 fatcat:vxeer4itzbalhbpowlk6qv5feq

Inference of recombination maps from a single pair of genomes and its application to ancient samples

Gustavo V. Barroso, Nataša Puzović, Julien Y. Dutheil, Bret Payseur
2019 PLoS Genetics  
from a single pair of unphased genomes.  ...  We exploit this possibility and reconstruct the recombination maps of ancient hominins.  ...  Here we introduce a new modeling framework (iSMC) to infer the variation in the recombination rate along the genome, using a single pair of unphased genomes.  ... 
doi:10.1371/journal.pgen.1008449 pmid:31725722 pmcid:PMC6879166 fatcat:zo3frmfrgzcyjdnvz2txj6j6nu

A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic [article]

Simon Pollett, Matthew A Conte, Mark A Sanborn, Richard G Jarman, Grace M Lidl, Kayvon Modjarrad, Irina Maljkovic Berry
2021 bioRxiv   pre-print
These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.  ...  We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event.  ...  A full acknowledgments list is submitted as Supplemental Table 5  ... 
doi:10.1101/2021.03.07.434287 fatcat:qahconpe4nhkdhmg4nugxj4lo4

A scalable analytical approach from bacterial genomes to epidemiology [article]

Xavier Didelot, Julian Parkhill
2021 bioRxiv   pre-print
Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations.  ...  Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available.  ...  Acknowledgments We acknowledge funding from the National Institute for Health Research (NIHR) Health Protection Research Unit in Genomics and Enabling Data.  ... 
doi:10.1101/2021.11.19.469232 fatcat:malwawkxzngyha7modpjtsc5ra

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations

Nicolas Radomski, Sabrina Cadel-Six, Emeline Cherchame, Arnaud Felten, Pauline Barbet, Federica Palma, Ludovic Mallet, Simon Le Hello, François-Xavier Weill, Laurent Guillier, Michel-Yves Mistou
2019 Frontiers in Microbiology  
) on six different genomic features (i.e., SNPs, SNPs excluding recombination events, genes, kmers, cgMLST alleles, and wgMLST alleles) to discriminate outbreak cases (i.e., positive control: C+) from  ...  The freely available non-parametric method written in R has been designed to be independent of both the phylogenomic reconstruction and the detection methods of genomic features (i.e., SNPs, genes, kmers  ...  This recommendation also applies to the non-parametric approach; if recombination events only appear in a C+ genome the likelihood of wrong assignment to C− would increase, and the method could fail to  ... 
doi:10.3389/fmicb.2019.02413 pmid:31708892 pmcid:PMC6821717 fatcat:ian4ikmwi5eohod5paf5vxeupa

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

Paul A. Jenkins, Yun S. Song, Rachel B. Brem, John J. Welch
2012 PLoS ONE  
The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable  ...  Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories.  ...  A recombination event was placed uniformly at random on the branches of the tree, and the new recombinant lineage was allowed to migrate and to recoalesce with the tree at the prior rate specified for  ... 
doi:10.1371/journal.pone.0046947 pmid:23226196 pmcid:PMC3511476 fatcat:n2v7vtcgbbadtbdnrni6l4ujvm

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

Simon R Harris, Ian N Clarke, Helena M B Seth-Smith, Anthony W Solomon, Lesley T Cutcliffe, Peter Marsh, Rachel J Skilton, Martin J Holland, David Mabey, Rosanna W Peeling, David A Lewis, Brian G Spratt (+12 others)
2012 Nature Genetics  
Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources.  ...  Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships  ...  S.R.H. is grateful for the opportunity to discuss this project at the Permafrost conference. This work was funded by the Wellcome Trust grant number WT076964. B.G.S. was funded by the Wellcome Trust.  ... 
doi:10.1038/ng.2214 pmid:22406642 pmcid:PMC3378690 fatcat:ldsyrbu4sndupfjvsiqri6uvbe

Current Methods for Recombination Detection in Bacteria

Anton E. Shikov, Yury V. Malovichko, Anton A. Nizhnikov, Kirill S. Antonets
2022 International Journal of Molecular Sciences  
In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination.  ...  In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.  ...  To handle the inference of ARGs on a large genomic scale, a computationally efficient alternative has been proposed.  ... 
doi:10.3390/ijms23116257 pmid:35682936 pmcid:PMC9181119 fatcat:qrp4jjmrxbavtdctlqhxoyqi74

Population genomics in natural microbial communities

Rachel J. Whitaker, Jillian F. Banfield
2006 Trends in Ecology & Evolution  
scale.  ...  Here, we discuss how population-genomic analysis of these data can be used to determine how selection and genetic exchange shape the evolution of new microbial lineages.  ...  Funding was provided by a grant from the NSF Biocomplexity Program, EAR0221768.  ... 
doi:10.1016/j.tree.2006.07.001 pmid:16859806 fatcat:jdvp5welrnhsdb74axq4yj5roq
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