@article{torrance_burton_diop_bobay_2024, title={Evolution of homologous recombination rates across bacteria}, url={https://doi.org/10.1073/pnas.2316302121}, DOI={10.1073/pnas.2316302121}, abstractNote={Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate—as a trait—remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate—as a trait—is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.}, journal={Proceedings of the National Academy of Sciences}, author={Torrance, Ellis L. and Burton, Corey and Diop, Awa and Bobay, Louis-Marie}, year={2024}, month={Apr} }
 @article{torrance_diop_bobay_2024, title={Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes}, url={https://doi.org/10.1101/2024.05.31.596828}, DOI={10.1101/2024.05.31.596828}, abstractNote={Abstract Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores ( i.e. replicational halves of circular chromosomes) and most species have genomic hotpots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.}, author={Torrance, Ellis L. and Diop, Awa and Bobay, Louis-Marie}, year={2024}, month={Jun} }
 @article{diop_bobay_2024, title={Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy}, url={https://doi.org/10.1101/2024.05.09.593304}, DOI={10.1101/2024.05.09.593304}, abstractNote={Abstract Most bacteria engage in gene flow and that this may act as a force maintaining species cohesiveness like it does in sexual organisms. However, introgression (gene flow between the genomic backbone of distinct species) has been reported in bacteria and is associated with fuzzy species borders in some lineages, but its prevalence and impact on the delimitation of bacterial species has not been systematically characterized. Here, we quantified the patterns of introgression across 50 major bacterial lineages. Our results reveal that bacteria present various levels of introgression, with an average of 2% of introgressed core genes and up to 12% in Campylobacter . Furthermore, our results show that some species are more prone to introgression than others within the same genus and introgression is most frequent between highly related species. We found evidence that the various levels of introgression across lineages are likely related to ecological proximity between species. Introgression can occasionally lead to fuzzy species borders, although many of these cases are likely instances of ongoing speciation. Overall, our results indicate that introgression has substantially shaped the evolution and the diversification of bacteria, but this process does not substantially blur species borders.}, author={Diop, Awa and Bobay, Louis-Marie}, year={2024}, month={May} }
 @article{benlaïfaoui_richard_diop_naimi_belkaid_bernet_veyrier_elkrief_bobay_routy_et al._2023, title={Tractidigestivibacter montrealensis</i> sp. nov., a new member of human gut microbiota isolated from a healthy volunteer}, volume={370}, ISSN={1574-6968}, url={http://dx.doi.org/10.1093/femsle/fnad058}, DOI={10.1093/femsle/fnad058}, abstractNote={Abstract}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={Benlaïfaoui, Myriam and Richard, Corentin and Diop, Awa and Naimi, Sabrine and Belkaid, Wiam and Bernet, Eve and Veyrier, Frederic and Elkrief, Arielle and Bobay, Louis-Marie and Routy, Bertrand and et al.}, year={2023} }
 @article{martinez-hernandez_diop_garcia-heredia_bobay_martinez-garcia_2022, title={Correction to: Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth}, volume={16}, url={https://doi.org/10.1038/s41396-021-01182-8}, DOI={10.1038/s41396-021-01182-8}, number={4}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Martinez-Hernandez, Francisco and Diop, Awa and Garcia-Heredia, Inmaculada and Bobay, Louis-Marie and Martinez-Garcia, Manuel}, year={2022}, month={Apr}, pages={1199–1199} }
 @article{diop_torrance_stott_bobay_2022, title={Gene flow and introgression are pervasive forces shaping the evolution of bacterial species}, volume={23}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/s13059-022-02809-5}, DOI={10.1186/s13059-022-02809-5}, abstractNote={Abstract}, number={1}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Diop, Awa and Torrance, Ellis L. and Stott, Caroline M. and Bobay, Louis-Marie}, year={2022}, month={Nov} }
 @article{ligaba-osena_salehin_numan_wang_choi_jima_bobay_guo_2022, title={Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress}, volume={12}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-022-23844-z}, DOI={10.1038/s41598-022-23844-z}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Ligaba-Osena, Ayalew and Salehin, Mohammad and Numan, Muhammad and Wang, Xuegeng and Choi, Sang-Chul and Jima, Dereje and Bobay, Louis-Marie and Guo, Wanli}, year={2022}, month={Nov} }
 @article{martinez-hernandez_diop_garcia-heredia_bobay_martinez-garcia_2022, title={Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth}, volume={16}, ISSN={1751-7362 1751-7370}, url={http://dx.doi.org/10.1038/s41396-021-01150-2}, DOI={10.1038/s41396-021-01150-2}, abstractNote={Abstract}, number={4}, journal={The ISME Journal}, publisher={Oxford University Press (OUP)}, author={Martinez-Hernandez, Francisco and Diop, Awa and Garcia-Heredia, Inmaculada and Bobay, Louis-Marie and Martinez-Garcia, Manuel}, year={2022}, pages={1025–1035} }
 @article{buton_bobay_2021, title={Evolution of Chi motifs in Proteobacteria}, volume={11}, url={https://doi.org/10.1093/g3journal/jkaa054}, DOI={10.1093/g3journal/jkaa054}, abstractNote={Abstract}, number={1}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Buton, Angélique and Bobay, Louis-Marie}, editor={Zetka, MEditor}, year={2021}, month={Mar}, pages={1–7} }
 @article{harris_torrance_raymann_bobay_2020, title={CoreCruncher</i>: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets}, volume={38}, ISSN={1537-1719}, url={http://dx.doi.org/10.1093/molbev/msaa224}, DOI={10.1093/molbev/msaa224}, abstractNote={Abstract}, number={2}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Harris, Connor D and Torrance, Ellis L and Raymann, Kasie and Bobay, Louis-Marie}, editor={Ouangraoua, AidaEditor}, year={2020}, month={Sep}, pages={727–734} }
 @article{bobay_2020, title={CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination}, volume={21}, url={https://doi.org/10.1186/s12859-020-03619-x}, DOI={10.1186/s12859-020-03619-x}, abstractNote={Abstract}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Science and Business Media LLC}, author={Bobay, Louis-Marie}, year={2020}, month={Dec} }
 @article{buton_bobay_2020, title={Evolution of Chi motifs in Proteobacteria}, volume={8}, url={https://doi.org/10.1101/2020.08.13.249359}, DOI={10.1101/2020.08.13.249359}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Buton, Angélique and Bobay, Louis-Marie}, year={2020}, month={Aug} }
 @article{stott_bobay_2020, title={Impact of homologous recombination on core genome phylogenies}, url={https://doi.org/10.21203/rs.3.rs-29898/v2}, DOI={10.21203/rs.3.rs-29898/v2}, abstractNote={Abstract}, author={Stott, Caroline Marie and Bobay, Louis-Marie}, year={2020}, month={Dec} }
 @article{stott_bobay_2020, title={Impact of homologous recombination on core genome phylogenies}, url={https://doi.org/10.21203/rs.3.rs-29898/v1}, DOI={10.21203/rs.3.rs-29898/v1}, abstractNote={Abstract}, author={Stott, Caroline Marie and Bobay, Louis-Marie}, year={2020}, month={Jun} }
 @article{stott_bobay_2020, title={Impact of homologous recombination on core genome phylogenies}, volume={21}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-020-07262-x}, DOI={10.1186/s12864-020-07262-x}, abstractNote={Abstract}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Stott, Caroline M. and Bobay, Louis-Marie}, year={2020}, month={Nov} }
 @article{bobay_o’donnell_ochman_2020, title={Recombination events are concentrated in the spike protein region of Betacoronaviruses}, volume={16}, url={https://doi.org/10.1371/journal.pgen.1009272}, DOI={10.1371/journal.pgen.1009272}, abstractNote={The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.}, number={12}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Bobay, Louis-Marie and O’Donnell, Angela C. and Ochman, Howard}, editor={Tang, HuaEditor}, year={2020}, month={Dec}, pages={e1009272} }
 @article{bobay_wissel_raymann_2020, title={Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome}, volume={5}, ISSN={2379-5042}, url={http://dx.doi.org/10.1128/msphere.00694-20}, DOI={10.1128/msphere.00694-20}, abstractNote={The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.}, number={4}, journal={mSphere}, publisher={American Society for Microbiology}, author={Bobay, Louis-Marie and Wissel, Emily F. and Raymann, Kasie}, editor={Campbell, Barbara J.Editor}, year={2020}, month={Aug} }
 @misc{bobay_2020, title={The Prokaryotic Species Concept and Challenges}, ISBN={9783030382803 9783030382810}, url={http://dx.doi.org/10.1007/978-3-030-38281-0_2}, DOI={10.1007/978-3-030-38281-0_2}, abstractNote={Abstract}, journal={The Pangenome}, publisher={Springer International Publishing}, author={Bobay, Louis-Marie}, year={2020}, pages={21–49} }
 @article{bobay_raymann_2019, title={Population Genetics of Host-Associated Microbiomes}, volume={5}, ISSN={2198-6428}, url={http://dx.doi.org/10.1007/s40610-019-00122-y}, DOI={10.1007/s40610-019-00122-y}, number={3}, journal={Current Molecular Biology Reports}, publisher={Springer Science and Business Media LLC}, author={Bobay, Louis-Marie and Raymann, Kasie}, year={2019}, month={Jul}, pages={128–139} }
 @article{bobay_ochman_2018, title={Biological species in the viral world}, volume={115}, url={https://doi.org/10.1073/pnas.1717593115}, DOI={10.1073/pnas.1717593115}, abstractNote={Significance}, number={23}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Bobay, Louis-Marie and Ochman, Howard}, year={2018}, month={Jun}, pages={6040–6045} }
 @article{bobay_ellis_ochman_2018, title={ConSpeciFix</i>: classifying prokaryotic species based on gene flow}, volume={34}, ISSN={1367-4803 1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/bty400}, DOI={10.1093/bioinformatics/bty400}, abstractNote={Abstract}, number={21}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Bobay, Louis-Marie and Ellis, Brian Shin-Hua and Ochman, Howard}, editor={Hancock, JohnEditor}, year={2018}, month={May}, pages={3738–3740} }
 @article{bobay_ochman_2018, title={Factors driving effective population size and pan-genome evolution in bacteria}, volume={18}, url={https://doi.org/10.1186/s12862-018-1272-4}, DOI={10.1186/s12862-018-1272-4}, abstractNote={Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species. However, attempts at estimating effective population sizes (Ne) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries.In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne; and that contrary to theoretical expectations, Ne was unaffected by recombination rate. Additionally, we found that Ne shapes the evolution and diversity of total gene repertoires of prokaryotic species.Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution.}, number={1}, journal={BMC Evolutionary Biology}, publisher={Springer Science and Business Media LLC}, author={Bobay, Louis-Marie and Ochman, Howard}, year={2018}, month={Dec} }
 @article{bobay_2018, title={Heredity: A Very Short Introduction}, volume={9}, url={https://doi.org/10.1093/jmammal/gyy106}, DOI={10.1093/jmammal/gyy106}, journal={Journal of Mammalogy}, publisher={Oxford University Press (OUP)}, author={Bobay, Louis-Marie}, year={2018}, month={Oct} }
 @article{raymann_bobay_moran_2017, title={Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome}, volume={27}, ISSN={0962-1083 1365-294X}, url={http://dx.doi.org/10.1111/mec.14434}, DOI={10.1111/mec.14434}, abstractNote={Abstract}, number={8}, journal={Molecular Ecology}, publisher={Wiley}, author={Raymann, Kasie and Bobay, Louis‐Marie and Moran, Nancy A.}, year={2017}, month={Dec}, pages={2057–2066} }
 @article{bobay_ochman_2017, title={Biological Species Are Universal across Life’s Domains}, volume={9}, ISSN={1759-6653}, url={http://dx.doi.org/10.1093/gbe/evx026}, DOI={10.1093/gbe/evx026}, abstractNote={Delineation of species is fundamental to organizing and understanding biological diversity. The most widely applied criterion for distinguishing species is the Biological Species Concept (BSC), which defines species as groups of interbreeding individuals that remain reproductively isolated from other such groups. The BSC has broad appeal; however, many organisms, most notably asexual lineages, cannot be classified according to the BSC. Despite their exclusively asexual mode of reproduction, Bacteria and Archaea can transfer and exchange genes though homologous recombination. Here we show that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes. By analyzing the impact of recombination on the polymorphisms in thousands of genome sequences, we find that over half of named bacterial species undergo continuous recombination among sequenced constituents, indicative of true biological species. However, nearly a quarter of named bacterial species show sharp discontinuities and comprise multiple biological species. These interruptions of gene flow are not a simple function of genome identity, indicating that bacterial speciation does not uniformly proceed by the gradual divergence of genome sequences. The same genomic approach based on recombinant polymorphisms retrieves known species boundaries in sexually reproducing eukaryotes. Thus, a single biological species definition based on gene flow, once thought to be limited only to sexually reproducing organisms, is applicable to all cellular lifeforms.}, number={3}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Bobay, Louis-Marie and Ochman, Howard}, year={2017}, month={Mar}, pages={491–501} }
 @article{bobay_ochman_2017, title={Impact of Recombination on the Base Composition of Bacteria and Archaea}, volume={34}, ISSN={0737-4038 1537-1719}, url={http://dx.doi.org/10.1093/molbev/msx189}, DOI={10.1093/molbev/msx189}, abstractNote={The mutational process in bacteria is biased toward A and T, and most species are GC-rich relative to the mutational input to their genome. It has been proposed that the shift in base composition is an adaptive process-that natural selection operates to increase GC-contents-and there is experimental evidence that bacterial strains with GC-rich versions of genes have higher growth rates than those strains with AT-rich versions expressing identical proteins. Alternatively, a nonadaptive process, GC-biased gene conversion (gBGC), could also increase the GC-content of DNA due to the mechanistic bias of gene conversion events during recombination. To determine what role recombination plays in the base composition of bacterial genomes, we compared the spectrum of nucleotide polymorphisms introduced by recombination in all microbial species represented by large numbers of sequenced strains. We found that recombinant alleles are consistently biased toward A and T, and that the magnitude of AT-bias introduced by recombination is similar to that of mutations. These results indicate that recombination alone, without the intervention of selection, is unlikely to counteract the AT-enrichment of bacterial genomes.}, number={10}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Bobay, Louis-Marie and Ochman, Howard}, year={2017}, month={Jul}, pages={2627–2636} }
 @article{bobay_ochman_2017, title={The Evolution of Bacterial Genome Architecture}, volume={8}, ISSN={1664-8021}, url={http://dx.doi.org/10.3389/fgene.2017.00072}, DOI={10.3389/fgene.2017.00072}, abstractNote={The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes. These properties create the situation in which eukaryotes with very similar numbers of genes can have vastly different genome sizes, while in bacteria, gene number scales linearly with genome size. Some bacterial genomes, however, particularly those of species that undergo bottlenecks due to recent association with hosts, accumulate pseudogenes and mobile elements, conferring them a low gene content relative to their genome size. These non-functional sequences are gradually eroded and eliminated after long-term association with hosts, with the result that obligate symbionts have the smallest genomes of any cellular organism. The architecture of bacterial genomes is shaped by complex and diverse processes, but for most bacterial species, genome size is governed by a non-adaptive process, i.e., genetic drift coupled with a mutational bias towards deletions. Thus, bacteria with small effective population sizes typically have the smallest genomes. Some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.}, journal={Frontiers in Genetics}, publisher={Frontiers Media SA}, author={Bobay, Louis-Marie and Ochman, Howard}, year={2017}, month={May} }
 @article{wexler_bao_whitney_bobay_xavier_schofield_barry_russell_tran_goo_et al._2016, title={Human symbionts inject and neutralize antibacterial toxins to persist in the gut}, volume={113}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1525637113}, DOI={10.1073/pnas.1525637113}, abstractNote={Significance}, number={13}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wexler, Aaron G. and Bao, Yiqiao and Whitney, John C. and Bobay, Louis-Marie and Xavier, Joao B. and Schofield, Whitman B. and Barry, Natasha A. and Russell, Alistair B. and Tran, Bao Q. and Goo, Young Ah and et al.}, year={2016}, month={Mar}, pages={3639–3644} }
 @article{douam_bobay_maurin_fresquet_calland_maisse_durand_cosset_féray_lavillette_2016, title={Specialization of Hepatitis C Virus Envelope Glycoproteins for B Lymphocytes in Chronically Infected Patients}, volume={90}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.02516-15}, DOI={10.1128/jvi.02516-15}, abstractNote={ABSTRACT}, number={2}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Douam, Florian and Bobay, Louis-Marie and Maurin, Guillemette and Fresquet, Judith and Calland, Noémie and Maisse, Carine and Durand, Tony and Cosset, François-Loïc and Féray, Cyrille and Lavillette, Dimitri}, editor={Diamond, M. S.Editor}, year={2016}, month={Jan}, pages={992–1008} }
 @article{bobay_traverse_ochman_2015, title={Impermanence of bacterial clones}, volume={112}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1501724112}, DOI={10.1073/pnas.1501724112}, abstractNote={
            Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in
            Escherichia coli
            for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the
            E. coli
            genome.
          }, number={29}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Bobay, Louis-Marie and Traverse, Charles C. and Ochman, Howard}, year={2015}, month={Jul}, pages={8893–8900} }
 @article{henry_bobay_chevallereau_saussereau_ceyssens_debarbieux_2015, title={The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae}, volume={10}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0117163}, DOI={10.1371/journal.pone.0117163}, abstractNote={In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.}, number={1}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Henry, Marine and Bobay, Louis-Marie and Chevallereau, Anne and Saussereau, Emilie and Ceyssens, Pieter-Jan and Debarbieux, Laurent}, editor={Dąbrowska, KrystynaEditor}, year={2015}, month={Jan}, pages={e0117163} }
 @article{bobay_touchon_rocha_2014, title={Pervasive domestication of defective prophages by bacteria}, volume={111}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1405336111}, DOI={10.1073/pnas.1405336111}, abstractNote={Significance}, number={33}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Bobay, Louis-Marie and Touchon, Marie and Rocha, Eduardo P. C.}, year={2014}, month={Aug}, pages={12127–12132} }
 @article{touchon_bobay_rocha_2014, title={The chromosomal accommodation and domestication of mobile genetic elements}, volume={22}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2014.09.010}, DOI={10.1016/j.mib.2014.09.010}, abstractNote={Prokaryotes are constantly being infected by large mobile genetic elements (MGEs) such as conjugative elements and temperate phages. The fitness of these elements is tightly linked with the evolutionary success of the host. This leads to selection against disruptive effects their integration might have on the organization and structure of the chromosome. Seamless genetic accommodation of the mobile elements also involves silencing infectious mechanisms and expressing functions adaptive to the host. Ironically, these characteristics favor the host ability to domesticate the mobile element. Recent data suggest that the domestication of mobile elements might be frequent. Importantly, it might affect the evolution of chromosome organization and drive the diversification of social traits.}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Touchon, Marie and Bobay, Louis-Marie and Rocha, Eduardo PC}, year={2014}, month={Dec}, pages={22–29} }
 @article{raymann_bobay_doak_lynch_gribaldo_2013, title={A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria}, volume={3}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.112.005231}, DOI={10.1534/g3.112.005231}, abstractNote={Abstract}, number={3}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Raymann, Kasie and Bobay, Louis-Marie and Doak, Thomas G and Lynch, Michael and Gribaldo, Simonetta}, year={2013}, month={Mar}, pages={505–516} }
 @article{bobay_touchon_rocha_2013, title={Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability}, volume={9}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1003825}, DOI={10.1371/journal.pgen.1003825}, abstractNote={Phages, like many parasites, tend to have small genomes and may encode autonomous functions or manipulate those of their hosts'. Recombination functions are essential for phage replication and diversification. They are also nearly ubiquitous in bacteria. The E. coli genome encodes many copies of an octamer (Chi) motif that upon recognition by RecBCD favors repair of double strand breaks by homologous recombination. This might allow self from non-self discrimination because RecBCD degrades DNA lacking Chi. Bacteriophage Lambda, an E. coli parasite, lacks Chi motifs, but escapes degradation by inhibiting RecBCD and encoding its own autonomous recombination machinery. We found that only half of 275 lambdoid genomes encode recombinases, the remaining relying on the host's machinery. Unexpectedly, we found that some lambdoid phages contain extremely high numbers of Chi motifs concentrated between the phage origin of replication and the packaging site. This suggests a tight association between replication, packaging and RecBCD-mediated recombination in these phages. Indeed, phages lacking recombinases strongly over-represent Chi motifs. Conversely, phages encoding recombinases and inhibiting host recombination machinery select for the absence of Chi motifs. Host and phage recombinases use different mechanisms and the latter are more tolerant to sequence divergence. Accordingly, we show that phages encoding their own recombination machinery have more mosaic genomes resulting from recent recombination events and have more diverse gene repertoires, i.e. larger pan genomes. We discuss the costs and benefits of superseding or manipulating host recombination functions and how this decision shapes phage genome structure and evolvability.}, number={9}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Bobay, Louis-Marie and Touchon, Marie and Rocha, Eduardo P. C.}, editor={Casadesús, JosepEditor}, year={2013}, month={Sep}, pages={e1003825} }
 @article{deghorain_bobay_smeesters_bousbata_vermeersch_perez-morga_drèze_rocha_touchon_van melderen_2012, title={Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages}, volume={194}, ISSN={0021-9193 1098-5530}, url={http://dx.doi.org/10.1128/jb.01085-12}, DOI={10.1128/jb.01085-12}, abstractNote={ABSTRACT}, number={21}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Deghorain, Marie and Bobay, Louis-Marie and Smeesters, Pierre R. and Bousbata, Sabrina and Vermeersch, Marjorie and Perez-Morga, David and Drèze, Pierre-Alexandre and Rocha, Eduardo P. C. and Touchon, Marie and Van Melderen, Laurence}, year={2012}, month={Nov}, pages={5829–5839} }
 @article{bobay_rocha_touchon_2012, title={The Adaptation of Temperate Bacteriophages to Their Host Genomes}, volume={30}, ISSN={1537-1719 0737-4038}, url={http://dx.doi.org/10.1093/molbev/mss279}, DOI={10.1093/molbev/mss279}, abstractNote={Rapid turnover of mobile elements drives the plasticity of bacterial genomes. Integrated bacteriophages (prophages) encode host-adaptive traits and represent a sizable fraction of bacterial chromosomes. We hypothesized that natural selection shapes prophage integration patterns relative to the host genome organization. We tested this idea by detecting and studying 500 prophages of 69 strains of Escherichia and Salmonella. Phage integrases often target not only conserved genes but also intergenic positions, suggesting purifying selection for integration sites. Furthermore, most integration hotspots are conserved between the two host genera. Integration sites seem also selected at the large chromosomal scale, as they are nonrandomly organized in terms of the origin-terminus axis and the macrodomain structure. The genes of lambdoid prophages are systematically co-oriented with the bacterial replication fork and display the host high frequency of polarized FtsK-orienting polar sequences motifs required for chromosome segregation. matS motifs are strongly avoided by prophages suggesting counter selection of motifs disrupting macrodomains. These results show how natural selection for seamless integration of prophages in the chromosome shapes the evolution of the bacterium and the phage. First, integration sites are highly conserved for many millions of years favoring lysogeny over the lytic cycle for temperate phages. Second, the global distribution of prophages is intimately associated with the chromosome structure and the patterns of gene expression. Third, the phage endures selection for DNA motifs that pertain exclusively to the biology of the prophage in the bacterial chromosome. Understanding prophage genetic adaptation sheds new lights on the coexistence of horizontal transfer and organized bacterial genomes.}, number={4}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Bobay, Louis-Marie and Rocha, Eduardo P.C. and Touchon, Marie}, year={2012}, month={Dec}, pages={737–751} }
 @article{lynch_bobay_catania_gout_rho_2011, title={The Repatterning of Eukaryotic Genomes by Random Genetic Drift}, volume={12}, ISSN={1527-8204 1545-293X}, url={http://dx.doi.org/10.1146/annurev-genom-082410-101412}, DOI={10.1146/annurev-genom-082410-101412}, abstractNote={ Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces. }, number={1}, journal={Annual Review of Genomics and Human Genetics}, publisher={Annual Reviews}, author={Lynch, Michael and Bobay, Louis-Marie and Catania, Francesco and Gout, Jean-François and Rho, Mina}, year={2011}, month={Sep}, pages={347–366} }
 @book{douam_bobay_martin_2010, place={Paris}, title={L'évolution c'est tout simple!}, ISBN={9782311002201}, publisher={Vuibert}, author={Douam, Florian and Bobay, Louis-Marie and Martin, Olivier}, year={2010} }