Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.pdf

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the USA. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of twenty V. cholerae and four V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as four clinical V. metoecus strains were sequenced and compared to reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. V. metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin co-regulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. V. metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01264332
http://hal.upmc.fr/hal-01264332
http://hal.upmc.fr/hal-01264332/document
http://hal.upmc.fr/hal-01264332/file/Genome%20Biol%20Evol-2015-Orata-gbe_evv193.pdf
DOI : 10.1093/gbe/evv193

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.
ISSN: 1932-6203

hal-01544765
https://hal.archives-ouvertes.fr/hal-01544765
DOI : 10.1371/journal.pone.0082402

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P.chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P.chromatophora that are related to P.ovalis and found one SCG assembly to contain -cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
ISSN: 0022-3646

hal-01544797
https://hal.archives-ouvertes.fr/hal-01544797
DOI : 10.1111/jpy.12028

Éditeur(s) : HAL CCSD HUMANA PRESS INC
Résumé : International audience
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of ``type 1 coalitions'' (functionally related units with genetic exchanges, aka ``friends with genetic benefits''), ``type 2 coalitions'' (functionally related units without genetic exchanges), ``communal interactions,'' and ``emergent evolutionary properties.'' On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2

ISBN : 978-1-61779-584-8
hal-01544801
https://hal.archives-ouvertes.fr/hal-01544801
DOI : 10.1007/978-1-61779-585-5_4