Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species

Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes

<p>Abstract</p> <p>Background</p> <p><it>Legionella pneumophila </it>is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of <it>Legionella </it>species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely <it>L. pneumophila </it>Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis.</p> <p>Results</p> <p>We show that <it>L. pneumophila </it>Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between <it>L. pneumophila </it>strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different <it>Legionella </it>species.</p> <p>Conclusion</p> <p>Horizontal gene transfer among bacteria and from eukaryotes to <it>L. pneumophila </it>as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.</p

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

International audienceBACKGROUND: Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages. PRINCIPAL FINDINGS: We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome. CONCLUSION: LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82

Utilisation de la génomique en microbiologie et en écologie microbienne

Genomics is a modern science that has taken off thanks to the evolution of sequencing and optical mapping technologies. In just a few years, we have gone from studying a gene to studying an entire complex ecosystem. The resulting knowledge is multiple and affects a very wide range of fields of biology: microbiology, health, agronomy, ecology, paleontology, ecotoxicology, etc., ranging from fundamental to applied. The knowledge provided by genomics initially made it possible to better understand the functioning of genomes and now opens up the possibility of studying the existing relationships between organisms in an ecosystem.In this manuscript, I will present various uses of genomics to answer different scientific questions. Comparison of the highlight of structural variants in plants, the study of an anthropogenic ecosystem, the analysis of the main actors that compose it and the search for alternative solutions to conventional plastics which are responsible for emerging pollution, will be discussed.La génomique est une science moderne qui a eu son essor grâce à l’évolution des technologies de séquençage et de cartographie optique. En seulement quelques années nous sommes passés de l’étude d’un gène à celle de tout un écosystème complexe. Les connaissances qui en découlent sont multiples et touchent un très large éventail des domaines de la biologie : la microbiologie, la santé, l’agronomie, l’écologie, la paléontologie, l’écotoxicologie…., allant du fondamental à l’appliqué. Les connaissances apportées par la génomique a permis dans un premier temps de mieux comprendre le fonctionnement des génomes et ouvre désormais la possibilité d’étudier les relations existantes entre les organismes d’un écosystème.Dans ce mémoire, je vais vous présenter diverses utilisations de la génomique pour répondre à des questions scientifiques différentes. La comparaison de la mise en évidence de variants structuraux chez les plantes, l’étude d’un écosystème anthropique, l’analyse des acteurs principaux qui le composent et la recherche de solutions alternatives aux plastiques conventionnels qui sont responsables d’une pollution émergente, seront abordés

Utilisation de la génomique en microbiologie et en écologie microbienne

Genomics is a modern science that has taken off thanks to the evolution of sequencing and optical mapping technologies. In just a few years, we have gone from studying a gene to studying an entire complex ecosystem. The resulting knowledge is multiple and affects a very wide range of fields of biology: microbiology, health, agronomy, ecology, paleontology, ecotoxicology, etc., ranging from fundamental to applied. The knowledge provided by genomics initially made it possible to better understand the functioning of genomes and now opens up the possibility of studying the existing relationships between organisms in an ecosystem.In this manuscript, I will present various uses of genomics to answer different scientific questions. Comparison of the highlight of structural variants in plants, the study of an anthropogenic ecosystem, the analysis of the main actors that compose it and the search for alternative solutions to conventional plastics which are responsible for emerging pollution, will be discussed.La génomique est une science moderne qui a eu son essor grâce à l’évolution des technologies de séquençage et de cartographie optique. En seulement quelques années nous sommes passés de l’étude d’un gène à celle de tout un écosystème complexe. Les connaissances qui en découlent sont multiples et touchent un très large éventail des domaines de la biologie : la microbiologie, la santé, l’agronomie, l’écologie, la paléontologie, l’écotoxicologie…., allant du fondamental à l’appliqué. Les connaissances apportées par la génomique a permis dans un premier temps de mieux comprendre le fonctionnement des génomes et ouvre désormais la possibilité d’étudier les relations existantes entre les organismes d’un écosystème.Dans ce mémoire, je vais vous présenter diverses utilisations de la génomique pour répondre à des questions scientifiques différentes. La comparaison de la mise en évidence de variants structuraux chez les plantes, l’étude d’un écosystème anthropique, l’analyse des acteurs principaux qui le composent et la recherche de solutions alternatives aux plastiques conventionnels qui sont responsables d’une pollution émergente, seront abordés

Utilisation de la génomique en microbiologie et en écologie microbienne

Genomics is a modern science that has taken off thanks to the evolution of sequencing and optical mapping technologies. In just a few years, we have gone from studying a gene to studying an entire complex ecosystem. The resulting knowledge is multiple and affects a very wide range of fields of biology: microbiology, health, agronomy, ecology, paleontology, ecotoxicology, etc., ranging from fundamental to applied. The knowledge provided by genomics initially made it possible to better understand the functioning of genomes and now opens up the possibility of studying the existing relationships between organisms in an ecosystem.In this manuscript, I will present various uses of genomics to answer different scientific questions. Comparison of the highlight of structural variants in plants, the study of an anthropogenic ecosystem, the analysis of the main actors that compose it and the search for alternative solutions to conventional plastics which are responsible for emerging pollution, will be discussed.La génomique est une science moderne qui a eu son essor grâce à l’évolution des technologies de séquençage et de cartographie optique. En seulement quelques années nous sommes passés de l’étude d’un gène à celle de tout un écosystème complexe. Les connaissances qui en découlent sont multiples et touchent un très large éventail des domaines de la biologie : la microbiologie, la santé, l’agronomie, l’écologie, la paléontologie, l’écotoxicologie…., allant du fondamental à l’appliqué. Les connaissances apportées par la génomique a permis dans un premier temps de mieux comprendre le fonctionnement des génomes et ouvre désormais la possibilité d’étudier les relations existantes entre les organismes d’un écosystème.Dans ce mémoire, je vais vous présenter diverses utilisations de la génomique pour répondre à des questions scientifiques différentes. La comparaison de la mise en évidence de variants structuraux chez les plantes, l’étude d’un écosystème anthropique, l’analyse des acteurs principaux qui le composent et la recherche de solutions alternatives aux plastiques conventionnels qui sont responsables d’une pollution émergente, seront abordés

Optimized Methods for High Molecular Weight Genomic DNA Isolation

International audienc

Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages

Supplementary Figures S1-S3 and Tables S1-8 and have been included in this submission. All auxiliary files for phylogenetics and other analyses, unmerged FISH microscopy images, as well as the genomes of Buchnera and co-obligate endosymbionts are available online at https://doi.org/10.5281/zenodo.6394197 (Manzano-Marín, Coeur d’acier, and Jousselin, 2022). Newly sequenced and annotated genomes have been deposited in the European Nucleotide Archive (ENA).International audienceAphids are a large family of phloem-sap feeders. They typically rely on a single bacterial endosymbiont, Buchnera aphidicola, to supply them with essential nutrients lacking in their diet. This association with Buchnera was described in model aphid species from the Aphidinae subfamily and has been assumed to be representative of most aphids. However, in two lineages, Buchnera has lost some essential symbiotic functions and is now complemented by additional symbionts. Though these cases break our view of aphids harbouring a single obligate endosymbiont, we know little about the extent, nature, and evolution of these associations across aphid subfamilies. Here, using metagenomics on 25 aphid species from nine subfamilies, re-assembly and re-annotation of 20 aphid symbionts previously sequenced, and 16S rRNA amplicon sequencing on 223 aphid samples (147 species from 12 subfamilies), we show that dual symbioses have evolved anew at least six times. We also show that these secondary co-obligate symbionts have typically evolved from facultative symbiotic taxa. Genome-based metabolic inference confirms interdependencies between Buchnera and its partners for the production of essential nutrients but shows contributions vary across pairs of co-obligate associates. Fluorescent in situ hybridisation microscopy shows a common bacteriocyte localisation of two newly acquired symbionts. Lastly, patterns of Buchnera genome evolution reveal that small losses affecting a few key genes can be the onset of these dual systems, while large gene losses can occur without any co-obligate symbiont acquisition. Hence, the Buchnera-aphid association, often thought of as exclusive, seems more flexible, with a few metabolic losses having recurrently promoted the establishment of a new co-obligate symbiotic partner

EmbRS a new two-component system that inhibits biofilm formation and saves Rubrivivax gelatinosus from sinking

Photosynthetic bacteria can switch from planktonic lifestyle to phototrophic biofilm in mats in response to environmental changes. The mechanisms of phototrophic biofilm formation are, however, not characterized. Herein, we report a two-component system EmbRS that controls the biofilm formation in a photosynthetic member of the Burkholderiales order, the purple bacterium Rubrivivax gelatinosus. EmbRS inactivation results in cells that form conspicuous bacterial veils and fast-sinking aggregates in liquid. Biofilm analyses indicated that EmbRS represses the production of an extracellular matrix and biofilm formation. Mapping of transposon mutants that partially or completely restore the wild-type (WT) phenotype allowed the identification of two gene clusters involved in polysaccharide synthesis, one fully conserved only in Thauera sp., a floc-forming wastewater bacterium. A second two-component system BmfRS and a putative diguanylate cyclase BdcA were also identified in this screen suggesting their involvement in biofilm formation in this bacterium. The role of polysaccharides in sinking of microorganisms and organic matter, as well as the importance and the evolution of such regulatory system in phototrophic microorganisms are discussed