Vibrio cholerae genomic diversity within and between patients

Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed ‘waves’ of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

Additional file 15. Summary of whole genome sequencing statistics

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.Some computations were performed on Tirant III of the Spanish Supercomputing Network (“Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin–Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation program Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. D.P. is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. Q.K.L. was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB−1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. C.R.L. holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by an NSERC Discovery Grant.Peer reviewe

Reproduction system, dispersal and reproductive success in a threatened vegetal species : example of Biscutella neustriaca, (Brassicaceae), a self-incompatible and micro-endemic species

Chez les espèces sexuées, les systèmes de reproduction et la dispersion peuvent jouer un rôle important dans la viabilité des petites populations en ayant un impact direct sur les succès reproducteurs des individus. Chez les plantes, la reproduction et la dispersion sont principalement des processus passifs et dépendent donc de la densité locale en partenaires, de l’isolement entre populations et des relations génétiques entre individus. Chez Biscutella neustriaca, une espèce végétale micro-endémique de la vallée de la Seine, nous mettons en évidence une forte isolation génétique entre populations, corroborée par la fragmentation de l’habitat et les faibles capacités de dispersion de l’espèce. Nous déterminons également, par des approches moléculaires et phénotypiques, que B. neustriaca est strictement auto- incompatible. Dans un tel contexte d’isolement et de structuration spatiale de la diversité génétique, nous nous demandons dans quelles mesures la dispersion et l’auto-incompatibilité ont un impact sur les succès reproducteurs des individus. Par une approche expérimentale ex situ, nous mettons en évidence les effets de la limitation pollinique et une diminution de la disponibilité en partenaires compatibles sur la diminution du succès reproducteur maternel. Dans quatre populations naturelles, nous identifions le potentiel reproducteur individuel et la densité locale en partenaires disponibles comme les principaux facteurs expliquant la variabilité des succès reproducteurs mâle et femelle. Des facteurs génétiques tels que la consanguinité et l’auto-incompatibilité semblent également influencer les succès reproducteurs dans certaines populations. Nous discutons de l’importance de prendre en compte un grand nombre de facteurs lors d’actions de conservation menées dans une population, de la nécessité de connaître le système de reproduction et les capacités de dispersion de l’espèce, indissociables d’un suivi des populations ciblées, où les effets de ces facteurs ne seront détectables qu’à certaines échelles spatiales et temporelles. Nous illustrons nos travaux par une action de renforcement dans l’une des populations étudiées.In sexual species, reproduction systems and dispersal could involve in viability of small populations by having directly an impact on individuals’ reproductive success. In plants, reproduction and dispersal are mainly passive processes and thus depend of local density in mates, isolation between populations and genetic relationships among individuals. In Biscutella neustriaca, a micro-endemic plant of the Seine river valley, we highlight a strong genetic isolation between populations corroborated by habitat fragmentation and low dispersal abilities of the species. By using phenotypic and molecular approaches, we determine that B. neustriaca is strictly self-incompatible. In this context of isolation and spatially structured genetic diversity, we wonder to what extent dispersal and self-incompatibility impact individuals’ reproductive successes. Through an ex situ experiment, we highlight both effects of pollen limitation and decrease in local density of compatible mates on maternal reproductive success decrease. In four natural populations, we identify individual reproductive potential and local density of available mates as main factors explaining male and female reproductive successes variability. Genetic factors as inbreeding depression and self-incompatibility also seem to evolve in reproductive successes in some populations. We discuss about importance of considering many factors when acting for conservation in a threatened population, the need to know the reproductive system and dispersal abilities of the species, inseparable from a monitoring of targeted populations, where effects of these factors are only detectable at certain temporal and spatial scales. We illustrate our works by a concrete conservation action in one of the studied populations

Système de reproduction, dispersion et succès reproducteurs chez une espèce végétale menacée (exemple de Biscutella neustriaca (Brassicaceae), une espèce auto-incompatible et micro-endémique)

Chez les espèces sexuées, les systèmes de reproduction et la dispersion peuvent jouer un rôle important dans la viabilité des petites populations en ayant un impact direct sur les succès reproducteurs des individus. Chez les plantes, la reproduction et la dispersion sont principalement des processus passifs et dépendent donc de la densité locale en partenaires, de l isolement entre populations et des relations génétiques entre individus. Chez Biscutella neustriaca, une espèce végétale micro-endémique de la vallée de la Seine, nous mettons en évidence une forte isolation génétique entre populations, corroborée par la fragmentation de l habitat et les faibles capacités de dispersion de l espèce. Nous déterminons également, par des approches moléculaires et phénotypiques, que B. neustriaca est strictement auto- incompatible. Dans un tel contexte d isolement et de structuration spatiale de la diversité génétique, nous nous demandons dans quelles mesures la dispersion et l auto-incompatibilité ont un impact sur les succès reproducteurs des individus. Par une approche expérimentale ex situ, nous mettons en évidence les effets de la limitation pollinique et une diminution de la disponibilité en partenaires compatibles sur la diminution du succès reproducteur maternel. Dans quatre populations naturelles, nous identifions le potentiel reproducteur individuel et la densité locale en partenaires disponibles comme les principaux facteurs expliquant la variabilité des succès reproducteurs mâle et femelle. Des facteurs génétiques tels que la consanguinité et l auto-incompatibilité semblent également influencer les succès reproducteurs dans certaines populations. Nous discutons de l importance de prendre en compte un grand nombre de facteurs lors d actions de conservation menées dans une population, de la nécessité de connaître le système de reproduction et les capacités de dispersion de l espèce, indissociables d un suivi des populations ciblées, où les effets de ces facteurs ne seront détectables qu à certaines échelles spatiales et temporelles. Nous illustrons nos travaux par une action de renforcement dans l une des populations étudiées.In sexual species, reproduction systems and dispersal could involve in viability of small populations by having directly an impact on individuals reproductive success. In plants, reproduction and dispersal are mainly passive processes and thus depend of local density in mates, isolation between populations and genetic relationships among individuals. In Biscutella neustriaca, a micro-endemic plant of the Seine river valley, we highlight a strong genetic isolation between populations corroborated by habitat fragmentation and low dispersal abilities of the species. By using phenotypic and molecular approaches, we determine that B. neustriaca is strictly self-incompatible. In this context of isolation and spatially structured genetic diversity, we wonder to what extent dispersal and self-incompatibility impact individuals reproductive successes. Through an ex situ experiment, we highlight both effects of pollen limitation and decrease in local density of compatible mates on maternal reproductive success decrease. In four natural populations, we identify individual reproductive potential and local density of available mates as main factors explaining male and female reproductive successes variability. Genetic factors as inbreeding depression and self-incompatibility also seem to evolve in reproductive successes in some populations. We discuss about importance of considering many factors when acting for conservation in a threatened population, the need to know the reproductive system and dispersal abilities of the species, inseparable from a monitoring of targeted populations, where effects of these factors are only detectable at certain temporal and spatial scales. We illustrate our works by a concrete conservation action in one of the studied populations.LILLE1-Bib. Electronique (590099901) / SudocSudocFranceF

What Is Speciation?

Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation “in the act” and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent

What Is Speciation?

Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation "in the act" and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent

Units of species and speciation.

<p>The Neo-Darwinian view of the Modern Synthesis is that "speciation genes" are the units driving speciation across the genome. Alternatively, if gene sets (including consortia of genes like plasmids or other mobile genetic elements) are sufficiently decoupled from their host genomes, this will lead to "gene ecology," in which gene sets, not species, determine reproductive isolation and/or adapt to ecological niches. Speciation could also be maintained (or potentially driven) by microbial symbionts or by host genes that select for particular symbionts, resulting in hologenome species. All of these speciation mechanisms can potentially be driven by selection or drift, and the list of units and mechanisms (arrows) is not exhaustive.</p

Models of speciation under different regimes of selection and recombination.

<p>In all models, a single population of chromosomes (circles) splits into two nascent species, distinguishable by sets of genetic differences. At each time point, the most frequent multilocus genotype is shown, but other chromosomes could be segregating in the population at lower frequencies. Different haplotypes (or clonal frames) are shown as black or white circles. The ancestral niche is shown in blue and a new niche in orange. Gene flow (recombination) between species is indicated by horizontal connections between branches. (<b>A</b>) In the simplest model of speciation with gene flow, a single mutation controlling sexual isolation (but not under selection) is the only divergent locus (yellow square), with other loci experiencing gene flow between incipient species. (<b>B</b>) Selection during speciation can produce a pattern of genetic diversity across the genome very similar to (A), but species are expected to be longer-lived. Mutations under selection at early and later stages of speciation are shown as orange stars. (<b>C</b>) Allopatric speciation with a population bottleneck and neutral divergence of species. As in (A), competitive exclusion should lead to the extinction of one species if they come back into contact. (<b>D</b>) Without gene flow, the mutation under selection between species (orange star) will purge diversity genome-wide as it sweeps through one population, resulting in genome-wide divergence from the other population.</p

Self-incompatibility in Brassicaceae: identification and characterization of SRK-like sequences linked to the S-locus in the tribe Biscutelleae.

International audienceSelf-incompatibility (SI) is a genetic system that prevents self-fertilization in many Angiosperms. Although plants from the Brassicaceae family present an apparently unique SI system that is ancestral to the family, investigations at the S-locus responsible for SI have been mostly limited to two distinct lineages (Brassica and Arabidopsis-Capsella, respectively). Here, we investigated SI in a third deep-branching lineage of Brassicaceae: the tribe Biscutelleae. By coupling sequencing of the SI gene responsible for pollen recognition (SRK) with phenotypic analyses based on controlled pollinations, we identified 20 SRK-like sequences functionally linked to 13 S-haplotypes in 21 individuals of Biscutella neustriaca and 220 seedlings. We found two genetic and phylogenetic features of SI in Biscutelleae that depart from patterns observed in the reference Arabidopsis clade: (1) SRK-like sequences cluster into two main phylogenetic lineages interspersed within the many SRK lineages of Arabidopsis; and (2) some SRK-like sequences are transmitted by linked pairs, suggesting local duplication within the S-locus. Strikingly, these features also were observed in the Brassica clade but probably evolved independently, as the two main SRK clusters in Biscutella are distinct from those in Brassica. In the light of our results and of what has been previously observed in other Brassicaceae, we discuss the ecological and evolutionary implications on SI plant populations of the high diversity and the complex dominance relationships we found at the S-locus in Biscutelleae