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Next-generation sequencing (NGS), through the implementation of metagenomic protocols,has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocolsare still laborious and costly to implement, and the technique has not yet become routine for everydayvirus characterization. Within the context of CRESS DNA virus studies, we implemented twoalternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledgeof the viral genome) and the other that use specific primers to target a virus (with a priori). Agnosticand specific long read NGS-based assembled genomes of two capulavirus strains were compared tothose obtained using the gold standard technique of Sanger sequencing. Both protocols allowed thedetection and accurate full genome characterization of both strains. Globally, the assembled genomeswere very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in thehomopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGSapproach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has provento be a credible alternative in the context of CRESS DNA virus study and could offer a new range ofapplications not previously accessible.

Background: Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results: metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion: metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.

"En plus de fournir des services écologiques primordiaux, les forêts du Canada constituent d’importants moteurs de développement économique et social. Cependant, les feux, les attaques d’insectes ainsi que tous les facteurs de stress induits par les événements climatiques extrêmes sont autant de menaces qui impactent de plus en plus nos forêts. À l'échelle mondiale, la réduction de la disponibilité en eau du sol devient l'un des facteurs les plus critiques responsables de la vulnérabilité croissante des arbres forestiers. [...]"

Many rice-growing areas are affected by high concentrations of arsenic (As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability (PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic (1600K SNPs) and phenotypic (grain As content, grain yield and days to flowering) data of the Bengal and Assam Aus Panel. Under the base-line single-environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As content, respectively; the three prediction methods (Bayesian Lasso, genomic best linear unbiased prediction and reproducing kernel Hilbert spaces) were considered to perform similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17K, without negative effect on PA of genomic predictions. Single-environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for genotype × environment interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest predictive ability (0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the Bengal and Assam Aus Panel. Genomic prediction can also be applied to breeding for other complex traits under multiple environments.

The Indian Ocean represents a central migration zone for bovine (Bos taurus) and ovine (Ovis aries) populations accompanying human populations between East Africa, the Middle East and Southeast Asia, but their genetic diversity as well as their demographic and adaptive histories remain poorly known. The main objective of the thesis was to study the demographic and adaptive histories of cattle and sheep in the Indian Ocean, based on medium and high density genotyping data, with particular attention to the breeds of the western part of the zone located on the island of Mayotte, in the Comoros (never before phenotypically and genetically characterized) and on the island of Madagascar. For this purpose, a first phenotypic characterization was conducted on the sheep and cattle populations of Mayotte, allowing to highlight their phenotypic heterogeneity and to contribute to the recognition of the Zebu breed of Mayotte as a local French breed. This phenotypic characterization revealed a malformation of the external ear in 20% of the studied sheep, which present reduced or totally atrophied ears (microtia). The study of SNP-HD data of current cattle from Mayotte and Madagascar by comparing them to those of a larger panel of breeds representative of the bovine genetic diversity of the world has allowed to highlight a great genetic proximity (predominantly indicine ancestry and weak African taurine ancestry) between these two breeds, having diverged in the 16th century, at the time of the arrival of the Europeans. Their common ancestral population is the result of a crossbreeding event involving an African zebu population (African taurine x zebu) and an Indian index population dating back to the 12th century. A sharp increase in the size of the estimated populations is observed between the 16th and 17th centuries and coincides with the expansion of the livestock trade to supply European ships in particular. The origin of the cattle populations of the western Indian Ocean isla

Grapevine breeding needs to address two main issues over the next few years: reducing pesticide use and adaptating to climate change. If the selection of new resistant grapevine cultivars has been accelerated, breeding remains a long and costly process for a perennial species such as grapevine. That is why I tested and compared different methodologies for optimizing the breeding of new grapevine varieties. The first is genomic prediction (GP), which relies on the use of molecular markers to train a model to predict genetic values. The second is phenomic prediction (PP), which relies on the use of spectra measured on plant tissues, which is cheaper and more high-throughput than genotyping. I used GP and PP under different configurations to evaluate their interest in breeding programs. For that, I used three grapevine populations with contrasted relatedness, both genotyped and phenotyped. First, I compared univariate and multivariate GP models in a bi-parental population (N=188), on 14 traits related to drought. Multivariate methods did not perform better than univariate ones, and ranking between methods depended on the genetic architecture and heritability of the trait. Secondly, I tested across-population GP (a more applicable configuration for breeding) for 15 traits, by training the prediction model in a diversity panel (N=277) and using 10 bi-parental families of a half-diallel (N=622) as validation sets. For that, I first predicted the average genetic value of each family (for the first selection step of future crosses to be made) and then the genetic values of individuals within each family (for the second selection step of offspring within crosses once they have been realized). Prediction accuracy for these two steps appeared to be satisfying for the application of GP in breeding programs, compared to within-population prediction accuracy. Finally, I tested for the first time the application of PP in grapevine, by using near-infrared spectra measured on wood a

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.

En agronomie et plus spécifiquement en amélioration génétique, le génotypage haut débit a été largement mis à profit, depuis maintenant plus de 20 ans, pour accéder à une information génétique toujours plus riche et abondante. Celle-ci a permis d'identifier les positions le long du génome impliquées dans la variabilité de caractères d'intérêt. Plus récemment, les méthodes de phénotypage haut débit ont fait leur apparition. Elles donnent accès au suivi de l'évolution de plusieurs caractères phénotypiques au cours du temps. Ces données, longitudinales, permettent d'étudier finement la dynamique évolutive de ces caractères tout en identifiant les facteurs environnementaux qui influencent leur variabilité selon les stades de développement. Cependant, l'analyse de telles données soulève plusieurs défis statistiques. Cette thèse propose des développements méthodologiques afin de prendre en compte les dépendances entre observations et entre variables, de sélectionner les variables génétiques ou environnementales pertinentes, ou encore d'estimer des effets qui évoluent au cours du temps. Le cadre bayésien est un formalisme statistique élégant pour répondre à ces différentes problématiques notamment au travers de la construction de lois a priori. Nous étudions et comparons différentes lois a priori pour simultanément inférer et sélectionner les effets fixes et/ou aléatoires quand ceux-ci peuvent être nombreux. Nous considérons différents cadres de modélisation statistique classiquement utilisés pour l'analyse de données longitudinales. En particulier, nous nous focaliserons sur les modèles à coefficients variants, les modèles linéaires mixtes ou encore la régression sur signal. Ce travail a été motivé par différentes applications pratiques portant sur l'évolution temporelle de l'architecture génétique, la détection de QTL ou l'impact des variations climatiques sur la variabilité phénotypique. Trois jeux de données, issus de contextes agronomiques variés, sont utilisés pour i

For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of biallelic markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called SnappNet, as it extends the Snapp method inferring evolutionary trees under the multispecies coalescent model, to networks. SnappNet is available as a package of the well-known beast 2 software. Recently, the MCMC_BiMarkers method, implemented in PhyloNet, also extended Snapp to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, SnappNet relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of SnappNet and MCMC_BiMarkers. We show that both methods enjoy similar abilities to recover simple networks, but SnappNet is more accurate than MCMC_BiMarkers on more complex network scenarios. Also, on complex networks, SnappNet is found to be extremely faster than MCMC_BiMarkers in terms of time required for the likelihood computation. We finally illustrate SnappNet performances on a rice data set. SnappNet infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.

Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.

Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.

We describe a new strain named Bartonella gabonensis sp. nov. strain 669T (CSURB1083). The entire genome of this strain is described here. It was isolated from a savannah rodent, a brush-furred rat (Lophuromys sp.), trapped the city of Franceville in Gabon, in Central Africa. B. gabonensis is an aerobic, rod-shaped and Gram-negative bacterium. On the basis of the organism's features, and following a taxonogenomic approach, we propose the creation of the species Bartonella gabonensis sp. nov.

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration.

Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pan-domestication set – and overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication.

Wheat blast is a devastating disease caused by the pathogenic fungusPyricularia oryzae.Wheat blast first emerged in South America before more recently reaching Bangladesh. Even thoughthe pathogen can spread locally by air-dispersed spores, long-distance spread is likely to occur viainfected wheat seed or grain. Wheat blast epidemics are caused by a genetic lineage of the fungus,called theTriticumlineage, only differing from the otherP. oryzaelineages by less than 1% geneticdivergence. In order to prevent further spread of this pathogen to other wheat-growing areas inthe world, sensitive and specific detection tools are needed to test for contamination of traded seedlots by theP. oryzae Triticumlineage. In this study, we adopted a comparative genomics approach toidentify new loci specific to theP. oryzae Triticumlineage and used them to design a set of new markersthat can be used in conventional polymerase chain reaction (PCR), real-time PCR, or loop-mediatedisothermal amplification (LAMP) for the detection of the pathogen, with improved inclusivity andspecificity compared to currently available tests. A preliminary biological enrichment step of theseeds was shown to improve the sensitivity of the tests, which enabled the detection of the targetat an infection rate as low as 0.25%. Combined with others, this new toolkit may be particularlybeneficial in preventing the trade of contaminated seeds and in limiting the spread of the disease.

Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.

The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research.

Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence.

Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water‐conducting systems, secondary metabolism, stress defense mechanisms, and small RNA‐mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole‐genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.

Background: The small, dense LDL phenotype is associated with an increased cardiovascular disease risk. A genome-wide scan performed on the Quebec Family Study (QFS) revealed a quantitative trait locus for LDL peak particle diameter (LDL-PPD) on the 17q21 region. A positional candidate gene – the fatty acid synthase gene (FASN) – encodes a key enzyme in the biogenesis of membrane lipids. FASN may play a role in the regulation of feeding and may be a potential therapeutic target for obesity and insulin resistance. Methods: Analyses were performed on 592 subjects of the QFS. Dietary fat was estimated by a 3-day food record. LDL-PPD was measured by gradient gel electrophoresis on polyacrylamide gradient gels. Results: Five single nucleotide polymorphisms were genotyped in FASN gene. FASN rs4246444 was associated with LDL-PPD, but only when fat intake was taken into account (p = 0.001). High and low lipid consumers were defined using a cutoff of 35% of dietary fat intake. Carriers of the variant allele showed smaller LDL-PPD only when consuming a high amount of fat. This association remained significant after adjustments for age, sex, body mass index and plasma triglyceride levels. Conclusion: The results suggest that dietary fat intake may modify the effect of the FASN rs4246444 polymorphism on LDL-PPD.

Tests that feature genomic indicators can now be used to guide the pharmacological treatment of patients. To better identify the needs and preferences of patients and health care providers in facilitating their understanding of information related to such pharmacogenomic tests (PGx), a review of literature on knowledge translation and health literacy in the context of testing was conducted. Using a grounded theory-based approach, a comparative analysis of data from 36 studies meeting the criteria for the meta-data analysis has revealed the recurrence of three principal themes: (a) knowledge and understanding of genetics and pharmacogenomics; (b) experiences with genetic, genomic, or PGx testing (decision about the test, information delivery, and understanding of test results); and (c) educational/informational resources. This synthesis sheds light on each theme from the standpoint of both patients and health care providers and suggests avenues in which to direct efforts to support the introduction of pharmacogenomic tests in current practice.

Aeromonas salmonicida strains are roughly classified into two categories, typical and atypical strains. The latter mainly regroup isolates that present unusual phenotypes or hosts, comparatively to the typical strains that belong to the salmonicida subspecies. This study focuses on an uncharacterized atypical strain, M18076-11, isolated from lumpfish (Cyclopterus lumpus) and not part of the four recognized Aeromonas salmonicida subspecies. This isolate presents an unreported phenotype in the A. salmonicida species: the formation of large granular aggregates. Granules are formed of a heterogeneous mix of live and dead cells, with live cells composing the majority of the population. Even if no mechanism was determined to cause cellular aggregation, small globular structures at the cell surface were observed, which might affect granular formation. Pan-genome phylogenetic analysis indicated that this strain groups alongside the masoucida subspecies. However, phenotypic tests showed that these strains have diverging phenotypes, suggesting that M18076-11 might belong to a new subspecies. Also, a pAsal1-like plasmid, which was only reported in strains of the subspecies salmonicida, was discovered in M18076-11. This study sheds light on unsuspected diversity in A. salmonicida subspecies and stresses the need of thorough identification when a new strain is encountered, as unique traits might be discovered.

OBJECTIVE: To support the introduction of pharmacogenomic tests in current practice, this study identifies the factors associated with a better understanding of the information related to genetic, genomic and/or pharmacogenomic tests by patients and health care professionals. METHODS: Following a scoping review methodology, a search for literature was conducted with keywords related to health literacy and knowledge translation in the context of pharmacogenomic tests. Since only 6 articles were identified, the context of genetic or genomic testing were added to the inclusion criteria, leading to 24 articles. RESULTS: Fourteen of the studies analyzed focused on genetic predictive, diagnostic or carrier tests, or concerned genetics in general, while ten addressed or included the use of pharmacogenomic tests. Demographic, individual, experiential and contextual factors were associated with a better understanding of the information related to genetic, genomic and/or pharmacogenomic tests among the targeted populations. RESEARCH IMPLICATIONS: Our review shows that there is currently little empirical research available to identify the factors to consider in order to develop educational tools and resources specific to pharmacogenomics. CONCLUSION: Expanding our review to include genetic and genomic testing factors can serve as a starting point for the evidence to be validated in future empirical research.

Background : Few genes have been associated with the metabolic syndrome (MS), although its genetic component is well accepted. The aim of this study was to compare the adipose tissue gene expression profiles of obese men with and without the MS and to apply an integrative genomic approach to propose new candidate genes. Methods : Affymetrix HG-U133 plus 2 arrays have been used for expression profiling of omental adipose tissue of non-diabetic obese men with (n=7) and without (n=7) the MS, as defined by the NCEP-ATPIII, that undergo a bariatric operation. Results ; Omentum expresses a total of 23 055 transcripts. Overall, 489 genes were differentially expressed between the two groups. A total of 80 differentially expressed genes were located within a previously identified region of linkage. In this subset of genes, zinc finger protein 36 (ZFP36) gene has been identified as the most promising genetic target for the MS-based mean fold expression differences and on biological plausibility. 2 out of 5 identified ZFP36 gene polymorphisms have been genotyped in a cohort of 698 obese subjects. The minor allele of these polymorphisms was associated with a lower body weight in women (rs251864; P≤0.01) and glucose level in men (c.1564_1565delTT; P<0.05). The haplogenotype was associated with plasma LDL-cholesterol levels in men and women (P≤0.02), and weight in women (P≤0.05). The haplogenotype was also associated with omental adipose tissue ZFP36 mRNA levels (n=83 women; P=0.02), and explained 10.1% of its variance. Conclusion : These results suggest that converging genomics is helpful to prioritize MS-related candidate genes and that ZFP36 is a promising candidate gene for obesity-associated metabolic complications.

The bacterium Aeromonas salmonicida is known since long time as a major fish pathogen unable to grow at 37 °C. However, some cases of human infection by putative mesophilic A. salmonicida have been reported. The goal of the present study is to examine two clinical cases of human infection by A. salmonicida in Spain and to investigate the pathogenicity in mammals of selected mesophilic A. salmonicida strains. An evaluation of the pathogenicity in a mouse model of clinical and environmental A. salmonicida strains was performed. The genomes of the strains were sequenced and analyzed in order to find the virulence determinants of these strains. The experimental infection in mice showed a gradient in the virulence of these strains and that some of them can cause necrotizing fasciitis and tissue damage in the liver. In addition to demonstrating significant genomic diversity among the strains studied, bioinformatics analyses permitted also to shed light on crucial elements for the virulence of the strains, like the presence of a type III secretion system in the one that caused the highest mortality in the experimental infection. Clinicians and microbiologists should consider these results for the inclusion of A. salmonicida in diagnosis tests since it is now clear that some mesophilic strains are also pathogens for humans.

Background: Bacteriophage replication depends on bacterial proteins and inactivation of genes coding for such host factors should interfere with phage infection. To gain further insights into the interactions between S. pneumoniae and its pneumophages, we characterized S. pneumoniae mutants selected for resistance to the virulent phages SOCP or Dp-1. Results: S. pneumoniae R6-SOCPR and R6-DP1R were highly resistant to the phage used for their selection and no cross-resistance between the two phages was detected. Adsorption of SOCP to R6-SOCPR was partly reduced whereas no difference in Dp-1 adsorption was noted on R6-DP1R. The replication of SOCP was completely inhibited in R6-SOCPR while Dp-1 was severely impaired in R6-DP1R. Genome sequencing identified 8 and 2 genes mutated in R6-SOCPR and R6-DP1R , respectively. Resistance reconstruction in phage-sensitive S. pneumoniae confirmed that mutations in a GntR-type regulator, in a glycerophosphoryl phosphodiesterase and in a Mur ligase were responsible for resistance to SOCP. The three mutations were additive to increase resistance to SOCP. In contrast, resistance to Dp-1 in R6-DP1R resulted from mutations in a unique gene coding for a type IV restriction endonuclease. Conclusion: The characterization of mutations conferring resistance to pneumophages highlighted that diverse host genes are involved in the replication of phages from different families.

Lactic acid bacteria (LAB) are essential for the manufacture of fermented dairy products. Studies on the physiology, biochemistry and genetics of these microorganisms over the last century have contributed considerably to the improvement of fermentation processes and have resulted in better and safer products. Nevertheless, the potential of LAB is far from being maximized. The sophistication of biotechnologies and the availability of complete genome sequences have opened the door to the metabolic engineering of LAB. In this regard, the recent publication of the complete genome sequences of two Streptococcus thermophilus strains will provide a key tool to facilitate the genetic manipulation of this important dairy species.

Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.