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We report four draft genome sequences of Nocardia spp. The strains are the Nocardia cyriacigeorgica DSM 44484 pathogenic type strain; two environmental isolates, Nocardia cyriacigeorgica EML446 and EML1456; and the Nocardia asteroides ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of Nocardia spp.

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos

We report the genome sequence of a Pseudomonas sp. strain isolated from olive knot galls. The genome size is 6.101 Mbp with a G+C content of 58%. A total of 6,137 coding DNA sequences (CDS) were predicted, including 52 tRNA and 4 rRNA genes.

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry., A fruitful genomic resource Detailed genomic maps from the fruit-bearing trees of the Prunus genus should greatly accelerate the breeding of superior cultivars. These plants produce a variety of popular fruits, but until relatively recently, breeders had only limited genetic information with which to work. Pere Arús of Spain’s Institute of Agrifood Research and Technology and colleagues have now reviewed the rapid advances in Prunus genomics that have taken place since 2010, when researchers completed the first genome assembly for this genus. In the ensuing decade, increasingly high-quality genomes from the peach, Japanese apricot, and cherry have allowed scientists to home in on chromosomal regions associated with key traits such as fruit quality and disease resistance. These data also offer valuable genetic markers that agronomists can use to guide the production of healthier trees and more commercially desirable fruits.

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode.

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. Aims and methods This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years. Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

International audience

Fusarium graminearum is a major fungal pathogen that induces Fusarium head blight (FHB), a devastating disease of small-grain cereals worldwide. This announcement provides the whole-genome sequence of a highly virulent and toxin-producing French isolate, MDC_Fg1.

International audience; We investigated unusual carbapenemase-producing Enterobacter cloacae complex isolates (n = 8) in the novel sequence type (ST) 873, which caused nosocomial infections in 2 hospitals in France. Whole-genome sequence typing showed the 1-year persistence of the epidemic strain, which harbored a blaVIM-4 ST1-IncHI2 plasmid, in 1 health institution and 2 closely related strains harboring blaCTX-M-15 in the other. These isolates formed a new subgroup in the E. hormaechei metacluster, according to their hsp60 sequences and phylogenomic analysis. The average nucleotide identities, specific biochemical properties, and pangenomic and functional investigations of isolates suggested isolates of a novel species that had acquired genes associated with adhesion and mobility. The emergence of this novel Enterobacter phylogenetic lineage within hospitals should be closely monitored because of its ability to persist and spread.

The gastrointestinal parasite Haemonchus contortus is the most pathogenic nematode of veterinary interest and a model for many aspects of parasitic nematode biology. Using single-worm whole genome sequencing, we have performed the most exhaustive survey of genome-wide diversity undertaken for any parasitic nematode, considering 19 populations spanning five continents. Phylogenetic inference supports an African origin for the species. However, contemporary global distribution has been mediated by modern human movement, with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia presented. Like other veterinary and human parasitic nematodes, H. contortus infections are controlled by widespread administration of anthelmintic drugs. Strong selection in response to benzimidazole treatment has impacted genetic diversity surrounding the β-tubulin locus independently throughout the world. Further, regions of high diversifying selection were enriched in genes involved in response to drugs as well as other anthelmintic-associated biological functions including pharyngeal pumping and oviposition. From these analyses, we identified genes putatively linked to ivermectin resistance that could be used in monitoring drug resistance. Finally, we describe genetic signatures of climate-driven adaptation, revealing that epigenetic regulation and components of the dauer pathway may play a role in adaptation in the face of climatic fluctuations. These results are the first to identify signatures of genetic adaptation to climate in a parasitic nematode, and provides insight into the ongoing expansion in the range of Haemonchus contortus, which may have consequences for the management of this parasite.

Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus., Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus. Genome lengths of the strains varied between 2,982,864 and 3,288,331 bp, with G+C contents of 72.23 to 73.50%.

Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through different ecotypes. Here, we present the draft genome sequences of 20 bacterial strains belonging to the contrasted psychrotolerant and thermotolerant ecotypes.

Background It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. Results Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., SCCmec XI element, Tn916 transposon and non φ3-prophages) in a majority of BSI isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections. The analysis of prophage content in all 76 BSI isolates showed an increasing prevalence of polylysogeny over time. Overall, over the course of the last 10 years, the BSI isolates appear to have acquired increasing numbers of genetic features previously shown to contribute to bacterial adaptation and virulence in animal models of staphylococcal infections. Conclusions We hypothesize that lysogeny has played a significant role in increasing the ability of the ST398 clone to cause infections in humans. Our findings highlight the risk that the ST398 lineage will increase its threat to public health by continuing to acquire virulence and/or multiple antibiotic-resistance genes from hospital-associated clones of Staphylococcus aureus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3516-x) contains supplementary material, which is available to authorized users.

We report here the complete genome sequences of two Myoviridae phages that infect various avian-pathogenic Escherichia coli strains and that are closely related to phage phAPEC8.

The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak's hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ∼1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding.

International audience; The 1000 bull genomes reference population makes it possible to impute whole genome sequences for a large number of animals. Even if imputation accuracy is still limited for rare variants, it becomes possible to directly pinpoint the causal mutations, or at least variants in very high linkage disequilibrium with them.However, sequence data (i.e. tens of millions of variants for several thousand animals) cannot be used in routine genomic evaluation and only the most predictive part of them should be identified and used. In this study, we propose to construct virtual chips containing 50k variants (V50K) selected from the whole genome sequence, compatible with a routine use.About 3,000 bulls from the French Montbéliarde breed were studied for a panel of ten traits related to milk production and composition, fertility, and conformation. This population was divided in training and validation sets. GWAS analyses were carried out at the sequence level on the training population using Wombat software. V50K were then designed considering different criteria: GWAS results, minor allele frequency, variant distribution over the genome, and functional annotations.BayesCπ approach was applied on these V50K and on the Illumina Bovine SNP50 Beadchip® (IB50K) to predict breeding values in the validation set based on the phenotypes (DYD) and genotypes of the training set. GEBV accuracy for each chip was then estimated through correlations between DYD and GEBV in the validation set. Most of the tested scenarios failed to improve accuracy of GEBV obtained with the IB50K. Nevertheless, a good choice of the variants can outperform results of the standard IB50K.

Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the environment. To better understand t~e genetic control of these components, quantitative trait loci (QTL) have been mapped for years. Today the genome sequence availability changes the paradigm of genetic approaches. QTL have been first identified using linkage mapping populations and positional cloning identified a few QTLs. However Iinkage mapping is Iimited to the analysis of traits differing between two parentallines. Genome-wide association (GWA) has then been proposed to assess a large range ofvariability. ln tomato, we have shown that GWAstudy is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAsuccess is limited in sorne regions due to the low decay of linkage disequilibrium, which varies along the genome. Rare alleles are also difficult to detect with GWA studies. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditionallinkage and GWAs by increasing the precision of QTLmapping but with equilibrated allelic frequencies. We have developed a MAGICpopulation by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequèncing to detect candidate single nuc\eotide polymorphisms (SNP) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, will be discussed.

Invitation d'un laboratoire; Bread wheat whole genome sequence assembly. Colloque EPGV 2016, Détection Gestion et Analyse du Polymorphisme des Génomes Végétaux

In this study, we describe the draft genome sequence of a Campylobacter jejuni clinical isolate issued from a French patient suffering from severe campylobacteriosis. This atypical strain is characterized by an unusual resistance to oxygen and the ability to grow under an aerobic atmosphere, a characteristic as-of-yet unique to this species.

International audience; Plant biology in general, and plant evo-devo in particular would strongly benefit from a broader range of available model systems. In recent years, technological advances have facilitated the analysis and comparison of individual gene functions in multiple species, representing now a fairly wide taxonomic range of the plant kingdom. Because genes are embedded in gene networks, studying evolution of gene function ultimately should be put in the context of studying the evolution of entire gene networks, since changes in the function of a single gene will normally go together with further changes in its network environment. For this reason, plant comparative biology/evo-devo will require the availability of a defined set of 'super' models occupying key taxonomic positions, in which performing gene functional analysis and testing genetic interactions ideally is as straightforward as, e.g., in Arabidopsis. Here we review why petunia has the potential to become one of these future supermodels, as a representative of the Asterid Glade. We will first detail its intrinsic qualities as a model system. Next, we highlight how the revolution in sequencing technologies will now finally allows exploitation of the petunia system to its full potential, despite that petunia has already a long history as a model in plant molecular biology and genetics. We conclude with a series of arguments in favor of a more diversified multi-model approach in plant biology, and we point out where the petunia model system may further play a role, based on its biological features and molecular toolkit.

International audience

International audience

Background: Sequence data can potentially increase the reliability of genomic predictions, because such data include causative mutations instead of relying on linkage disequilibrium (LD) between causative mutations and prediction variants. However, the location of the causative mutations is not known, and the presence of many variants that are in low LD with the causative mutations may reduce prediction reliability. Our objective was to investigate whether the use of variants at quantitative trait loci (QTL) that are identified in a multi-breed genome-wide association study (GWAS) for milk, fat and protein yield would increase the reliability of within- and multi-breed genomic predictions in Holstein, Jersey and Danish Red cattle. A wide range of scenarios that test different strategies to select prediction markers, for both within-breed and multi-breed prediction, were compared.[br/] Results: For all breeds and traits, the use of variants selected from a multi-breed GWAS resulted in substantial increases in prediction reliabilities compared to within-breed prediction using a 50 K SNP array. Reliabilities depended highly on the choice of the prediction markers, and the scenario that led to the highest reliability varied between breeds and traits. While genomic correlations across breeds were low for genome-wide sequence variants, the effects of the QTL variants that yielded the highest reliabilities were highly correlated across breeds.[br/] Conclusions: Our results show that the use of sequence variants, which are located near peaks of QTL that are detected in a multi-breed GWAS, can increase reliability of genomic predictions.

With the recent development of approaches using high throughput genotyping and sequencing, identifying the causal mutation underlying a genetic defect from several cases has become much simpler. However, cases, or their corresponding biological material, are not always available. This article presents two approaches relying on high throughput data analysis to identify recessive lethal mutations or to efficiently orient their research from genome sequence. The first approach uses genotyping data to look for genomic régions presenting a deficit in homozygotes. This method has proven to be efficient with several mutations already characterized in each analyzed bovine breed. In the second approach, DNA variants are searched in the available whole genome sequences, with strong annotations suggesting that they are not tolerated in the homozygous state. The number of false positives is relatively high but these variants can orient the observation step toward mating at risk or homozygous animals and, in the most favorable cases, to anticipate the outbreak of the defect. Examples are provided with the RP1 gene responsible for retina degeneration or the EDAR gene responsible for the ectodermal anhidrotic syndrome.; Avec le récent développement des approches reposant sur le génotypage et séquençage à haut débit, identifier la mutation responsable d’une anomalie à partir de quelques cas est beaucoup plus simple qu’auparavant. Toutefois, il n’est pas toujours possible d’observer des cas et de disposer du matériel biologique correspondant. Cet article présente deux approches reposant sur l’analyse de données à haut débit, permettant d’identifier des mutations récessives létales ou d’orienter plus efficacement leur recherche à partir des données de séquence du génome. La première approche utilise les données de génotypage à haut débit pour rechercher des régions du génome présentant un déficit en homozygotes. Cette méthode a déjà permis de caractériser plusieurs mutations dans chacune des races bovines analysées. Dans la seconde approche, on recherche dans les données de séquence disponibles des variants dont l’annotation suggère qu’ils ne sont pas tolérés à l’état homozygote. Le nombre de faux positifs est élevé, mais ces données permettent d’orienter la phase d’observation et de diagnostic plus efficacement et, dans les cas les plus favorables, d’anticiper l’émergence de l’anomalie. Des exemples sont fournis avec le gène RP1 responsable de dégénérescence rétinienne ou le gène EDAR responsable de l’absence de poils et de dents.

Isolates of peste des petits ruminants virus (PPRV) can be segregated genetically into four lineages. For decades, lineages I–III have been reported across Africa whilst lineage IV has predominantly circulated across Asia. However, the lineage distribution is currently changing in Africa. Importantly, full genome sequence data for African field isolates have been lacking. Here, we announce the first complete genome sequence of a field isolate of peste des petits ruminants virus (PPRV) from East Africa. This isolate was derived from the intestine of a goat suffering from severe clinical disease during the 2010 outbreak in Ethiopia. The full genome sequence of this isolate, PPRV Ethiopia/2010, clusters genetically with other lineage IV isolates of PPRV, sharing high levels of sequence identity across the genome. Further, we have carried out a phylogenetic analysis of all of the available African partial N gene and F gene PPRV sequences to investigate the epidemiology of PPRV with a focus on the emergence of different lineages of PPRV in Africa.

Key message This paper describes how the combination of genomics, genetic engineering, and 3D structural characterization has helped clarify the redox regulatory networks in poplar with consequences not only in system biology in plants but also in bacteria and mammalian systems.[br/] Context Tree genomes are increasingly available with a large number of orphan genes coding for proteins, the function of which is still unknown.[br/] Aims and methods Modern techniques of genome analysis coupled with recombinant protein technology and massive 3D structural determination of tree proteins should help elucidate the function of many of the proteins encoded by orphan genes. X-ray crystallography and NMR will be the methods of choice for protein structure determination.[br/] Results In this review, we provide examples illustrating how the above-mentioned techniques improved our understanding of redox regulatory circuits in poplar, the first forest tree species sequenced. We showed that poplar peroxiredoxins use either thioredoxin or glutaredoxin as electron donors to reduce hydrogen peroxide. That glutaredoxin could be a reductant was unknown at the time of this discovery even in other biological organisms and was later confirmed notably by the observation that the two genes are fused in some bacteria and by the resolution of the structure of the bacterial hybrid protein. Similarly, genome analysis coupled to in vitro analysis of enzymatic properties led to the discovery that some plant methionine sulfoxide reductases can also use both thioredoxins and glutaredoxins as electron donors. Besides their disulfide reductase activity, it has been demonstrated that some poplar glutaredoxins are also involved in iron-sulfur center biogenesis and assembly. The original 3D structure determination has been made with poplar glutaredoxin C1 and then confirmed in a variety of other biological organisms including human. Our work also showed that in plants, so-called glutathione peroxidases use thioredoxins and not glutathione as electron donors. This is true for all non-selenocysteine-containing glutathione peroxidases. Finally, connections between the thioredoxin and glutaredoxin systems have been elucidated through the study of atypical poplar thioredoxins.[br/] Conclusion Altogether, these data illustrate how the combination of genetic engineering and structural biology improves our understanding of biological processes and helps fuel systems biology for trees and other biological species.

The oomycota Pythium oligandrum Po37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of the P. oligandrum Po37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.

SE-vdA is supported by BBSRC grant BB/M014207/1. Sequencing was funded by BBSRC grant BB/F000642/1 to the University of Leeds and grant BB/F00334X/1 to the Wellcome Trust Sanger Institute). DRL was supported by a fellowship from The James Hutton Institute and the School of Biological Sciences, University of Edinburgh. GK was supported by a BBSRC PhD studentship. The James Hutton Institute receives funding from the Scottish Government. JAC and NEH are supported by the Wellcome Trust through its core funding of the Wellcome Trust Sanger Institute (grant 098051). This work was also supported by funding from the Canadian Safety and Security Program, project number CRTI09_462RD. Background. The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results. We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions. These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action. Publisher PDF

Avec le récent développement des approches reposant sur le génotypage et séquençage à haut débit, identifier la mutation responsable d’une anomalie à partir de quelques cas est beaucoup plus simple qu’auparavant. Toutefois, il n’est pas toujours possible d’observer des cas et de disposer du matériel biologique correspondant. Cet article présente deux approches reposant sur l’analyse de données à haut débit, permettant d’identifier des mutations récessives létales ou d’orienter plus efficacement leur recherche à partir des données de séquence du génome. La première approche utilise les données de génotypage à haut débit pour rechercher des régions du génome présentant un déficit en homozygotes. Cette méthode a déjà permis de caractériser plusieurs mutations dans chacune des races bovines analysées. Dans la seconde approche, on recherche dans les données de séquence disponibles des variants dont l’annotation suggère qu’ils ne sont pas tolérés à l’état homozygote. Le nombre de faux positifs est élevé, mais ces données permettent d’orienter la phase d’observation et de diagnostic plus efficacement et, dans les cas les plus favorables, d’anticiper l’émergence de l’anomalie. Des exemples sont fournis avec le gène RP1 responsable de dégénérescence rétinienne ou le gène EDAR responsable de l’absence de poils et de dents., With the recent development of approaches using high throughput genotyping and sequencing, identifying the causal mutation underlying a genetic defect from several cases has become much simpler. However, cases, or their corresponding biological material, are not always available. This article presents two approaches relying on high throughput data analysis to identify recessive lethal mutations or to efficiently orient their research from genome sequence. The first approach uses genotyping data to look for genomic régions presenting a deficit in homozygotes. This method has proven to be efficient with several mutations already characterized in each analyzed bovine breed. In the second approach, DNA variants are searched in the available whole genome sequences, with strong annotations suggesting that they are not tolerated in the homozygous state. The number of false positives is relatively high but these variants can orient the observation step toward mating at risk or homozygous animals and, in the most favorable cases, to anticipate the outbreak of the defect. Examples are provided with the RP1 gene responsible for retina degeneration or the EDAR gene responsible for the ectodermal anhidrotic syndrome.

Sequence data is expected to increase the reliability of genomic prediction by containing causative mutations directly, especially in cases where low linkage disequilibrium between markers and causative mutations limits prediction reliability, such as across breed prediction in dairy cattle. In practice, the causative mutations are unknown, and prediction with only variants in perfect linkage disequilibrium with the causative mutations is not realistic, leading to a reduced reliability compared to knowing the causative variants. Our objective was to use sequence data to investigate the potential benefits of sequence data for the prediction of genomic relationships and consequently reliability of genomic breeding values. We used sequence data from five dairy cattle breeds, and a larger number of imputed sequences for two of the five breeds. We focused on the influence of linkage disequilibrium between markers and causative mutations, and assumed that a fraction of the causative mutations was shared across breeds and had the same effect across breeds. By comparing the loss in reliability of different scenarios, varying the distance between markers and causative mutations, using either all genome wide markers from commercial SNP chips, or only the markers closest to the causative mutations, we demonstrate the importance of using only variants very close to the causative mutations, especially for across breed prediction. Rare variants improved prediction only if they were very close to rare causative mutations and all causative mutations were rare. Our results show that sequence data can potentially improve genomic prediction, but careful selection of markers is essential.

Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious disease, affecting livestock, wild animals, and sometimes humans. We report the draft genome sequence of a Mycobacterium bovis strain isolated from wild boar of spoligotype SB0120 (or BCG-like) also present in wildlife-livestock multi-host systems.

Tomato is a model species for genetic analyses since a long time. Many mutations controlled by a single gene were discovered and the underlying genes were mapped first on the tomato genetic map. Most of these genes are involved in fruit colour and shape, in plant growth and architecture and in disease resistances. With the construction of high-density molecular genetic maps, many genes were located on the genome and subsequently several of them were fine-mapped and further identified by positional cloning. Today with the availability of the tomato genome sequence these genes are physically located on the genome and the identification of new ones is being considerably accelerated. The alignment of the physical and genetic maps allowed the identification of hot spots of recombination and of large regions where recombination is almost suppressed, whatever the progeny studied. The impact of this heterogeneity in recombination is discussed.

Background: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.Results: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.Conclusions: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.

Cryptococcus sp. strain Mo29 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. Here, we present the draft genome sequence of this basidiomycetous yeast strain, which has highlighted its biotechnological potential as revealed by the presence of genes involved in the synthesis of secondary metabolites and biotechnologically important enzymes.

Article en open access; International audience; Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species. With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species. Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes. Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.

La disponibilité de la séquence du génome complet de nombreux individus, rendue possible par l’évolution très rapide des technologies de séquençage d’ADN, constitue un apport majeur pour l’identification des anomalies génétiques. L’approche conventionnelle par phénotypage des individus, cartographie de l’anomalie, et identification de la mutation, gagne en rapidité et puissance lorsque l’on dispose d’une grande base de référence pour filtrer les variants candidats. Mais le s données de séquence permettent également d’envisager d’autres approches, en particulier pour les anomalies dont le phénotype est difficilement identifiable et qui passent encore inaperçues. Par exemple, la cartographie des déficits en homozygotes à partir des données de génotypage, suivie de l’analyse des données de séquence d’ individus porteurs, a permis l’identification de plusieurs mutations responsables de mortalité embryonnaire dans différentes ra ces. De façon plus prospective, on peut identifier des polymorphismes délétères dans les données de séquence à partir de leur annotation fonctionnelle, puis caractériser leur effet potentiel par le phénotypage d’animaux porteurs. Cette approche est illustrée avec une anomalie de la vision en race Normande. L’augmentation rapide du nombre d’anomalies génétiques résolues ces dernières années démontre la puissance apportée par le séquençage de génomes complets et ce phénomène s’amplifiera à l’avenir. L’approche comporte cependant des limites, l’annotation encore très incomplète des polymorphismes du génome ou la caractérisation phénotypique, souvent compliquée mais essentielle pour la compréhension des effets des mutations. Enfin, le nombre croissant d’anomalies découvertes dans chaque race nécessitera des stratégies de contre-sélection plus complexe s que l’éradication directe, The availability of whole genome sequences (WGS) of many individuals, made possible by the rapid evolution of DNA sequencing technologies, is a major factor for genetic defect identification. The conventional approach consisting in phenotyping affected animals, mapping and identification of the causal mutation gains speed and power with the availability of large sequence databases to filter out candidate variants. WGS also open new avenues, especially for defects with non specific phenotypes which may remain unobserved. Mapping of regions showing homozygous deficiency with massive genotyping data, followed by analysis of the genome sequences of carriers, enables the identification of several causal mutations responsible for embryonic lethality in different breeds. In a more prospective way, one can identify deleterious polymorphisms in WGS on the basis of their functional annotation, and then characterize their potential effect on carrier animals. Here this approach is illustrated by a defect affecting vision in the Normandy cattle breed. The rapid increase in the number of resolved genetic defects during the last years illustrates the power brought by WGS and this will continue in the future. These approaches still suffer from important limitations, especially the incomplete annotation of the biological effects of variants on the genome, or the phenotypic characterization of the mutations, oft n complex but necessary for a full comprehension of their effects. Finally, the increasing number of known defects in each breed requires new selection strategies, more complex than a direct elimination.

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International audience

Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.

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International audience

Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. A successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. Although some of these processes are well understood today many of the molecular mechanisms underlying SNF, especially in chickpea, remain unclear. Here, we reannotated our previously published transcriptome data generated by deepSuperSAGE (Serial Analysis of Gene Expression) to the recently published draft genome of chickpea to assess the root- and nodule-specific transcriptomes of the eukaryotic host cells. The identified gene expression patterns comprise up to 71 significantly differentially expressed genes and the expression of twenty of these was validated by quantitative real-time PCR with the tissues from five independent biological replicates. Many of the differentially expressed transcripts were found to encode proteins implicated in sugar metabolism, antioxidant defense as well as biotic and abiotic stress responses of the host cells, and some of them were already known to contribute to SNF in other legumes. The differentially expressed genes identified in this study represent candidates that can be used for further characterization of the complex molecular mechanisms underlying SNF in chickpea.