Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract\ud \ud \ud \ud Background\ud Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences.\ud \ud \ud \ud Results\ud Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations.\ud \ud \ud \ud Conclusions\ud This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.AI is funded by a PhD grant from INRA-SPE and region Pays de la Loire, France. EG was funded by a PhD grant from the French Ministry of National Education and Research and French Guyana. SC, EG, MA, EL and LDN are funded by the LABEX TULIP (ANR-10-LABX-41), LSG is funded by ANR-2010-GENM-013 Xanthomix

Diversity and Evolution of Nucleotide Landscapes in Plants

Le paysage nucléotidique – la manière dont la composition nucléotidique varie le long du génome – est une caractéristique marquante de l'organisation des génomes et varie fortement entre espèces. Plusieurs hypothèses émergent des nombreux débats autour des mécanismes évolutifs à l'origine de ces hétérogénéités du taux de GC, parmi lesquelles la conversion génique biaisée vers G et C (BGC) et la sélection sur l'usage du code (SUC). La BGC est un processus neutre associé à la recombinaison qui favorise les allèles en G ou C au détriment des allèles en A ou T. La SUC est une force de sélection qui favorise les codons dits « préférés », ceux dont la traduction serait la plus efficace. Contrairement à ceux des vertébrés, les paysages nucléotidiques des plantes sont peu connus. La plupart des études ont été consacrées au génome d'Arabidopsis thaliana, pauvre en GC et homogène, et à celui du riz, riche en GC et hétérogène. Le contraste entre ces deux génomes a souvent été généralisé comme une dichotomie entre dicotylédones et monocotylédones, mais cette vision est clairement phylogénétiquement biaisée.Les objectifs de ce travail de thèse sont de caractériser les paysages nucléotidiques des angiospermes à une large échelle phylogénétique et de mieux comprendre quels sont les mécanismes évolutifs jouant sur l'évolution de ces paysages nucléotidiques. Comment varient les paysages nucléotidiques le long de la phylogénie des angiospermes ? SUC et BGC façonnent-elles ces paysages nucléotidiques ? Les différents taxons sont-ils affectés avec la même intensité ?Pour répondre à ces questions, j'ai utilisé une approche de génomique comparative basée sur l'analyse de données EST chez plus de 230 espèces d'angiospermes et de gymnospermes. L'exploration des paysages nucléotidiques de ce large éventail de plantes a montré que les patrons d'hétérogénéité des paysages nucléotidiques suivent un continuum le long de la phylogénie, avec des groupes particulièrement riches et hétérogènes en GC, les graminées par exemple. Mes résultats suggèrent que les paysages nucléotidiques des plantes pourraient avoir été façonnés par la BGC et, dans une moindre mesure, par la SUC. Des épisodes indépendants d'enrichissement et d'appauvrissement en GC ont vraisemblablement eu lieu au cours de l'évolution des plantes, et pourraient être expliqués par des variations d'intensité de ces mécanismes. En utilisant une prédiction du degré d'expression des EST, j'ai également mis en évidence une diversité dans les codons préférés entre espèces. Les préférences d'usage des codons se sont révélées plus labiles au cours de l'évolution pour les codons des acides aminés au code quatre et six fois dégénéré. J'ai pu lier l'évolution des préférences d'usage des codons à l'évolution de la composition nucléotidique des génomes. Mes résultats suggèrent que la composition en base des génomes, affectée en partie par la BGC, orienterait la coévolution entre préférence d'usage du code et ARNt.The nucleotide landscape – the way base composition varies along a genome – is a striking feature of genome organization and is highly variable between species. The evolutionary causes of such heterogeneity in GC content have been much debated. Biased gene conversion towards G and C (BGC) and selection on codon usage (SCU) are thought to be main forces. BGC is a neutral process associated with recombination favouring G and C alleles over A and T ones. SCU is a selection process favouring the so-called “preferred” codons, i.e., those whose translation is the most efficient. Contrary to vertebrates, plant nucleotide landscapes are still poorly known. Most studies focused on the GC-poor and homogeneous Arabidopsis thaliana genome and on the GC-rich and heterogeneous rice genome. The contrast between these two genomes was often generalized as a dicot/monocot dichotomy but this vision is clearly phylogenetically biased.The objectives of this study are to characterize angiosperm nucleotide landscapes on a wide phylogenetic scale and to better understand the evolutionary mechanisms acting upon the evolution of nucleotide landscapes. To what extent do nucleotide landscapes vary across angiosperm phylogeny? Are nucleotide landscapes shaped by BGC and SCU? Are taxa affected with the same intensity?To tackle these issues, I used a comparative genomic approach relying on EST data analysis on over 230 angiosperm and gymnosperm species. Through the nucleotide landscape survey for such a wide range of species I found a continuum of GC-heterogeneity patterns across phylogeny, some taxa such as Poaceae being strikingly GC-rich and heterogeneous. My results suggest that nucleotide landscapes could have been shaped by BGC and, to a lesser extent, by SCU. GC-content enrichment and impoverishment are likely to have occurred several times independently during plant evolution and could be explained by intensity variations of BGC and SCU. Using a proxy for EST expression level, I also characterized the diversity of preferred codons between species. Codon usage preferences were shown to be evolutionarily more unstable for four- and six-fold degenerate codon families. Finally, I could link the evolution of codon usage preferences to the evolution of genome base composition. My results suggest that genome base composition, partially shaped by BGC, seems to drive the coevolution between codon usage preferences and tRNAs

Patterns and evolution of nucleotide landscapes in seed plants

International audienceNucleotide landscapes, which are the way base composition is distributed along a genome, strongly vary among species. The underlying causes of these variations have been much debated. Though mutational bias and selection were initially invoked, GC-biased gene conversion (gBGC), a recombination-associated process favoring the G and C over A and T bases, is increasingly recognized as a major factor. As opposed to vertebrates, evolution of GC content is less well known in plants. Most studies have focused on the GC-poor and homogeneous Arabidopsis thaliana genome and the much more GC-rich and heterogeneous rice (Oryza sativa) genome and have often been generalized as a dicot/monocot dichotomy. This vision is clearly phylogenetically biased and does not allow understanding the mechanisms involved in GC content evolution in plants. To tackle these issues, we used EST data from more than 200 species and provided the most comprehensive description of gene GC content across the seed plant phylogeny so far available. As opposed to the classically assumed dicot/monocot dichotomy, we found continuous variations in GC content from the probably ancestral GC-poor and homogeneous genomes to the more derived GC-rich and highly heterogeneous ones, with several independent enrichment episodes. Our results suggest that gBGC could play a significant role in the evolution of GC content in plant genomes

tpc093674SupplementalDS4

List of Genbank accession used for the EST dataset of the articl

Natural triploids of wild cherry

International audienceResearch of triploid individuals was carried out in the French wild cherry (Prunus avium L.) collection at the Institut National de la Recherche Agronomique (INRA), Orléans, France, using 12 microsatellite markers and the S gametophytic incompatibility marker. For 11 of 312 clones (3.5%), we found three different alleles or two different alleles included one doubled allele for 10–12 markers spread along five of the eight chromosome pairs in wild cherry. The cytometry analysis confirmed that triploidy was genome-wide. No new allele was observed among the triploids compared with the diploids of the wild cherry collection: these triploids probably result from diploids through the production of unreduced gametes, and not from interspecific hybridation. A comparison of the height growth, diameter growth, and resistance to leaf spot among 38–85 clones in four 6- to 10-year-old clonal field trials showed that six triploids were among the best compared with the diploids. The dimensions of the leaves were somewhat larger, and the petals were always larger for nine triploids compared with 20 diploids observed on plants of the wild cherry collection of INRA. Three triploids are already used as clonal variety or component of a seed orchard. We discuss the need to include more triploids in the wild cherry breeding programme.Une recherche d’individus triploïdes a été réalisée dans la collection française de merisier (Prunus avium L.) de l’Institut National de la Recherche Agronomique (INRA) d’Orléans, à l’aide de 12 marqueurs microsatellites et du marqueur d’incompatibilité S. Onze clones sur 312 (3,5 %) présentaient trois allèles différents, ou deux allèles différents dont un doublé, pour 10–12 marqueurs répartis sur cinq sur les huit paires de chromosomes que compte le merisier. Une analyse par cytométrie a confirmé que la triploïdie concernait le génome entier. Les allèles des triploïdes ne sont pas différents de ceux observés chez les diploïdes : ces triploïdes sont donc probablement issus de diploïdes grâce à la non réduction de certains gamètes, et non de croisements interspécifiques. La croissance en hauteur et en circonférence, ainsi que la résistance à la cylindrosporiose semble meilleure que celle des diploïdes, pour six triploïdes observés dans quatre tests forestiers, âgés de 6 à 10 ans et mettant en comparaison 38–85 clones. Les dimensions des feuilles et surtout des pétales (parfaitement discriminants) sont plus grandes chez neuf triploïdes, comparés à 20 diploïdes, observés sur les plants de la collection de l’INRA. Trois triploïdes sont déjà utilisés comme cultivar ou composant de verger à graines. L’intérêt d’utiliser plus largement les triploïdes dans le programme d’amélioration du merisier est discuté

tpc093674SupplementalDS5

Acession numbers for the complete genome dataset of the articl

Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

International audienceBackground: Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. Results: To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. Conclusions: Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers

High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119.

International audienceWe report here the high-quality draft genome sequences of two strains of Xanthomonas axonopodis pv. glycines, the causal agent of bacterial pustule on soybeans. Comparison of these genomes with those of phylogenetically closely related pathovars of Xanthomonas spp. will help to understand the mechanisms involved in host specificity and adaptation to host plants