ECCB2014_Poster_B24

<p>How to Design a good RNA-Seq experiment in an<br>interdisciplinary context?</p

Online exploration of transcription profiles along B. subtilis and S. aureus

International audienceGenoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome data sets available for Bacillus subtilis and Staphylococcus aureus. Websites and source code freely accessible at https:/

Comparative analysis of transposable elements in the Magnaporthe oryzae/grisea clade

Magnaporthe oryzae is a successful pathogen of crop plants and a major threat for food production. This species gathers pathogens of different Poaceaes, and causes the main fungal disease of rice worldwide and severe epidemics on wheat in South America. The evolutionary genomics of Magnaporthe oryzae project aims at characterizing genomic determinants and evolutionary events involved in the adaptation of this fungus to different host plants. Such evolution may be driven by variations in Transposable Elements (TEs) and gene content as well as modifications of coding and regulatory sequences. Indeed, TEs are essential for shaping genomes and are a source of mutations and genome re-organizations. We performed a comparative analysis of TEs in 9 isolates from the M. oryzae/grisea clade differing in their host specificity using a reference TEs consensus library (Mg7015_Refs_TE) made from M. oryzae 70-15 reference genome. We used REPET pipelines (http://urgi.versailles.inra.fr/Tools/REPET) to detect ab initio and classify TEs in M. oryzae 70-15 according to functional features (LTR, ITR, RT, transposase, etc.). After manual curation on consensus provided by the TEdenovo pipeline, we used the resulting consensus of TE families (Mg7015_Refs_TE) to annotate the 9 genome copies including nested and degenerated ones using TEannot pipeline. We will present results obtained for Mg7015_Refs_TE classification, their annotation and preliminary comparison in M. oryzae/grisea species studied regarding correlation with phylogeny

Distribution and evolution of transposable elements in the Magnaporthe oryzae/grisea clade

Magnaporthe oryzae is a successful pathogen of crop plants and a major threat for food production. This species gathers pathogens of different Poaceaes, and causes the main fungal disease of rice worldwide and severe epidemics on wheat in South America. The evolutionary genomics of Magnaporthe oryzae project aims at characterizing genomic determinants and evolutionary events involved in the adaptation of fungus to different host plants. Such evolution may rely on variations in Transposable Elements (TEs) and gene content as well as modification of coding and regulatory sequences. Indeed, TEs are essential for shaping genomes and are a source of mutations and genome re-organizations. We performed a comparative analysis of TEs in 9 isolates from the M. oryzae/grisea clade differing in their host specificity using a reference TEs consensus library (Mg7015_Refs_TE) made from M. grisea 70-15 reference genome. We used REPET pipelines (http://urgi.versailles.inra.fr/Tools/REPET) to detect ab initio and classify TEs in M. grisea 70-15 according to functional features (LTR, ITR, RT, transposase, etc.). After manual curation on consensus provided by the TEdenovo pipeline, we used the resulting consensus of TE families (Mg7015_Refs_TE) to annotate the 9 genome copies including nested and degenerated ones using TEannot pipeline. We will present results obtained for Mg7015_Refs_TE classification, their annotation, distribution along the genome and preliminary results provided by comparison in M. oryzae/grisea species studied regarding correlation with phylogeny and host specificity

Deciphering regulatory networks of the fish pathogen Flavobacterium psychrophilum by primary transcriptome mapping

Deciphering regulatory networks of the fish pathogen [i]Flavobacterium psychrophilum[/i] by primary transcriptome mapping. 4. International Conference on Flavobacterium - Flavobacterium 201

How to Design a good RNA-Seq experiment in an interdisciplinary context?

How to Design a good RNA-Seq experiment in an interdisciplinary context?. European conference on Computational Biolog

Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis.

In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis. Rho inactivation strongly affected gene expression in B. subtilis, as assessed by transcriptome and proteome analysis of a rho-null mutant during exponential growth in rich medium. Subsequent physiological analyses demonstrated that a considerable part of Rho-controlled transcription is connected to balanced regulation of three mutually exclusive differentiation programs: cell motility, biofilm formation, and sporulation. In the absence of Rho, several up-regulated sense and antisense transcripts affect key structural and regulatory elements of these differentiation programs, thereby suppressing motility and biofilm formation and stimulating sporulation. We dissected how Rho is involved in the activity of the cell fate decision-making network, centered on the master regulator Spo0A. We also revealed a novel regulatory mechanism of Spo0A activation through Rho-dependent intragenic transcription termination of the protein kinase kinB gene. Altogether, our findings indicate that distinct Rho-controlled transcripts are functional and constitute a previously unknown built-in module for the control of cell differentiation in B. subtilis. In a broader context, our results highlight the recruitment of the termination factor Rho, for which the conserved biological role is probably to repress pervasive transcription, in highly integrated, bacterium-specific, regulatory networks

The GEMO project: Analysis and comparison of genomes of the fungal pathogen Magnaporthe oryzae

Poster + Résumé Court proceeding online open accèsGEMO is a project of comparative fungal genomics focusing on related species and sub-species from the Magnaporthe grisea/oryzae species complex. The dataset gathered by the GEMO project encompasses 10 Magnaporthe genomes: 9 M. oryzae genomes from isolates specifically pathogenic on Oryza sativa, Triticum sp, Setaria sp or Eleusine sp, and 1 from a M. grisea isolate specifically pathogenic on Digitaria sp. In this project, the MIG in collaboration with the URGI-Bioger platform are realizing a comparative analysis of these genomes which consists of automatic annotation of genes, structural comparison of these genomes and detection of positive selection in orthologs across this taxonomic sampling [1]. In addition, a detailed evolutionary and syntenic analysis will be performed on two particular groups of genes encoding putative effectors known to be involved in pathogenicity: small secreted proteins (SSPs) and genes involved in the biosynthesis of secondary metabolites. The first step will be to establish the repertory of genes belonging to these families in the 10 available genomes. Different sources of information will be used, such as a set of lists of secondary metabolism genes already established [1], a list of SSP to be compiled fromdifferent sources (transcriptomes, proteomes, effectomes), the automatic annotations of the 10available genomes, and RNAseq data from in planta early infection. We will then address three questions: 1) Are SSP and secondary metabolism genes more subject to birth/death/duplication processes and to horizontal gene transfers, than the rest of the coding genome? 2) Are transposable elements more frequently associated with SSP and secondarymetabolism genes than in the rest of the coding genome? 3) Are SSP and secondary metabolism genes more targeted by positive selection than the rest of the coding genome? All this information will allow depicting the evolutionary history of some pathogenicity and host-specificity related genes in Magnaporthe. [1] Collemare 2007. Communication entre les plantes et leurs agents pathogènes : rôle des métabolites secondaires dans la reconnaissance du champignon Magnaporthe grisea par le riz. PhD Thesis

GEMO project: Genetic bases of pathogenicity and host specificity analyzed through comparative and evolutionary genomics in the model fungus Magnaporthe

Session 3 : Génomique des Champignons Poster n°3.4absen