Expressed Sequence Tags from the oomycete Plasmopara halstedii, an obligate parasite of the sunflower

<p>Abstract</p> <p>Background</p> <p>Sunflower downy mildew is a major disease caused by the obligatory biotrophic oomycete <it>Plasmopara halstedii</it>. Little is known about the molecular mechanisms underlying its pathogenicity. In this study we used a genomics approach to gain a first insight into the transcriptome of <it>P. halstedii</it>.</p> <p>Results</p> <p>To identify genes from the obligatory biotrophic oomycete <it>Plasmopara halstedii </it>that are expressed during infection in sunflower (<it>Helianthus annuus </it>L.) we employed the suppression subtraction hybridization (SSH) method from sunflower seedlings infected by <it>P. halstedii</it>. Using this method and random sequencing of clones, a total of 602 expressed sequence tags (ESTs) corresponding to 230 unique sequence sets were identified. To determine the origin of the unisequences, PCR primers were designed to amplify these gene fragments from genomic DNA isolated either from <it>P. halstedii </it>sporangia or from <it>Helianthus annuus</it>. Only 145 nonredundant ESTs which correspond to a total of 373 ESTs (67.7%) proved to be derived from <it>P. halstedii </it>genes and that are expressed during infection in sunflower. A set of 87 nonredundant sequences were identified as showing matches to sequences deposited in public databases. Nevertheless, about 7% of the ESTs seem to be unique to <it>P. halstedii </it>without any homolog in any public database.</p> <p>Conclusion</p> <p>A summary of the assignment of nonredundant ESTs to functional categories as well as their relative abundance is listed and discussed. Annotation of the ESTs revealed a number of genes that could function in virulence. We provide a first glimpse into the gene content of <it>P. halstedii</it>. These resources should accelerate research on this important pathogen.</p

Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara halstedii race 300.

International audienceThe resistance of sunflower to Plasmopara halstedii is conferred by major resistance genes denoted Pl. Previous genetic studies indicated that the majority of these genes are clustered on linkage groups 8 and 13. The Pl6 locus is one of the main clusters to have been identified, and confers resistance to several P. halstedii races. In this study, a map-based cloning strategy was implemented using a large segregating F2 population to establish a fine physical map of this cluster. A marker derived from a bacterial artificial chromosome (BAC) clone was found to be very tightly linked to the gene conferring resistance to race 300, and the corresponding BAC clone was sequenced and annotated. It contains several putative genes including three toll-interleukin receptor-nucleotide binding site-leucine rich repeats (TIR-NBS-LRR) genes. However, only one TIR-NBS-LRR appeared to be expressed, and thus constitutes a candidate gene for resistance to P. halstedii race 300

Analyse transcriptomique du développement du grain de blé (Triticum aestivum) (implication des E3 ligases et des gènes relatifs aux hormones)

Le blé tendre, Triticum aestivum, représente une grande ressource dans l alimentation humaine mais également dans l industrie. En conséquence, la taille finale du grain de blé constitue une cible privilégiée des programmes de sélections variétales. Pour ces raisons, comprendre les mécanismes moléculaires qui contrôlent le développement du grain, en particulier lors des phases précoces de la mise en place des structures cellulaires et leur remplissage par des réserves, constitue un enjeu majeur. Le développement du grain de blé est un processus complexe qui nécessite l intervention séquentielle ou combinée d un très grand nombre de gènes et de voies métaboliques. Parmi ces voies, le métabolisme carboné (en particulier celui du saccharose), les voies de signalisation par les hormones et la voie Ubiquitine / Protéasome 26S (UPS) semblent jouer un rôle déterminant dans la taille finale et donc le rendement en grain chez les céréales. Pour étudier le développement du grain de blé tendre, des plantes de la variété Récital ont été cultivées en serre dans des conditions optimales sans contraintes. Les grains ont été récoltés à onze stades de développement après floraison, allant de 40CJ (soit deux jours après floraison) à 500CJ (soit 25 jours après floraison). Les ARN totaux ont été extraits à partir de ces grains et utilisés pour analyser l expression des gènes par une approche transcriptomique, soit en utilisant une lame dédiée , soit en utilisant une lame Nimblegen comprenant 39 179 gènes. Une analyse différentielle utilisant le test LIMMA a permis d identifier 9284 gènes différentiellement exprimés. L analyse globale de ces gènes a montré que des modifications transcriptionnelles majeures ont lieu entre les stades 80 et 120 CJ ainsi qu entre 220 et 240CJ. La répartition de ces 9284 en 10 clusters, en fonction de leurs profils d expression, permet d identifier les gènes activés en début de la phase de division cellulaire chez le grain, ceux activés pendant la phase de remplissage et ceux présentant un profil dit en cloche . Parmi les gènes différentiellement exprimés, nous nous sommes intéressés à ceux qui codent pour des E3 ligases impliquées dans la voie UPS et aux gènes relatifs à 7 hormones végétales (auxine, acide abscissique, acide jasmonique, brassinostéroïdes, cytokinines, gibbérellines et éthylène). Nous avons alors identifié 173 gènes codant pour des E3 ligases (dont certaines sont également des récepteurs hormonaux) et 126 gènes impliqués dans les voies hormonales. Un modèle global décrivant la chronologie d intervention de ces gènes a été proposé. La majorité des gènes E3 de type SCF (SKP1-Cullin-Fbox), APC/C, Cul3-BTB et Ubox interviendrait dans les phases précoces du développement du grain de blé. Parallèlement, la majorité des gènes relatifs à l auxine, à l acide jasmonique et aux brassinostéroïdes interviendrait lors des phases de divisions cellulaires alors que les gènes relatifs à l éthylène et à l acide abscissique interviendraient dans les phases de remplissage. Par ailleurs, une méta-analyse a été réalisée et a permis d identifier 26 gènes candidats codants pour des E3 ligases ainsi que de 12 gènes candidats impliqués dans les voies hormonales qui seraient préférentiellement exprimés dans l albumen, un tissu du grain à haute valeur agro-économique. Le modèle proposé et l identification de ces gènes candidats établissent un cadre pour de futures études visant à comprendre les mécanismes moléculaires contrôlant le développement du grain de blé.Wheat grain is an important source of food, feed, and industrial raw materials, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the Ubiquitin-Proteasome System (UPS). Among several implications of the UPS, it has become clear that it plays an essential role in hormone signaling. In particular E3 ubiquitin ligases, from the UPS, have been demonstrated to play critical roles in hormone perception and signal transduction. During these work, wheat cv. Recital were grown in optimum growth conditions. By comparing eleven consecutive time-points from 40CJ (2 days after anthesis) to 500CJ (around 25 days after anthesis), 9284 differentially expressed genes were identified during this study. A comparison of these genes in terms of time revealed dynamic transcript accumulation profiles with major re-programming events that occurred during the time intervals of 80-120Cdays and 220-240Cdays. The gene expression comparison allows observing genes potentially involved in cell division or grain filling stage. An emphasis was made on the E3 ligases and hormone-related genes (Abscisic acid, Auxin, Brassinosteroid, Cytokinine, Gibberellic acid, Ethylene and Jasmonic acid). 173 E3 ligase coding genes and 126 hormone related genes were found to be differentially expressed during the cell division and grain filling stages, with a different expression profile for each family. A model describing the timing of the involvement of these genes is proposed to provide a framework for the design of future experiments and for the identification of genes and pathways for further characterization. A majority of the E3 SCF (SKP1-Cullin-F-box), APC/C, Cul3-BTB and Ubox are found expressed in early wheat developmental stages (cell division stage). A majority of auxin, jasmonic acid and brassinostéroïde related genes were found to be up-regulated in early wheat developmental stages while ethylene and abscisic acid related genes were found to be activated during grain filling stage. The differential expression of genes involved in E3 ligase pathways and plant hormone signalling suggested that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. A meta-analysis of these genes led to the identification of 26 E3 ligase candidate genes and 12 hormones-related candidate genes that are preferentially expressed in the endosperm. The functional model that we proposed and the identification of candidate genes should help to better understand wheat grain development.CLERMONT FD-Bib.électronique (631139902) / SudocSudocFranceF

Genome-wide analysis, classification, expression and interaction of Physcomitrella patens SKP1-like ( PpSKP ) and F-box ( FBX ) genes

International audienc

Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.).

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat

Characterization of 4 transcription factors TaNAC during the seed development in response to a thermal stress in the bread wheat Triticum aestivum

Poster ID 309Characterization of 4 transcription factors TaNAC during the seed development in response to a thermal stress in the bread wheat Triticum aestivum. Plant Biology Europe EPSO/FESP

Towards the understanding of the heat stress in wheat grain development

Poster ID 313Towards the understanding of the heat stress in wheat grain development. Plant Biology Europe EPSO/FESP

Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower-2

<p><b>Copyright information:</b></p><p>Taken from "Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower"</p><p>http://www.biomedcentral.com/1471-2180/7/110</p><p>BMC Microbiology 2007;7():110-110.</p><p>Published online 6 Dec 2007</p><p>PMCID:PMC2242796.</p><p></p>like protein [GenBank:]. NT indicates the N-terminus trauncation, L1 and L2 indicate two conserved loop. The asterisk indicates the conserved Tryptophane amino acid within the L2 loop. The potential Peptide signal is also indicated