title: Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences.
abstract: BACKGROUND
  Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, downy mildew remains a major threat to the sunflower crop. Very few genomic, genetic and molecular resources are currently available to study this pathogen. Using a 454 sequencing method, expressed sequence tags (EST) during the interaction between H. annuus and P. halstedii have been generated and a search was performed for sites in putative effectors to show polymorphisms between the different races of P. halstedii.
  
  
  RESULTS
  A 454 pyrosequencing run of two infected sunflower samples (inbred lines XRQ and PSC8 infected with race 710 of P. halstedii, which exhibit incompatible and compatible interactions, respectively) generated 113,720 and 172,107 useable reads. From these reads, 44,948 contigs and singletons have been produced. A bioinformatic portal, HP, was specifically created for in-depth analysis of these clusters. Using in silico filtering, 405 clusters were defined as being specific to oomycetes, and 172 were defined as non-specific oomycete clusters. A subset of these two categories was checked using PCR amplification, and 86% of the tested clusters were validated. Twenty putative RXLR and CRN effectors were detected using PSI-BLAST. Using corresponding sequences from four races (100, 304, 703 and 710), 22 SNPs were detected, providing new information on pathogen polymorphisms.
  
  
  CONCLUSIONS
  This study identified a large number of genes that are expressed during H. annuus/P. halstedii compatible or incompatible interactions. It also reveals, for the first time, that an infection mechanism exists in P. halstedii similar to that in other oomycetes associated with the presence of putative RXLR and CRN effectors. SNPs discovered in CRN effector sequences were used to determine the genetic distances between the four races of P. halstedii. This work therefore provides valuable tools for further discoveries regarding the H. annuus/P. halstedii pathosystem.
authors: INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France.
authors: Falah
authors: F
authors: As-sadi
authors: Sébastien
authors: S
authors: Carrere
authors: Quentin
authors: Q
authors: Gascuel
authors: Thibaut
authors: T
authors: Hourlier
authors: David
authors: D
authors: Rengel
authors: Marie-Christine
authors: MC
authors: Le Paslier
authors: Amandine
authors: A
authors: Bordat
authors: Marie-Claude
authors: MC
authors: Boniface
authors: Dominique
authors: D
authors: Brunel
authors: Jérôme
authors: J
authors: Gouzy
authors: Laurence
authors: L
authors: Godiard
authors: Patrick
authors: P
authors: Vincourt
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D020451:Contig Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D006368:Helianthus / Q000235:genetics* / Q000469:parasitology; D008969:Molecular Sequence Data; D009868:Oomycetes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D013997:Time Factors; D059467:Transcriptome