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SESSION 1: FUSARIUM – GENETICS, GENOMICS AND SYSTEMS BIOLOGY P1 - RNA-Seq analysis reveals new gene models and alternative splicing in the Fusarium graminearum C. Zhao 1,2,3,4 , C. Waalwijk 1,2 , P. J. G. M. de Wit 2,5 , D. Tang 3 , T. van der Lee 1,2 1 Plant Research International, Wageningen, The Netherlands; 2 Graduate School Experimental Plant Sciences, Wageningen, The Netherlands; 3 State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; 4 Graduate University of Chinese Academy of Sciences, Beijing 100049, China; 5Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands E-mail: theo.vanderlee@wur.nl The genome of Fusarium graminearum has been sequenced and annotated, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum. In total 25,720,650 reads were generated from RNA-Seq. Using the genome annotation in Broad database, transcripts were detected for 84% of the predicted genes. 74.8% of the reads matched to exonic regions, 10.6% to untranslated regions (UTRs), 12.9% to intergenic regions and only 1.7% to intronic regions. We identified and revised 655 incorrectly predicted gene models (10% of all tested gene models), including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. In-frame analysis showed that the majority of the alternatively spliced transcripts identified in F. graminearum cause premature termination codons (PTCs), of which most are located in intronic regions and these transcripts are potential targets of the nonsense mediated mRNA decay (NMD). Apart from PTC isoforms, some alternatively spliced transcripts encoding proteins with diverse length were identified. The effects of the diversity in length on the biological function of proteins are still unknown, but several functions including binding properties, intracellular localization, enzymatic activity or stability might be affected. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that some of these could be genes that were missed in the annotation. Finally, we identified the 5’ UTR and/or 3’ UTR sequences of 7666. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons. Our results demonstrate that posttranscriptional regulations can be studied efficiently using our developed RNA-Seq analysis pipeline and may be important in adaptation of F. graminearum to changing external environmental conditions that occur during different growth stages. Keywords: transcription, RNA-Seq, regulation, secondary metabolism 93
SESSION 1: FUSARIUM – GENETICS, GENOMICS AND SYSTEMS BIOLOGY P2 - Genome-wide transcriptional response to ambient pH and Pac1 regulatory factor in Fusarium graminearum J. Merhej 1 , N. Ponts 1 , F. Richard-Forget 1 , C. Barreau 1,2 1 INRA, UR1264 MycSA, 71 Avenue Edouard Bourlaux, CS20032, 33883 Villenave d'Ornon-France; 2 CNRS, UR1264 MycSA, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon-France E-mail: cbarreau@bordeaux.inra.fr The pathogenic fungus Fusarium graminearum produces type B trichothecene mycotoxins during cereal plants infection. Trichothecenes accumulate in cereal grains and represent a threat for health. Expression studies of the Tri genes implicated in trichothecene biosynthesis have demonstrated that acidic extracellular pH is a determinant inducer. Actually, it has been shown that the FgPac1 pH regulatory factor negatively regulates the expression of Tri genes under neutral or basic pHs. Beside their role in regulating secondary metabolites in fungi, Pac transcription factors are known to regulate various classes of genes, especially the genes whose roles involve communication with the environment. In this study, a genome-wide transcriptional analysis conducted in two different pH conditions using a strain deleted for FgPac1 and a strain expressing a constitutively active form of FgPac1was carried out to investigate the global regulation by the pH in F. graminearum. The data obtained identified a set of genes related to various functions whose expression is affected by the change in pH. Our results also point toward a potential role of a regulation by calcium in response to the ambient pH and identified a γ-aminobutyric acid (GABA) shunt activated in response to acidic pH. Finally, a clustering approach followed by cisregulatory motifs search highlights the presence of complex stress-response regulatory circuits impacted by the change in external pH. Keywords: Fusarium, pH, Pac1, microarrays 94
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Bordeaux EFS12 12 th European Fusar
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TABLE OF CONTENTS Welcome from the
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4 SPONSORSHIP The 12 th European Fu
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8 13:00 - 14:00 Lunch 14:00 - 15:00
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10 Session 4: Genetics of Hosts - P
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12 Thursday, May 16 th Session 6: F
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Evidence for birth-and-death evolut
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Future challenges of Fusarium and m
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P35 - Screening deoxynivalenol in o
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P76 - Fusarium verticillioides and
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P113 - Agronomic practices and risk
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ORAL PRESENTATIONS 25
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KEYNOTE LECTURE SESSION 1: FUSARIUM
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SESSION 1: FUSARIUM - GENETICS, GEN
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KEYNOTE LECTURE SESSION 2: SECONDAR
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SESSION 6: FUTURE CHALLENGE FOR EUR
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de Hoog G. S., 89, 114, 236 de Kler
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Ponts N., 33, 36, 82, 94, 104, 106,
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BOKU-University of Natural Resource
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touatisihem03@yahoo.fr He Xinyao In
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steve.oliver@bioc.cam.ac. uk Ortega
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Subramaniam Gopal Agriculture and A
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