EFS12- Book of abstracts - Contact
EFS12- Book of abstracts - Contact
EFS12- Book of abstracts - Contact
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SESSION 1: FUSARIUM – GENETICS, GENOMICS AND SYSTEMS BIOLOGY<br />
P1 - RNA-Seq analysis reveals new gene models and<br />
alternative splicing in the Fusarium graminearum<br />
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<br />
1 Plant Research International, Wageningen, The Netherlands; 2 Graduate School Experimental Plant<br />
Sciences, Wageningen, The Netherlands; 3 State Key Laboratory <strong>of</strong> Plant Cell and Chromosome<br />
Engineering, Institute <strong>of</strong> Genetics and Developmental Biology, Chinese Academy <strong>of</strong> Sciences, Beijing<br />
100101, China; 4 Graduate University <strong>of</strong> Chinese Academy <strong>of</strong> Sciences, Beijing 100049, China;<br />
5Wageningen University, Laboratory <strong>of</strong> Phytopathology, Wageningen, The Netherlands<br />
E-mail: theo.vanderlee@wur.nl<br />
The genome <strong>of</strong> Fusarium graminearum has been sequenced and annotated, but<br />
correct gene annotation remains a challenge. In addition, posttranscriptional<br />
regulations, such as alternative splicing and RNA editing, are poorly understood in<br />
F. graminearum. Here we took advantage <strong>of</strong> RNA-Seq to improve gene<br />
annotations and to identify alternative splicing and RNA editing in F.<br />
graminearum. In total 25,720,650 reads were generated from RNA-Seq. Using the<br />
genome annotation in Broad database, transcripts were detected for 84% <strong>of</strong> the<br />
predicted genes. 74.8% <strong>of</strong> the reads matched to exonic regions, 10.6% to<br />
untranslated regions (UTRs), 12.9% to intergenic regions and only 1.7% to<br />
intronic regions. We identified and revised 655 incorrectly predicted gene models<br />
(10% <strong>of</strong> all tested gene models), including revisions <strong>of</strong> intron predictions, intron<br />
splice sites and prediction <strong>of</strong> novel introns. 231 genes were identified with two or<br />
more alternative splice variants, mostly due to intron retention. In-frame analysis<br />
showed that the majority <strong>of</strong> the alternatively spliced transcripts identified in F.<br />
graminearum cause premature termination codons (PTCs), <strong>of</strong> which most are<br />
located in intronic regions and these transcripts are potential targets <strong>of</strong> the<br />
nonsense mediated mRNA decay (NMD). Apart from PTC is<strong>of</strong>orms, some<br />
alternatively spliced transcripts encoding proteins with diverse length were<br />
identified. The effects <strong>of</strong> the diversity in length on the biological function <strong>of</strong><br />
proteins are still unknown, but several functions including binding properties,<br />
intracellular localization, enzymatic activity or stability might be affected.<br />
Interestingly, the expression ratios between different transcript is<strong>of</strong>orms appeared<br />
to be developmentally regulated. Surprisingly, no RNA editing was identified in F.<br />
graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were<br />
identified and our analysis indicates that some <strong>of</strong> these could be genes that were<br />
missed in the annotation. Finally, we identified the 5’ UTR and/or 3’ UTR<br />
sequences <strong>of</strong> 7666. A number <strong>of</strong> representative novel gene models and<br />
alternatively spliced genes were validated by reverse transcription polymerase<br />
chain reaction and sequencing <strong>of</strong> the generated amplicons.<br />
Our results demonstrate that posttranscriptional regulations can be studied<br />
efficiently using our developed RNA-Seq analysis pipeline and may be important<br />
in adaptation <strong>of</strong> F. graminearum to changing external environmental conditions<br />
that occur during different growth stages.<br />
Keywords: transcription, RNA-Seq, regulation, secondary metabolism<br />
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