title: RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum.
abstract: BACKGROUND
  The genome of Fusarium graminearum has been sequenced and annotated previously, 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.
  
  
  RESULTS
  We identified and revised 655 incorrectly predicted 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. 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 many of these could be missed genes. Finally, we identified the 5' UTR and/or 3' UTR sequences of 7666 genes. 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.
  
  
  CONCLUSIONS
  We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum.
authors: Plant Research International, P.O. Box 6708 PB, Wageningen, The Netherlands.
authors: Chunzhao
authors: C
authors: Zhao
authors: Cees
authors: C
authors: Waalwijk
authors: Pierre J G M
authors: PJ
authors: de Wit
authors: Dingzhong
authors: D
authors: Tang
authors: Theo
authors: T
authors: van der Lee
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D005670:Fusarium / Q000235:genetics* / Q000254:growth & development; D005800:Genes, Fungal / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011786:Quality Control; D017393:RNA Editing / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D022821:RNA Splice Sites; D012331:RNA, Fungal; D020506:Untranslated Regions