RNA-Seq for identifying novel transcripts, alternate splicing and improving current gene annotations in plant pathogen Phytophthora infestans

Phytophthora infestans is responsible for the late blight diseases of potato and tomato plants. Correct gene models and annotations are important for studying this pathogen. In this study we used RNA-Seq data to modify the current annotations of the P. infestans genome. Trinity and PASA were used to update the existing gene models, identify new genes, and identify alternative splicing events. We used genome-guided Trinity to first align the reads to the T30-4 reference genome, and then PASA to align the transcripts obtained by Trinity back to the genome. Out of 18,179 genes currently annotated in the latest public release of the genome, our analysis resulted in the modification of ~10,000 genes with additions of untranslated regions, changes in CDS boundaries, and gene merging. About ~800 genes exhibited alternative splicing, which involved intron retention, alternate start and ending exons and alternate donor/acceptor sites. Nearly 8,000 transcripts did not map to any genes in public annotation, and up to 400 of these appeared to represent new protein-coding genes. This study will help researchers since signal peptides and transcription factor binding sites can be more accurately identified once the 5' ends of genes are known, since protein function can be better-predicted, and since gene expression studies can assign transcripts to the proper open reading frame.