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 disease of potato and tomato plants. Several other Phytophthora species infect potato and tomato. Disease management strategies require correct identification of the pathogen as different species call for different controlling strategies. Correct gene models and annotations are key to successfully study any organism. In the present study we used RNA-Seq data to modify the gene annotations of P. infestans. We have used Trinity and PASA to update the existing gene models, identify novel genes and alternative splicing events. Altsplicing has been not been previously studied in P. infestans. We have used genomeguided Trinity to first align the reads to the genome and then PASA was used to align the transcripts obtained by Trinity back to the T30-4 genome. Out of 18,179 genes currently annotated in the genome, we have modified ~8,000 genes with additions of untranslated regions, changes in CDS boundaries and gene merging. We have also identified ~800 genes with alternative splicing which were initially not known. Apart from the current genome annotations, we have identified ~8,000 overlapping transcripts that were not having any corresponding genes in the current annotation. Out of these 8,000 transcripts we have identified ~400 P. infestans genes which were previously not annotated. This study will help researchers in many ways: correctly identifying any signal peptides present in the gene affecting their localization, identification of transcription factor binding sites, any additional exons affecting the enzymatic activity of certain genes. To conclude we find that RNA-Seq is a great tool to improve gene models and identify novel transcripts.