Arabidopsis thaliana Iso-Seq and Gene Annotation

The ability to generate full-length or nearly full-length transcripts with PacBio Iso-Seq allows us to re-examine both lightly and heavily-curated plant genome annotations. We report on an initial study of the Arabidopsis thaliana TAIR 10 annotation using approximately 23,000 Iso-Seq transcripts generated at the JGI. With this somewhat small sample we were able to recover close to 60% (16,342 gene models) of TAIR 10 gene models with full length support. In addition, new gene loci, some of which have functional domains, were also recovered. In terms of existing models, we were able to add the UTR on approximately 1,790 loci, and some support for existing model mergers or splits was found in 29 cases. With larger Iso-Seq data sets, we could address the issue of support for full set and alternative splicing in the TAIR10 annotation.