Plant Genome Reannotation Using NextGen Sequences

Gene structure annotation is a fundation for computational analysis of gene function and genome evolution. Therefore a high quality and stable gene set for a species is highly desirable. We have reannotated several plant genomes and highest mapping ratio is 90% between versions using our in-house gene annotation pipeline. Here we report a new pipeline, gene model improvement pipline (GMI). GMI uses transcriptome to update the gene set if and only if transcriptome data dictate. With short read transcriptome assemblies and/or ESTs/cDNA, we achieved about 95% mapping ratio in several plant genomes and 99% mapping ratio using Iso-Seq in Arabidopsis. The Iso-Seq raw reads were corrected. Iso-Seq sequences are near full length and high quality and mapping ratio by GMI using Iso-Seq is much better in Arabidopsis, one of the best annotated plant genomes.