Wheat Genome Structural Annotation using a Modular and Evidence-Combined Annotation Pipeline.

Bread wheat is a major global cereal grain essential to human nutrition. Research on improving important traits in wheat highly depending on knowing identities of trait associated gene loci. With the availability of high-quality wheat genome assembly sequence, one crucial objective in the post-genomics era is to identify functional genetic elements. Numerous pipelines have been developed for gene discovery. However, some are not suitable for annotating large and highly repetitive genome such as wheat, resulting in high false positive prediction rate, while others provide high quality annotation but are computational intensive, lack of reproducibility and require extensive manual processing steps. Here we introduce a custom pipeline MEGAP – modular and evidence-combined genome annotation pipeline – that leverages on strength of diverse gene evidence resources to increase prediction accuracy. Applying this pipeline on wheat genome, we masked 85% genome as repeat and identified 164,785 transcripts loci, of which 129,149 are high confidence gene models with average mRNA size of 1,271 bp. Overall, our annotation pipeline shows balance between annotation quality and efficiency, sustainability and reproducibility, which are essential for our new genome annotation projects in the future.