Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
Bottom Line: Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion.The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data.Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.
Affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.Show MeSH
Mentions: Through the evaluation, we discovered miss-annotated genes derived from the six-frame translation. To verify the reasons for the miss-annotation, we examined the detailed structure of each gene model and identified representative cases among the validation results (Fig. 3). We found that the miss-annotations from the six-frame translation were caused by the retention of introns and the translation of the inappropriate region or strand (Fig. 3). For the corresponding regions, ISGAP successfully performed the gene annotations (Fig. 3). Hence, ISGAP could detect and extract accurate exon regions based on the structure of the reference protein and ab initio gene models, whereas six-frame translation could not.Figure 3.
Affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.