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Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, Jeon J, Kim S, Kim DS, Sohn SH, Lee YH, Choi D - DNA Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.

Show MeSH
Representative cases of well-annotated genes predicted by ISGAP compared with the genes predicted by six-frame translation. The genes predicted by ISGAP and six-frame translation are shown, as well as the onion, RefSeq, reference, and ab initio gene models. The plus and minus signs in the brackets indicate the strand of mapped or predicted genes. (A and B) Cases of genes containing multiple exons; (C) gene annotation with the correct region. (D) Gene annotation with the correct strand.
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DSU035F3: Representative cases of well-annotated genes predicted by ISGAP compared with the genes predicted by six-frame translation. The genes predicted by ISGAP and six-frame translation are shown, as well as the onion, RefSeq, reference, and ab initio gene models. The plus and minus signs in the brackets indicate the strand of mapped or predicted genes. (A and B) Cases of genes containing multiple exons; (C) gene annotation with the correct region. (D) Gene annotation with the correct strand.

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.


Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, Jeon J, Kim S, Kim DS, Sohn SH, Lee YH, Choi D - DNA Res. (2014)

Representative cases of well-annotated genes predicted by ISGAP compared with the genes predicted by six-frame translation. The genes predicted by ISGAP and six-frame translation are shown, as well as the onion, RefSeq, reference, and ab initio gene models. The plus and minus signs in the brackets indicate the strand of mapped or predicted genes. (A and B) Cases of genes containing multiple exons; (C) gene annotation with the correct region. (D) Gene annotation with the correct strand.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379974&req=5

DSU035F3: Representative cases of well-annotated genes predicted by ISGAP compared with the genes predicted by six-frame translation. The genes predicted by ISGAP and six-frame translation are shown, as well as the onion, RefSeq, reference, and ab initio gene models. The plus and minus signs in the brackets indicate the strand of mapped or predicted genes. (A and B) Cases of genes containing multiple exons; (C) gene annotation with the correct region. (D) Gene annotation with the correct strand.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.

Show MeSH