title: Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
abstract: The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. 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.
authors.affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.
authors.forename: Seungill
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.
authors.forename: Myung-Shin
authors.initials: MS
authors.lastname: Kim
authors.affiliation: Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Kim
authors.affiliation: Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea Department of Horticulture, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea.
authors.forename: Seon-In
authors.initials: SI
authors.lastname: Yeom
authors.affiliation: Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.
authors.forename: Kyeongchae
authors.initials: K
authors.lastname: Cheong
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
authors.forename: Ki-Tae
authors.initials: KT
authors.lastname: Kim
authors.affiliation: Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea.
authors.forename: Jongbum
authors.initials: J
authors.lastname: Jeon
authors.affiliation: Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, Korea.
authors.forename: Sunggil
authors.initials: S
authors.lastname: Kim
authors.affiliation: National Institute of Horticultural and Herbal Science, RDA, Suwon, Korea.
authors.forename: Do-Sun
authors.initials: DS
authors.lastname: Kim
authors.affiliation: National Institute of Agricultural Science, RDA, Suwon, Korea.
authors.forename: Seong-Han
authors.initials: SH
authors.lastname: Sohn
authors.affiliation: Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Seoul National University, Seoul, Korea Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea doil@snu.ac.kr.
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
mesh_terms: D003001:Cloning, Molecular; D017343:Genes, Plant / Q000502:physiology*; D058977:Molecular Sequence Annotation; D019697:Onions / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics*; D059467:Transcriptome / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant
keywords: de novo transcriptome; gene prediction; non-coding sequence; onion; reference gene set