title: Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.
abstract: Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan yasyas@kais.kyoto-u.ac.jp mori@ishikawa-pu.ac.jp.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Yasui
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan.
authors.forename: Mariko
authors.initials: M
authors.lastname: Ueno
authors.affiliation: NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861-1192, Japan.
authors.forename: Katsuhiro
authors.initials: K
authors.lastname: Matsui
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Katsube-Tanaka
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan.
authors.forename: Soo Jung
authors.initials: SJ
authors.lastname: Yang
authors.affiliation: Faculty of Applied Life Science, Niigata University of Pharmacy and Applied Life Science, Akiha-ku, Niigata 956-8603, Japan.
authors.forename: Jotaro
authors.initials: J
authors.lastname: Aii
authors.affiliation: Faculty of Applied Life Science, Niigata University of Pharmacy and Applied Life Science, Akiha-ku, Niigata 956-8603, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Sato
authors.affiliation: Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 308 Suematsu, Nonoichi, Ishikawa 912-8836, Japan yasyas@kais.kyoto-u.ac.jp mori@ishikawa-pu.ac.jp.
authors.forename: Masashi
authors.initials: M
authors.lastname: Mori
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D020451:Contig Mapping; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019612:Fagopyrum / Q000235:genetics*; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D000069600:Plant Breeding; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: GBS marker; buckwheat; database usage; draft sequence; heteromorphic self-incompatibility