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Title: Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.
Authors: Yasui, Yasuo  kyouindb  KAKEN_id
Hirakawa, Hideki
Ueno, Mariko
Matsui, Katsuhiro
Katsube-Tanaka, Tomoyuki
Yang, Soo Jung
Aii, Jotaro
Sato, Shingo
Mori, Masashi
Author's alias: 安井, 康夫
Keywords: buckwheat
draft sequence
database usage
GBS marker
heteromorphic self-incompatibility
Issue Date: 1-Jun-2016
Publisher: Oxford University Press
Journal title: DNA research : an international journal for rapid publication of reports on genes and genomes
Volume: 23
Issue: 3
Start page: 215
End page: 224
Abstract: Buckwheat (Fagopyrum esculentumMoench; 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.
Description: 世界初となるソバの全ゲノム解読に成功 -ソバの安全性、高品質性、収量安定性の鍵となる遺伝情報の発見-. 京都大学プレスリリース. 2016-04-13.
Rights: © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
URI: http://hdl.handle.net/2433/210200
DOI(Published Version): 10.1093/dnares/dsw012
PubMed ID: 27037832
Related Link: https://www.kyoto-u.ac.jp/ja/research-news/2016-04-13
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