Integration of plant strain SNPs using NGS Sequence Read Archive and diversity statistics analysis

• Project/Area Number: 24500366
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: National Institute of Genetics
• Principal Investigator: KAMINUMA Eli 国立遺伝学研究所, 生命情報研究センター, 助教 (90314559)
• Co-Investigator(Renkei-kenkyūsha): NAGASAKI Hideki 国立遺伝学研究所, 生命情報研究センター, 特任研究員 (70624451) ; MOCHIZUKI Takako 情報・システム研究機構, 新領域融合研究センター, 特任研究員 (40709284)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: SNP / 次世代シークエンサ / Sequence Read Archive / 多様性指標 / データベース / 解析ワークフロー / 一塩基多型 / WGS / DNA多型 / 遺伝的多様性 / ゲノム多様性

Outline of Final Research Achievements

In this study, an integrated database of Single Nucleotide Polymorphisms of plant strains from Sequence Read Archive was constructed as DNA Polymorphism Annotation Database(DNAPod). The integrated database is accessible from DNAPod website(http://tga.nig.ac.jp/dnapod/). Moreover, an analytical workflow for DNAPod database was implemented as a function of DDBJ Pipeline (http://p.ddbj.nig.ac.jp/). The constructed DNAPod database can be a data resource of further genomic breeding research and genomic diversity research. The integrated SNPs of rice, sorghum and maize in DNAPod are available for experimental researchers as genetic markers such as trait mapping and diversity statistics analysis.

Research Products

• [Presentation] DNA Polymorphism Database from New-Generation Sequence Read Archive and Analytical Workflow (2015)
  • Author(s): Mochizuki T, Tanizawa Y, Fujisawa T, Nikoh N, Toyoda A, Fujiyama A, Kurata N, Nagasaki H, Shimizu T, Kaminuma E, Nakamura Y
  • Organizer: Plant & Animal Genome XXIII
  • Place of Presentation: San Diego (USA)
  • Year and Date: 2015-01-14
• [Presentation] 遺伝研スパコン概要と、NGSアーカイブデータを用いたSNP解析 (2014)
  • Author(s): 神沼英里、望月孝子、長崎英樹、谷沢靖洋、小笠原理、大久保公策、高木利久、中村保一
  • Organizer: 日本育種学会第126回講演会「NGS 使い倒し講座 - Breeding Informatics 研究 XIII」
  • Place of Presentation: 南九州大学(都城市)
  • Year and Date: 2014-09-26
  • Invited
• [Presentation] Constructing an integrated DNA polymorphism database and an analytical workflow for plants and bacteria (2014)
  • Author(s): Takako Mochizuki, Takatomo Fujisawa, Yasuhiro Tanizawa, Hideki Nagasaki, Eli Kaminuma, Tokurou Shimizu, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Naruo Nikoh and Yasukazu Nakamura
  • Organizer: Plant and Animal Genome XXII (PAG XXII) Conference
  • Place of Presentation: Town and Country Hotel, San Diego, USA
• [Presentation] NGS由来ゲノムワイド多型マーカ構築とそのRDF注釈情報統合化 (2013)
  • Author(s): Eli Kaminuma, Takatomo Fujisawa, Takako Mochizuki, Yasuhiro Tanizawa, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Tokurou Shimizu, Yasukazu Nakamura
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸国際会議場
• [Presentation] DNA多型統合データベースと解析ワークフローの構築 : 植物、微生物への取り組み (2013)
  • Author(s): 望月 孝子, 藤澤 貴智, 谷澤 靖洋, 長崎 英樹, 神沼 英里, 大柳 一, 清水 徳朗, 豊田 敦, 藤山 秋佐夫, 倉田 のり, 二河 成男, 中村 保一
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 新型シークエンサのアーカイブ配列と解析パイプライン：系統間SNP解析を事例として (2012)
  • Author(s): 神沼英里
  • Organizer: 第122回日本育種学会講演会ワークショップ06 "育種のための情報解析ツール使い倒し塾"
  • Place of Presentation: 京都産業大学
  • Invited
• [Book] 実験医学別冊「次世代シークエンス解析スタンダード」:Ⅵ-4 DDBJ Read Annotation Pipeline 解析パイプラインによるRNA-Seq de novo assemblyとイネ多型解析 (2014)
  • Author(s): 長崎英樹,望月孝子,谷沢靖洋,神沼英里,中村保一
  • Publisher: 羊土社
• [Remarks] DNApod: DNA Polymorphism annOtation Database
  • URL: http://tga.nig.ac.jp/dnapod/
• [Remarks] DNAPod database
  • URL: http://tga.nig.ac.jp/dnapod/
• [Remarks] DNA Polymorphism Annotation Database(DNAPod)
  • URL: http://tga.nig.ac.jp/dnapod/