Development of system to improve the quality of draft assemblies

• Project/Area Number: 26430200
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Institute of Physical and Chemical Research (2015-2017); Kazusa DNA Research Institute (2014)
• Principal Investigator: Kosugi Shunichi 国立研究開発法人理化学研究所, 統合生命医科学研究センター, 研究員 (30365457)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2016: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: アセンブリ / ゲノム / ヘテロ接合 / 次世代シークエンシング / 第３世代シークエンシング / ミスアセンブリ / パイプライン / ギャップ修復

Outline of Final Research Achievements

I constructed genome assemblies with the whole genome sequencing reads from budding yeast, nematoda, and rice, and determined the statistics for the metrics and error properties of the assemblies. Using the likelihood ratio of the alignment properties (i.e., alignment length, alignment identity, and mapping rate of paired-end short reads) between the true and false alignment data, I developed a gap-closing tool, GMcloser, that closes gaps in assemblies with high accuracy. In addition, I developed another too tools, GMvalue and Extrerm. GMvalue determines the metrics of misassemblies including the number of misassembles. Extreme reassembles a preassembled config set by extending the termini of the contigs followed by assembling the extended contigs with overlap-layout-consensus algorithm.

Research Products

• [Journal Article] Rice breeding based on whole genome sequencing using next-generation sequencer (2016)
  • Author(s): Akira Abe, Hiroki Takagi, Satoshi Natsume, Hiroki Yaegashi, Hideko Kikuchi, Kentaro Yoshida, Shunichi Kosugi, Hiromasa Saitoh, Naoya Urasaki, Hideo Matsumura, Hiroyuki Kanzaki, and Ryohei Terauchi
  • Journal Title: 生化学 Volume: 88 Issue: 1 Pages: 44-53
  • DOI: 10.14952/SEIKAGAKU.2016.880044
  • ISSN: 0037-1017
  • Year and Date: 2016-02-25
  • Peer Reviewed / Open Access
• [Journal Article] Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements (2016)
  • Author(s): Yoshida K, Saunders DG, Mitsuoka C, Natsume S, Kosugi S, Saitoh H, Inoue Y, Chuma I, Tosa Y, Cano LM, Kamoun S, Terauchi R
  • Journal Title: BMC Genomics Volume: 17 Issue: 1 Pages: 370-370
  • DOI: 10.1186/s12864-016-2690-6
  • NAID: 120005817905
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Sequencing and comparative analyses of the genomes of zoysiagrasses (2016)
  • Author(s): Tanaka H, Hirakawa H, Kosugi S, Nakayama S, Ono A, Watanabe A, Hashiguchi M, Gondo T, Ishigaki G, Muguerza M, Shimizu K, Sawamura N, Inoue T, Shigeki Y, Ohno N, Tabata S, Akashi R, Sato S
  • Journal Title: DNA Research Volume: 23 Issue: 2 Pages: 171-180
  • DOI: 10.1093/dnares/dsw006
  • Peer Reviewed / Open Access
• [Journal Article] 次世代シークエンサーを活用した全ゲノム解析によるイネ育種 (2016)
  • Author(s): 阿部 陽，高木 宏樹，夏目 俊，八重樫 弘樹，菊池 秀子，吉田 健太郎，小杉 俊一，齋藤 宏昌，浦崎 直也，松村 英生，神崎 洋之，寺内 良平
  • Journal Title: 生化学 Volume: 88 Pages: 44-53
  • Peer Reviewed / Open Access
• [Journal Article] GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments. (2015)
  • Author(s): Shunichi Kosugi, Hideki Hirakawa, and Satoshi Tabata
  • Journal Title: Bioinformatics Volume: 31 Issue: 23 Pages: 3133-3141
  • DOI: 10.1093/bioinformatics/btv465
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] MutMap accelerates breeding of a salt-tolerant rice cultivar (2015)
  • Author(s): Takagi, H., Tamiru, M., Abe, A., Yoshida, K., Uemura, A., Yaegashi, H., Obara, T., Oikawa, K., Utsushi, H., Kanzaki, E., Mitsuoka, C., Natsume, S., Kosugi, S., Kanzaki, H., Matsumura, H., Urasaki, N., Kamoun, S., Terauchi, R.
  • Journal Title: Nature Biotechnology Volume: 33 Issue: 5 Pages: 445-449
  • DOI: 10.1038/nbt.3188
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly (2015)
  • Author(s): H. Nishikawa, T Iijima, R Kajitani, et. al.
  • Journal Title: Nature Genetics Volume: 47 Issue: 4 Pages: 405-409
  • DOI: 10.1038/ng.3241
  • Peer Reviewed / Open Access
• [Journal Article] NESmapper: accurate prediction of leucine-rich nuclear export signals using activity-based profiles (2014)
  • Author(s): Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata
  • Journal Title: Plos Computational Biology Volume: 18 Issue: 9 Pages: e1003841-e1003841
  • DOI: 10.1371/journal.pcbi.1003841
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Structural variations in whole genome sequencing data from 1300 disease genomes (2017)
  • Author(s): 小杉俊一、桃沢幸秀、久保允人、鎌谷洋一郎
  • Organizer: 第6回生命医薬情報連合大会
• [Presentation] Comprehensive evaluation of strucutral variation calling tools and development of an integrated pipeline for merging calling results (2016)
  • Author(s): Shunichi Kosugi, Yoichiro Kamatani
  • Organizer: 第5回生命医薬情報連合大会
  • Place of Presentation: 東京お台場
  • Year and Date: 2016-09-29