Development of haplotype phased genome assembler
| Project/Area Number |
16H04719
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Genome biology
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| Research Institution | Tokyo Institute of Technology |
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Principal Investigator |
Itoh Takehiko 東京工業大学, 生命理工学院, 教授 (90501106)
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| Co-Investigator(Kenkyū-buntansha) |
豊田 敦 国立遺伝学研究所, ゲノム・進化研究系, 特任教授 (10267495)
梶谷 嶺 東京工業大学, 生命理工学院, 助教 (40756706)
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| Project Period (FY) |
2016-04-01 – 2019-03-31
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| Project Status |
Completed (Fiscal Year 2018)
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| Budget Amount *help |
¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000)
Fiscal Year 2018: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
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| Keywords | ゲノムアセンブラ / ヘテロ接合性 / ゲノムアセンブル / 次世代シークエンサー / ゲノム構築 / ハプロタイプ / ゲノム解析 / アセンブラ |
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| Outline of Final Research Achievements |
The ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions, where the haplotype sequences differ considerably and are likely to relate to various interesting biological phenomena. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee, which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for highly divergent regions.
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| Academic Significance and Societal Importance of the Research Achievements |
本研究を通じて開発されたPlatanua-alleeアセンブラは、そのアルゴリズムを論文にて公開する一方で、ホームページより利用可能な形のプログラムとして公開している。このプログラムを用いることで、従来はfosmid構築など特別なコストのかかる方法で配列決定をしないとアクセスできなかったようなゲノム領域に対し、安価なIlluminaデータの使用のみで迫ることができるようになったという点で、学術的な意義は極めて大きいと考えられる。
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Report
(4 results)
Research Products
(5 results)
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[Journal Article] Genome sequence and analysis of the Japanese morning glory Ipomoea nil.2016
Author(s)
Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, et al.
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Journal Title
Nature Communications
Volume: 7
Issue: 1
Pages: 132395-132395
DOI
NAID
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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