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2022 Fiscal Year Final Research Report

Development of a k-mer-based GWAS method for metagenomic analysis

Research Project

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Project/Area Number 21K19211
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionTokyo Institute of Technology

Principal Investigator

Itoh Takehiko  東京工業大学, 生命理工学院, 教授 (90501106)

Project Period (FY) 2021-07-09 – 2023-03-31
Keywordsメタゲノム / アセンブル
Outline of Final Research Achievements

In this study, we aimed to develop a method to efficiently extract environment-specific genomic regions from two groups of environmental samples by metagenomic sequencing and comparative analysis, respectively. Initially, we planned to achieve this region by extracting and assembling specific k-mer from short reads obtained from both environments. However, due to the difficulty of distinguishing k-mer from error-derived k-mer by frequency difference, we changed the plan and developed a method to extract the genomic regions specific to each environment from the “bubble structure” of the assembly graph after pan- metagenome assembly of the whole sequence data from both environments. By applying the method to real data, we succeeded in extracting regions of diversity within the same bacterial species depending on the environment, demonstrating the effectiveness of our method.

Free Research Field

ゲノム情報解析

Academic Significance and Societal Importance of the Research Achievements

近年、ある環境に生息する細菌群集からゲノムDNAを直接回収・解析するメタゲノム手法は注目されている研究分野の一つである。しかし、アセンブル・ビンニングにより各菌のゲノムを再構成させ、さらには表現型との因果関係まで繋げようとすると解析は極めて困難であると言わざるを得ない。このような問題に対して、二群間で異なる多様性を持つゲノム領域を効率的に抽出することを可能にする本成果の利用は、研究遂行を容易にする効果が期待される。残念ながらデータ量の不足などから、両群の表現型とのリンクまでを直接的に見出すことは、現時点で困難であるが、候補箇所の効率的な抽出による候補の絞り込みが可能となり、その意義は大きい。

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Published: 2024-01-30  

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