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Open Access Highly Accessed Methodology article

Systematic genome sequence differences among leaf cells within individual trees

Deepti Diwan1, Shun Komazaki1, Miho Suzuki1, Naoto Nemoto1, Takuyo Aita3, Akiko Satake2 and Koichi Nishigaki1*

Author Affiliations

1 Graduate School of Science and Engineering, Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan

2 Department of Science, Hokkaido University, Sapporo, Japan

3 Graduate School of Information Science and Technology, Osaka University, Suita, Japan

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BMC Genomics 2014, 15:142  doi:10.1186/1471-2164-15-142

Published: 19 February 2014

Abstract

Background

Even in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biological problems associated with DNA mutation rates, can assist efforts to elucidate essential mechanisms of cancer.

Results

Using genome profiling (GP), we detected considerable systematic variation in genome sequences among cells in individual woody plants. The degree of genome sequence difference (genomic distance) varied systematically from the bottom to the top of the plant, such that the greatest divergence was observed between leaf genomes from uppermost branches and the remainder of the tree. This systematic variation was observed within both Yoshino cherry and Japanese beech trees.

Conclusions

As measured by GP, the genomic distance between two cells within an individual organism was non-negligible, and was correlated with physical distance (i.e., branch-to-branch distance). This phenomenon was assumed to be the result of accumulation of mutations from each cell division, implying that the degree of divergence is proportional to the number of generations separating the two cells.

Keywords:
Genome sequence; Genomic distance; Mutation rate; Japanese beech; Yoshino cherry; Leaf genomes; Genome profiling (GP); Next-generation sequencing (NGS)