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Published on: May 21, 2020
Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data
Kanako Kawaura1, Keiichi Mochida, Akiko Enju
1Kihara Institute for Biological Research, Yokohama City University, Maioka-cho 641-12, Yokohama 244-0813, Japan. kawaura@yokohama-cu.ac.jp
BMC Genomics
|June 19, 2009
Summary
Researchers created a valuable full-length cDNA resource for wheat, aiding in genome annotation and functional studies. This collection helps understand gene expression and evolution in wheat and other cereals.
Area of Science:
- Plant genomics
- Molecular biology
- Bioinformatics
Background:
- Wheat possesses a large and complex genome, necessitating comprehensive expressed sequence tag (EST) accumulation for functional genomics and breeding.
- A systematic survey and sequencing of full-length cDNA clones were performed to validate ESTs and annotate the wheat genome.
- This sequence data serves as a crucial genetic resource for wheat functional genomics and comparative cereal genomics.
Purpose of the Study:
- To generate a high-quality full-length cDNA resource for common wheat.
- To analyze gene expression profiles in various wheat tissues and under stress conditions.
- To investigate gene variability and adaptive selection between wheat and rice.
Main Methods:
- Generation of a comprehensive collection of expressed sequence tags (ESTs) from diverse wheat tissues and stress conditions.
- Systematic survey and sequencing of full-length cDNA clones.
- In silico analysis of expression profiles and comparative genomics with rice, including Ka/Ks ratio calculation.
Main Results:
- A collection of 6,162 independent, high-accuracy full-length cDNA clones was generated from common wheat.
- Approximately 10% of the sequenced clones represented wheat-unique genes.
- Genes preferentially expressed in specific tissues or under stress exhibited higher variability (Ka/Ks) compared to others, suggesting adaptive selection.
Conclusions:
- A high-quality full-length cDNA resource for common wheat has been established, crucial for ongoing genome curation and annotation.
- Expression data across tissues and stress treatments, along with wheat-rice variability data, provides valuable tools for wheat functional and comparative cereal genomics.
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