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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes
Anna R Reineke1, Erich Bornberg-Bauer, Jenny Gu
1Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany.
Nucleic Acids Research
|April 8, 2011
Summary
Discovering plant regulatory motifs is hard due to short motifs and genome evolution. This study reveals differences between monocots and dicots, suggesting group-specific searches for novel motifs and highlighting limits for conserved non-coding sequence detection.
Area of Science:
- Bioinformatics
- Genomics
- Plant Biology
Background:
- Regulatory motif discovery in plants is challenging due to short motifs and genome diversification.
- Plant genomes have undergone events like duplication, impacting regulatory motif evolution.
Purpose of the Study:
- To conduct a phylogenomic comparison of plant upstream regions.
- To identify features of plant regulatory genomes for de novo motif discovery.
- To understand the impact of divergence times and duplication events on regulatory motifs.
Main Methods:
- Systematic phylogenomic comparison of plant upstream regions.
- Analysis of conserved non-coding sequence (CNS) detection limits.
- Investigation of motif decay rates over evolutionary time.
Main Results:
- Clear evolutionary differences in upstream regions between monocots and dicots were detected.
- Universal motifs like the TATA box are rare in plants.
- A divergence time of approximately 100 million years ago (mya) limits reliable CNS detection.
Conclusions:
- Separating monocots and dicots is recommended for novel regulatory motif searches.
- The findings provide a framework for identifying functional motifs by understanding CNS detection limits.
- This research aids in understanding plant regulatory genome evolution.
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