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06:34
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
Plant noncoding RNA gene discovery by "single-genome comparative genomics".
Chong-Jian Chen1, Hui Zhou, Yue-Qin Chen
1Institut de Génétique et Microbiologie, CNRS/UMR 8621, Université Paris Sud, Orsay, France.
RNA (New York, N.Y.)
|January 12, 2011
Summary
Most plant noncoding RNA (ncRNA) genes are duplicated, creating species-specific families. This study reveals intragenome comparison as a powerful method for discovering novel ncRNA genes in plants.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Plant genomes exhibit extensive gene family expansion due to multiple duplication events.
- While protein-coding genes have been well-studied, the impact of duplications on noncoding RNA (ncRNA) genes remains largely unknown.
Purpose of the Study:
- To systematically analyze duplicated regions in the rice genome for ncRNA repeats.
- To develop a computational method for discovering novel ncRNA gene families based on duplication footprints.
Main Methods:
- Systematic analysis of duplicated regions in the rice genome.
- Development of a Support Vector Machine (SVM) model for ncRNA candidate retrieval.
- Comparison of predicted ncRNA families with maize genomes.
Main Results:
- Most ncRNA genes in rice have undergone multiple duplications, leaving conserved sequence footprints.
- An SVM model identified nearly 4000 ncRNA families, with most being structured RNAs, not previously annotated snoRNAs or miRNAs.
- A significant portion of these ncRNA families are species-specific or of recent origin, with limited conservation in maize.
Conclusions:
- Intragenome comparison is a potent strategy for the large-scale computational annotation of ncRNA genes.
- A substantial fraction of rice ncRNA genes are duplicated and species-specific.
- Duplication events significantly shape the evolution and diversity of ncRNA gene families in plants.
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