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A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs
Guoqin Mai1, Ruiquan Ge2, Guoquan Sun1
1Shenzhen Institutes of Advanced Technology and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
Biomed Research International
|May 20, 2016
Summary
This study refines Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) detection by proposing a new definition and manual curation. Findings reveal significant variations in CRISPR elements across prokaryotic species and evolutionary manipulation by transposons.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are key prokaryotic genetic elements involved in regulating foreign gene expression.
- CRISPR-associated (Cas) systems, particularly Cas9, have been engineered into powerful genome editing tools.
- Current CRISPR detection programs may overlook weak signals due to inconsistent definitions.
Purpose of the Study:
- To manually curate and update annotations of CRISPR elements in prokaryotic genomes.
- To propose a new, comprehensive definition for CRISPR elements.
- To investigate the evolutionary dynamics and distribution of CRISPRs in prokaryotes.
Main Methods:
- Manual curation of all annotated CRISPR elements in prokaryotic genomes.
- Development of a new definition encompassing all CRISPR types.
- Comparative analysis of CRISPR element abundance across different taxonomic levels (domains, genera).
- Evolutionary analysis of CRISPR manipulation in the genus Thermoanaerobacter.
Main Results:
- 95 updates to existing CRISPR annotations were proposed.
- A new definition for CRISPR elements was established.
- High variability in CRISPR element numbers was observed, even among closely related species.
- Transposons were identified as frequent tools for splitting long CRISPR arrays in Thermoanaerobacter.
Conclusions:
- A refined definition and manual curation improve CRISPR detection accuracy.
- CRISPR element distribution is highly variable and subject to evolutionary pressures.
- Transposon-mediated rearrangement plays a significant role in CRISPR array evolution.
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