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Updated: Aug 4, 2026
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications
Gaurav Sablok1, Ting-Wen Chen2, Chi-Ching Lee2
1Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy.
Summary
ChloroMitoCU is a new web-based catalog analyzing codon usage patterns in organelle genomes. This resource aids in understanding biases and developing hyper-expression organelle transgenics.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Organelle genomes (chloroplasts, mitochondria) are believed to originate from bacterial endosymbiosis.
- Heterogeneity in base composition and codon usage within organelle genomes affects gene expression and phylogenetic analysis.
Purpose of the Study:
- To systematically analyze codon usage patterns in organelle genomes.
- To develop a comprehensive, web-based reference catalog for organelle codon usage.
- To facilitate the design of hyper-expression organelle transgenics.
Main Methods:
- Compilation of codon usage patterns from 328 chloroplast and 3,502 mitochondrial genomes.
- Development of a web-based platform (ChloroMitoCU) for data exploration and analysis.
- Implementation of phylogenetic comparison and predictive analysis tools.
Main Results:
- ChloroMitoCU provides pre-compiled codon usage data for 29,960 chloroplast and 49,066 mitochondrial coding sequences.
- The catalog enables genome-wide exploration and comparative analysis across diverse species.
- Tools for phylogenetic comparison and prediction of codon usage patterns are integrated.
Conclusions:
- ChloroMitoCU is the first curated catalog of organelle genome codon usage patterns.
- This resource enhances understanding of codon usage biases across multiple organelle clades.
- It supports advancements in organelle genetic engineering and functional genomics.
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