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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention
Konstantinos Giannakis1, Samuel J Arrowsmith2, Luke Richards3
1Department of Mathematics, University of Bergen, Bergen, Norway.
Cell Systems
|September 17, 2022
Summary
Mitochondrial and plastid gene retention is predicted by protein properties like binding energy, not just hydrophobicity. These universal features apply across eukaryotic organelle DNA (oDNA) and independent endosymbiotic events.
Area of Science:
- Evolutionary Biology
- Genomics
- Structural Biology
Background:
- Mitochondria and plastids are essential organelles that retain their own DNA (oDNA) genomes.
- The selective retention of specific genes within organelle DNA is a long-standing evolutionary question.
- Understanding gene retention mechanisms is key to comprehending organelle evolution and function.
Purpose of the Study:
- To identify the specific properties of genes that determine their retention in organelle DNA.
- To investigate the underlying molecular and biochemical mechanisms driving organelle gene retention.
- To test the universality of these retention features across different eukaryotic organelles and endosymbiotic events.
Main Methods:
- Analysis of over 15,000 organelle DNA sequences and 300 whole eukaryotic genomes.
- Application of structural biology, bioinformatics, and machine learning tools.
- Utilized Bayesian model selection to identify predictive features of gene retention.
Main Results:
- Gene retention in organelle DNA is predicted by protein hydrophobicity and binding energy centrality.
- Nucleic acid and amino acid biochemistry also influence gene retention.
- Identical features predict retention in both mitochondria and plastids, demonstrating universality.
Conclusions:
- A universal set of gene properties governs retention in organelle DNA across eukaryotes.
- These findings support the universality of retention mechanisms, even in recent endosymbiotic events.
- The study provides quantitative models for predicting organelle gene retention.
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