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Updated: Aug 25, 2025
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
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Does IR-loss promote plastome structural variation and sequence evolution?
Zi-Xun Wang1,2, Ding-Jie Wang1,3, Ting-Shuang Yi1,3
1Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
Frontiers in Plant Science
|October 17, 2022
Summary
Plastid genome (plastome) inverted repeats (IRs) are not the primary drivers of structural changes; instead, IR loss is a consequence of broader evolutionary processes affecting plastome stability and sequence evolution.
Area of Science:
- Plant molecular biology
- Genomics
- Evolutionary biology
Background:
- Plastids are key organelles in plant cells, with their genomes (plastomes) typically exhibiting a conserved quadripartite structure.
- This structure includes large single-copy (LSC) and small single-copy (SSC) regions flanking two copies of inverted repeats (IRs), which were thought to stabilize the plastome.
Purpose of the Study:
- To investigate the role of inverted repeats (IRs) in maintaining plastome structural stability and sequence evolution.
- To compare genome structure and sequence evolution in IR-lacking lineages versus their closest relatives with canonical IRs (CRCIRs).
Main Methods:
- Integrated comparative analysis of genome structure and sequence evolution.
- Examination of representative plastomes from nine IR-lacking lineages and their CRCIR relatives.
Main Results:
- Most IR-lacking plastomes showed significant structural rearrangements, gene loss/duplication, new repeat accumulation, and accelerated synonymous substitution compared to CRCIRs.
- However, IR-lacking plastomes exhibited comparable or even reduced structural variation metrics (rearrangement distance, repeat numbers, indel frequency, GC3 content) than some IR-present plastomes.
- This suggests IR loss is not the cause of these genomic changes.
Conclusions:
- Inverted repeat loss is likely a consequence, not a driver, of plastome structural and sequence evolution.
- Broader evolutionary processes appear to shape both structural integrity and sequence divergence in plastomes, irrespective of IR presence.
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