Plastid Genome Evolution in Angiosperms

Plastid genomes in flowering plants exhibit a conserved quadripartite organisation comprising two single-copy regions separated by a pair of inverted repeats. Over evolutionary time, these genomes have undergone expansions, contractions and rearrangements that shape gene content, structural stability and copy number. The inverted repeat region often contributes to genome stability and gene dosage by duplicating ribosomal RNA operons, while its contraction or loss can provoke compensatory increases in plastid DNA content. Gene losses, transfers to the nucleus and sequence inversions are widespread across diverse angiosperm lineages and underpin adaptations to different ecological niches. Structural variation in plastid genomes has been exploited to resolve phylogenetic relationships, trace biogeographic histories and develop molecular markers for crop improvement. Advances in long-read sequencing and bioinformatic assembly now permit comprehensive surveys of complex plastomes, revealing lineage-specific dynamics with implications for synthetic biology, species conservation and organelle genome stability.

Research from Nature Portfolio

Recent work has demonstrated that precise removal of the large inverted repeat from a model plastid genome reduces its size yet increases genome copy number, suggesting a direct link between repeat-mediated gene dosage and plastid ribosome abundance. Such streamlined plastomes facilitate synthetic biology applications by simplifying genome architecture. Foundational studies in legume subfamilies have uncovered tandem repeat expansions and shifts at inverted repeat boundaries that drive genome enlargement and accelerated evolution of key protein-turnover genes. An earlier investigation of a medicinal legume revealed hypermutation loci, gene losses and large inversions that generate heteroplasmic plastome variants, offering genetic markers to distinguish closely related varieties.

Plastid Genome Evolution in Angiosperms publication trend

The graph below shows the total number of articles in plastid genome evolution in angiosperms across all publications each year (not limited to Nature Index journals).

Technical terms

Plastid genome: The circular DNA molecule within plastids that encodes genes involved in photosynthesis and other plastid functions.

Inverted repeat: A duplicated DNA segment in reverse orientation, typically flanking the single-copy regions of the plastid genome.

Heteroplasmy: The occurrence of two or more variant plastid genome sequences within a single individual or cell.

Genome rearrangement: Structural changes in the genome such as inversions, deletions or expansions that alter gene order or content.

Gene dosage: The number of copies of a gene present in the genome, which can influence the level of gene expression.

References

1. Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number. Nature Plants (2024).
2. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP. Scientific Reports (2015).
3. Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus. Scientific Reports (2016).
4. Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica. Horticulture Research (2024).
5. Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure. Frontiers in Plant Science (2023).
6. Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae). BMC Plant Biology (2024).