Chloroplast Genome Phylogenetics and Evolution

Chloroplast genomes have become central to reconstructing plant evolutionary histories. These circular DNA molecules, known as plastomes, typically range from 120 to 160 kilobases and feature a quadripartite structure comprising two inverted repeats (IRs) separated by large and small single-copy regions. High conservation of gene content and order across land plants has enabled broad comparative analyses, while variation in non-coding regions and certain coding loci provides the phylogenetic signal needed to resolve both deep and shallow divergences. Advances in high-throughput sequencing and bioinformatics have streamlined the assembly and annotation of plastomes from diverse taxa, yielding genomic resources that inform divergence times, biogeographic patterns and adaptive shifts. Chloroplast phylogenomics has illuminated key events such as the radiation of angiosperms, the origins of major lineages and the dynamics of structural changes, including IR expansions and contractions. These insights not only refine the tree of life for green plants but also underpin applications in conservation, biodiversity assessment and crop improvement.

Research from Nature Portfolio

Recent studies have identified novel plastid regions with enhanced species-level resolution. The plastid gene ycf1 has emerged as the most variable locus across land plants, outperforming traditional barcodes such as matK and rbcL in distinguishing closely related taxa. Two subregions of ycf1 exhibit high amplification success and discriminatory power, enabling more accurate DNA barcoding and phylogeographic analyses. Primer sets targeting these loci have been developed and validated across a broad spectrum of angiosperms, offering a standardised approach for rapid species identification and genetic diversity studies.

Chloroplast Genome Phylogenetics and Evolution publication trend

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

Technical terms

Plastome: The complete circular genome of a plastid organelle, most often referring to the chloroplast, containing genes for photosynthesis and other essential functions.

Inverted repeats (IRs): Two identical or nearly identical DNA sequences in opposite orientations that separate the large and small single-copy regions in chloroplast genomes.

DNA barcoding: A method for species identification using a short, standardised DNA sequence from a specific genome region.

Heterotachy: Variation in the evolutionary rate of a gene or site over time or across different lineages, affecting phylogenetic analyses.

References

1. Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences. Horticultural Plant Journal (2023).
2. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology (2016).
3. Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding. PLOS ONE (2012).
4. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology (2009).
5. ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports (2015).
6. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Ecology and Evolution (2008).