Phylogenetic Analysis of Chloroplast Genomes in Angiosperms

Chloroplast genomes have become central to reconstructing the evolutionary history of flowering plants. Their relatively conserved structure, moderate size and uniparental inheritance make them ideal for resolving relationships at multiple taxonomic scales, from deep divergences among families to species‐level radiations. Advances in high‐throughput sequencing have enabled assembly of complete plastomes across diverse lineages, revealing the canonical quadripartite architecture with large single‐copy (LSC), small single‐copy (SSC) regions and a pair of inverted repeats (IRs). Comparative analyses of gene content, order and sequence variation provide both phylogenetic signal and insights into structural evolution. In particular, identification of mutational hotspots and positively selected genes has informed studies of adaptation to shaded understories, alpine environments and marine habitats. Integrating plastome data with nuclear markers and fossil calibration has improved divergence‐time estimation and clarified reticulate events such as ancient hybridisation and polyploidy. This body of work underpins global efforts to refine angiosperm classification, to develop DNA barcodes for biodiversity monitoring and to guide conservation of phylogenetic diversity.

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Phylogenetic Analysis of Chloroplast Genomes in Angiosperms publication trend

The graph below shows the total number of articles in phylogenetic analysis of chloroplast genomes in angiosperms across all publications each year (not limited to Nature Index journals).

Technical terms

Chloroplast genome: The circular DNA molecule within plant chloroplasts, typically 120–170 kb, encoding genes for photosynthesis and gene expression.

Large single‐copy (LSC) region: The major contiguous segment of the chloroplast genome, separated from the SSC by inverted repeats.

Small single‐copy (SSC) region: The smaller non‐repeated region flanked by the IRs, often variable in length.

Inverted repeat (IR): Two identical or nearly identical sequences in opposite orientation, contributing to genome stability.

Monophyletic: A group of organisms that form a clade, containing an ancestor and all its descendants.

Mutational hotspot: A genome region exhibiting elevated rates of nucleotide substitution, useful for phylogenetic resolution.

Positive selection: Process by which beneficial genetic variants increase in frequency, identified by elevated non‐synonymous substitution rates.

References

1. A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus Chrysosplenium. International Journal of Molecular Sciences (2023).
2. Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics. Frontiers in Plant Science (2023).
3. Chloroplast genomic comparison provides insights into the evolution of seagrasses. BMC Plant Biology (2023).
4. Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment. Genes (2022).