Chloroplast Genome Phylogenetics in Asteraceae Plants

The Asteraceae constitute one of the largest and most diverse families of flowering plants, encompassing economically important crops, ornamentals and medicinal species. Chloroplast genome phylogenetics has emerged as a powerful approach to resolve evolutionary relationships within this family by harnessing complete plastid sequences rather than a handful of traditional markers. Typical angiosperm plastomes exhibit a conserved quadripartite structure—two inverted repeats (IRs) flanking large (LSC) and small (SSC) single-copy regions—yet subtle variations in genome size, gene content and boundary dynamics can provide a wealth of phylogenetic signal. Comparative analyses of whole plastomes now underpin the reconstruction of backbone relationships across tribes and genera, the identification of cryptic lineages and the testing of taxonomic concepts. Advances in high-throughput sequencing and bioinformatic workflows have facilitated the assembly of dozens of plastomes per study, driving forward super-barcoding approaches that employ entire chloroplast genomes to delimit species and infer divergence times. This body of work has global significance for biodiversity assessment, conservation planning, crop and forage improvement, and the authentication of medicinal and ornamental germplasm. By integrating structural variation, repeat profiling and sequence divergence, chloroplast phylogenomics in Asteraceae continues to refine our understanding of diversification patterns, morphological convergence and biogeographical history across this vast plant family.

Research from Nature Portfolio

Recent studies have assessed the phylogenetic utility of chloroplast‐encoded ribosomal protein genes across a representative sampling of Asteraceae species. By sequencing and analysing the rps-11 gene from sixteen taxa, researchers constructed phylogenetic trees based both on nucleotide and deduced amino acid data. The amino acid-based topology revealed greater resolution of intergeneric relationships, with pairwise divergence values highlighting amino acid substitutions as particularly informative. In tandem, three-dimensional modelling of the RPS11 protein provided structural insights, identifying conserved and variable regions that may serve as future markers. Although the study highlighted the potential of rps-11 for resolving shallow to intermediate nodes, it also underlined the need for multi-locus plastome comparisons to validate its broader applicability in Asteraceae phylogenetics.

Chloroplast Genome Phylogenetics in Asteraceae Plants publication trend

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

Technical terms

Chloroplast genome: The circular DNA molecule of chloroplasts, typically 120–170 kb in size, containing genes essential for photosynthesis and gene expression.

Quadripartite structure: The organisation of a plastome into two inverted repeats (IRs) separated by large (LSC) and small (SSC) single-copy regions.

Inverted repeats (IRs): Two identical sequence blocks in opposite orientations that stabilise plastome structure and may shift in length.

Phylogenomic analysis: Reconstruction of evolutionary relationships using genome-scale data rather than individual loci.

Superbarcode: An approach employing entire organellar genomes as a high-resolution molecular marker for species identification and delimitation.

References

1. Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene. Scientific Reports (2024).
2. Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome. Frontiers in Plant Science (2024).
3. Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships. BMC Plant Biology (2023).