Introduction: Erigeron’s Global Footprint and Genomic Inquiry
Erigeron, commonly known as fleabane, is a diverse and nearly cosmopolitan genus within the tribe Astereae of the Asteraceae. With roughly 457 species spanning North American temperate regions to East Asia and the Juan Fernández Islands, Erigeron presents a compelling case for studying chloroplast genome evolution in a widely distributed lineage. Despite taxonomic revisions and frequent hybridization, cp genomes offer a stable, maternally inherited resource for inferring phylogenetic relationships, assessing genetic diversity, and identifying polymorphic markers suitable for population genetics and conservation work.
What the chloroplast genome tells us
The chloroplast (cp) genome is a small, circular DNA molecule with a conserved quadripartite structure: a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeats (IRs). Across the 25 Erigeron species analyzed here, cp genomes show remarkable conservation in structure, gene content, and overall size (roughly 152,100–153,430 bp). Each genome typically carries 112 unique genes (79 protein-coding, 29 tRNA, 4 rRNA), with the IRs duplicating a subset of these genes. This structural stability underpins their usefulness for broad-scale phylogenetics and finer-scale population studies alike.
Scope of the study: taxonomic breadth and data integration
To expand genomic resources for Erigeron, researchers de novo assembled the cp genomes of 16 species (including Erigeron bonariensis) and integrated 9 additional genomes from NCBI, bringing the total to 25 species. The sampling spans New World taxa (e.g., E. bonariensis, E. philadelphicus, E. canadensis), Old World taxa (e.g., E. alpinus, E. breviscapus), and Juan Fernández island endemics (e.g., E. fernandezianus, E. ingae). This breadth enables a thorough comparison of genome architecture, IR dynamics, sequence variation, and selective pressures across clades that reflect divergent ecological histories.
Key findings: genome architecture, IR dynamics, and selection
Genome structure was highly conserved across the 25 species. All cp genomes had 112 unique genes, with IRs duplicating a core set of genes including several rRNAs and tRNAs. Introns remained remarkably conserved in length and position, highlighting strong purifying selection on cp introns due to their regulatory roles in transcription and RNA processing. Intriguingly, IR boundary regions (the JLB, JSB, JSA, and JLA junctions) exhibited minimal variation, suggesting robust constraints maintaining plastid genome integrity in Erigeron.
Analyses of IR length variation revealed a clear phylogenetic signal: differences in IR length correlate with evolutionary distances (Mantel r = 0.767, p = 0.0001). This implies that even within this relatively conserved genome compartment, IR dynamics reflect lineage divergence over time.
Across coding regions, the cp genomes are under strong purifying selection (average Ka/Ks around 0.068). A targeted search for positive selection found limited evidence at the gene level, with ycf2 showing gene-wide episodic diversification. Codon-level signals point to episodic selection in accD, ndhF, rbcL, ycf1, and ycf2, suggesting occasional adaptive changes at specific sites superimposed on a backdrop of overall stability.
Markers for phylogeny and population studies
The study identified ten highly polymorphic intergenic spacer regions suitable as markers for phylogenetic and phylogeographic analyses. Notably, psaC–ndhD and ndhD–ccsA showed strong diversity (π values up to ~0.031), with other spacers such as trnT–trnL, psbI–trnS, ndhI–ndhG also among the top hits. Protein-coding genes generally exhibited lower variability, though rps19 and ycf1 showed relatively higher diversity within coding regions. The clade-specific patterns underscore that marker choice should consider the target group; what is most polymorphic in one subset (e.g., Chilean island taxa) may differ in another (e.g., Old World taxa).
Phylogenetic insights and taxonomic implications
The cp genome-based phylogeny of 25 Erigeron species confirms paraphyly for several traditional infrageneric sections (notably Erigeron and Trimorpha), aligning with prior molecular work. The study also places Conyza-type taxa—often treated as a separate genus—within Erigeron in cp genome analyses, supporting broader circumscription per POWO (Plants of the World Online). However, the authors caution that cp data alone may not resolve reticulate histories driven by hybridization; integrating nuclear data and morphological traits will be essential to test genus-level classifications robustly.
Future directions: integrating data for a robust taxonomy
As the cp genome signals reveal, Erigeron’s evolutionary narrative is shaped by a combination of long-term conservation and episodic, site-specific variation. The authors advocate integrating target-enrichment nuclear datasets (e.g., Angiosperms353), transcriptomics, and comprehensive morphology to construct a more stable framework for this diverse genus. Such integrative approaches are increasingly effective in Asteraceae, which often exhibit complex reticulate relationships at both tribal and subfamily levels.
Concluding remarks
This comparative chloroplast genomics study provides a foundational, phylogenomically informed view of Erigeron, highlighting conserved genome architecture and pinpointing polymorphic regions that can drive future population and phylogeographic research. The work advances our understanding of cp genome evolution in a widespread, taxonomically challenging group and lays the groundwork for integrative taxonomic revisions that better reflect evolutionary history.
