Introduction: Erigeron’s Global Footprint and the Chloroplast View
The genus Erigeron, commonly known as fleabanes, comprises hundreds of species distributed across temperate and mountainous regions worldwide. Despite its ecological versatility and near-cosmopolitan range, resolving Erigeron’s evolutionary relationships has been hampered by polyphyly, hybridization, and taxonomic ambiguity, especially among Old World taxa. Chloroplast (cp) genomes, with their conserved structure and uniparental inheritance, offer a valuable lens for comparative genomics and early phylogenetic signals within this complex group.
Scope of the Study: A Broad Comparative Sampling
This study expands cp genome resources by sequencing Erigeron bonariensis and assembling de novo cp genomes for 15 additional species, then integrating 9 publicly available Erigeron cp genomes for a total of 25 species. The sampling spans the New World, Old World, and island endemics from the Juan Fernández Archipelago, enabling a broad assessment of genomic features, intron dynamics, IR boundary evolution, and interspecific polymorphism. A single outgroup, Solidago decurrens, anchors the phylogeny within the Astereae tribe.
Genome Structure Is Highly Conserved, Yet Local Variation Tells the Story
All assembled Erigeron cp genomes share the classic quadripartite structure (LSC, SSC, and two IRs) with lengths ranging from 152,108 to 153,430 bp. Each genome harbors 112 unique genes (79 CDS, 29 tRNA, 4 rRNA). The IR regions duplicate 16 genes, including several rRNA and tRNA genes, a pattern consistent with other Asteraceae. Intron content is highly conserved, with 18 intron-containing genes showing stable positions across species. Intron length variation exists but is modest, with notable variability in rpl16, ndhA, and clpP introns, among others. Overall GC content sits around 37%, but IRs are GC-rich (up to ~43%) due to rRNA genes, underscoring functional constraints in the chloroplast.
IR Boundary Dynamics and Phylogenetic Signal
IR contraction and expansion across Erigeron species are subtle but meaningful. The JSB junction consistently houses a functional ycf1 gene, while a truncated Ψycf1 copies appears at JSA. The ndhF gene remains SSC-confined, and rps19 and rpl2 show near-constant junctional patterns with slight clade-specific deviations. Importantly, IR length variation correlates strongly with phylogenetic distance (Mantel r = 0.767, p = 0.0001), suggesting that even in a predominantly conserved cp genome, IR dynamics carry a detectable evolutionary signal that aligns with lineage divergence.
Evolutionary Pressures: Purifying Selection with Localized Positives
Across the cp CDS, purifying selection prevails (average Ka/Ks ~0.068). A targeted search for positive selection via BUSTED and MEME reveals limited gene-wide selection, with ycf2 showing episodic diversification and several codons in accD, ndhF, rbcL, ycf1, and ycf2 under site-specific diversifying selection. These findings indicate that cp genome evolution in Erigeron is largely constrained, punctuated by a few localized adaptive changes relevant to photosynthesis and plastid function.
Polymorphic Loci: Markers for Phylogeography and Population Studies
Intergenic spacers emerge as the most polymorphic regions, with psaC–ndhD and ndhD–ccsA showing π values above 0.02. Ten intergenic loci—psaC–ndhD, ndhD–ccsA, trnT–trnL, psbI–trnS, ndhI–ndhG, clpP–psbB, ccsA–trnL, ycf1–rps15, trnD–trnY, and ndhC–trnV—stand out as robust markers across diverse Erigeron clades, including a distinct Chilean group. Among coding regions, rps19 and ycf1 show relatively higher diversity, though overall coding-region variation remains low. These patterns emphasize the utility of cp markers for resolving phylogeography while highlighting the clade-specific nature of polymorphism in Erigeron.
Phylogenetic Insights: Non-M Monophyly and Taxonomic Implications
Phylogenomic reconstruction based on complete cp genomes reveals paraphyly within several traditional infrageneric sections. Sections Erigeron and Trimorpha are not monophyletic; E. muirii and E. denalii fall outside their respective sections, and E. alpinus and E. elongatus cluster with E. alpiniformis, challenging traditional circumscriptions. The unassigned E. breviscapus groups with Eurasian Trimorpha taxa, suggesting a possible affinity that invites taxonomic revision. The inclusion of Conyza-type taxa (e.g., E. bonariensis, E. canadensis) within Erigeron in cp-genome trees aligns with modern taxonomic treatments (as per POWO), though cp data alone cannot resolve the full monophyly of the genus in the face of potential hybridization and uniparental inheritance. The study advocates integrating nuclear genomic data and comprehensive morphological reassessment to achieve a robust, repeatable taxonomic framework for Erigeron and related groups in Asteroideae.
Concluding Perspectives: A Step Toward Taxonomic Clarity in Erigeron
This first comprehensive cp-genome comparison across 25 Erigeron species underscores the plastid genome’s role as a stable, mutationally slow record of evolutionary history. The conserved genome architecture contrasts with informative variation in IR boundaries and intergenic spacers, providing a foundation for resolving phylogeny and guiding population-level studies. The findings highlight both the promise and limitations of chloroplast data for dissecting complex reticulations in Erigeron, and they point to a path forward that includes broader taxon sampling, addition of nuclear data, and integrative taxonomy to clarify sectional delineations and genus circumscription within Asteraceae.
