Overview: Why Compare Erigeron Chloroplast Genomes?
Erigeron, commonly known as fleabanes, includes hundreds of species spread across temperate and mountainous regions worldwide. Unraveling their evolutionary relationships is challenging due to polyphyly, hybridization, and taxonomic ambiguity, especially among Old World taxa. A comprehensive comparative study of chloroplast (cp) genomes provides a stable, maternally inherited genetic framework to infer phylogenetic relationships, identify polymorphic loci for barcoding, and illuminate patterns of genome conservation and variation across a cosmopolitan genus.
What the Study Analyzed
The work consolidates cp genome data from 25 Erigeron species, encompassing New World, Old World, and island endemics from the Juan Fernández Islands. With 16 species newly assembled and 9 previously published cp genomes, researchers examined genome structure, gene content, introns, inverted repeats (IRs), codon usage, repeats, selection, nucleotide diversity, and phylogenetic relationships. The objective was to (a) characterize cp genome features, (b) reconstruct a preliminary Erigeron phylogeny from complete cp genomes, and (c) pinpoint highly polymorphic regions useful for future phylogenetic and population studies.
Conserved cp Genome Architecture Across Erigeron
The 25 Erigeron chloroplast genomes show remarkable structural conservation. Genome sizes range narrowly around 152,100–153,430 bp, with a classic quadripartite structure: large single-copy (LSC), small single-copy (SSC), and two inverted repeats (IRs). Each genome encodes 112 unique genes (79 protein-coding, 29 tRNA, 4 rRNA). IR regions duplicate a subset of genes, including rRNA genes, which reinforces higher GC content in IRs (~43%) relative to LSC and SSC (about 37% and 31%, respectively). Puntamental gene order and most intron positions are preserved, underscoring slow cp genome evolution in Erigeron and aligning with patterns observed in Asteraceae and broad angiosperm lineages.
IR Boundary Stability and Phylogenetic Signal
Analyses of IR contraction and expansion reveal only minor boundary variation among species. A Mantel test shows a strong correlation between IR length differences and phylogenetic distance (r = 0.767, p = 0.0001), indicating that while IR boundaries are conserved, they accumulate divergence with lineage split. This finding suggests that IR dynamics carry phylogenetic information, albeit secondary to sequence changes in non-repeated regions.
Selection, Variation, and Polymorphic Loci
Chloroplast genes experience strong purifying selection in Erigeron, with an average Ka/Ks around 0.068. A targeted search for episodic positive selection identified limited gene-wide signals, with ycf2 showing site-specific episodes of diversifying selection. MEME analyses highlight episodic selection at specific codons in accD, ndhF, rbcL, ycf1, and ycf2, indicating localized adaptive changes within an otherwise conserved cp genome.
Genome-wide, intergenic spacers are the most variable regions (π ≈ 0.0127), followed by introns and coding sequences. Ten highly polymorphic loci emerge as candidates for phylogenetic and population studies, primarily in intergenic spacers: psaC–ndhD, ndhD–ccsA, trnT–trnL, psbI–trnS, ndhI–ndhG, clpP–psbB, ccsA–trnL, ycf1–rps15, trnD–trnY, ndhC–trnV. Their variability makes them robust markers across broad Erigeron sampling, though lineage-specific differences mean clade-focused analyses may reveal alternate top polymorphic regions. Among coding regions, rps19, ycf1, rps15, and ndhF display higher diversity, but overall coding regions remain relatively conserved.
Phylogeny: What the cp Genomes Reveal
The cp-based phylogeny places Erigeron species into eight sections with notable paraphyly in several groups, including Erigeron and Trimorpha. Notably, former Conyza species (e.g., E. bonariensis and E. canadensis) cluster within Erigeron in cp-based trees, echoing taxonomic debates about genus circumscription. The unassigned E. breviscapus (East Asia) shows affinity with Eurasian Trimorpha taxa, hinting at broader Old World connections. Importantly, cp genomes alone may not resolve all reticulate histories, as maternal inheritance masks hybridization and biparental gene flow. This study therefore supports an integrative approach combining nuclear data and morphology for a robust taxonomic framework.
Implications for Taxonomy, Conservation, and Future Work
Few plant groups exhibit such a stable cp genome structure alongside meaningful variation in non-coding regions. The findings support current broad genus concepts (e.g., WoRld-wide Erigeron) and provide practical molecular tools for species identification, population genetics, and phylogeography. They also highlight the need for broader taxon sampling and incorporation of nuclear genomic data (e.g., Angiosperms353 targets or transcriptomics) to fully resolve Erigeron’s complex taxonomy and test monophyly across continents.
Takeaway
Comparative chloroplast genomics in Erigeron reveals a conserved genome backbone punctuated by informative non-coding regions and targeted codon-level signals of selection. This genomic portrait lays the groundwork for refined phylogenies, clearer taxonomy, and targeted conservation strategies across a genus of striking ecological breadth.
