Comparative chloroplast genomics of Erigeron (Asteroideae, Asteraceae)

The genus Erigeron L. (Astereae, Asteroideae, Asteraceae), commonly known as fleabanes, comprises approximately 457 species with a near-cosmopolitan distribution. However, taxonomic discrepancies persist within the genus. In this study, the complete chloroplast (cp.) genomes of 16 Erigeron species were sequenced and/or de novo assembled and compared with those of nine previously reported species. The complete cp. genomes ranged from 152,108 to 153,430 base pairs (bp) in length, with a large single-copy region of 84,250-85,191 bp, inverted repeat regions (each IRa and IRb) of 24,688-25,054 bp, and a small single-copy region of 18,093-18,530 bp. Each genome contained 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Comparative analyses revealed conserved gene order, GC content, codon usage patterns, simple sequence repeats, and substitution trends across Erigeron species. A consistently low transition-to-transversion ratio (mostly <1) was observed. Analysis of selective pressure revealed gene-wide positive selection acting on ycf2, while some codons of accD, ndhF, rbcL, and ycf1 showed signatures of positive selection. Furthermore, ten highly polymorphic loci were identified, including psaC-ndhD, ndhD-ccsA, trnT-trnL, psbI-trnS, and ndhI-ndhG. Phylogenetic analysis of 25 Erigeron species revealed paraphyly within sect. Erigeron and sect. Trimorpha. The former Conyza species were embedded within the Erigeron species. The species Erigeron breviscapus (Vaniot) Hand.-Mazz., which is endemic to China, showed close relationships with species of sect. Trimorpha. This study provides insights into the evolutionary dynamics of the cp. genome and the phylogeny of the genus, with the identified polymorphic loci offering robust and cost-effective markers for resolving phylogenetic relationships within Erigeron.