Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline

In phylogeographic studies, genetic distances between individuals are typically small: In the European endemic, declining medicinal plant Arnica montana L., range-wide biogeographic patterns so far remained obscure as sequence diversity in plastome marker regions is very low. While entire chloroplast genomes promise higher resolution, comparing them in great detail is a technical challenge, requiring high accuracy and repeatability in sequencing, assembly and annotation, automated across large sample sets. Using A. montana as our working example, we developed the PlastidPipeline, which consistently and repeatably provides structurally standardized and annotated, ready-to-analyze plastomes from short-read sequences. The PlastidPipeline combines well-tested standard software tools with own scripts, from data cleanup through plastome assembly, structural standardization, annotation, to quality control and raw read backmapping. Using publicly available read data of diverse provenance, we obtained plastid genomes for eight A. montana accessions across Europe, four further species of Arnica and three outgroup species. All A. montana plastomes formed a well-supported clade, split further into an Iberian and a Central/Northern European geographic group, which are, however, connected by patterns of potential heteroplasmy. Beyond demonstrating that pan-plastome phylogeography is both feasible and useful, we recommend the analysis of within-sample read variation, and improved standardization of newly reported plastomes.