Comparative plastome analyses and evolutionary relationships of all species and cultivars within the medicinal plant genus Atractylodes

Atractylodes DC., a member of the Asteraceae family, is a crucial medicinal plant in East Asia. However, determining the taxonomy and phylogeny of Atractylodes remains challenging due to its hybridization and similar morphological features. To address this issue, we conducted a study wherein we sequenced 21 complete plastomes of all species and cultivars in Atractylodes. Our analysis revealed that all the plastomes within this genus had a typical quadripartite structure and ranged from 153,129 to 153,300 bp in length. Comparative plastome analyses revealed ten highly variable regions (trnH-psbA, rps18-rpl20, trnL-trnF, psbA-trnK, ndhD-ccsA, rpl20, trnK-matK, psbC-trnS, trnL-rpl32, petA-psbJ). A total of 4 polymorphic SSRs among 21 Atractylodes samples and 8 polymorphic SSRs among a wild and two cultivated populations of A. macrocephala were identified. Our phylogenetic analysis based on both plastid and RAD datasets was highly supported and provided insights into the plastid capture events that occurred in the A. lancea complex through putative ancient hybridization. Overall, our study provides a robust phylogeny and a temporal framework for further research on phylogeographic and population genetics of Atractylodes. The genomic resources we have accumulated will also be available for genetic engineering and germplasm exploration of this medicinally and economically important genus.