Integrating plastome comparison and phylogenetic analyses reveals the phylogenetic relationships of Pachypleurum (Apiaceae)

BACKGROUND: Phylogenomic data rich in informative loci can significantly improve the support and resolution of phylogenetic tree and has been proven to be an effective tool for studying plant taxonomy and phylogeny. The genus Pachypleurum Ledeb., belonging to subfamily Apioideae (Apiaceae), comprises approximately seven species worldwide (six in China). Due to the long-standing taxonomic ambiguity of this genus, it is urgent need for investigation. RESULTS: In this current study, we obtained six Pachypleurum plastomes and performed comprehensively comparative analyses. The results showed that six Pachypleurum plastomes were conserved in genome structure, gene number, gene arrangement, codon bias and SSRs, but varied in genome size, GC content and SC/IR boundaries. These findings indicated that Pachypleurum plastomes showed both conservation and diversity. In addition, nine mutation hotspot regions (matK, rps16, atpF, clpP, ndhE, trnH-psbA, psbK-psbI, accD-psaI, ycf4-cemA) were identified that can serve as potential DNA barcodes for species identification within the genus Pachypleurum. Phylogenetic analyses based on 79 commonly shared PCGs and ITS sequences robustly supported that the non-monophyly of Pachypleurum and six Pachypleurum members fell into two clades: Selineae and Acronema Clade. The phylogenetic results also showed that Chinese Pachypleurum taxa may be circumscribed to only one species (P. alpinum) and other five species previously placed in this genus may be transferred out this genus and the systematic position of them were also discussed. Finally, combined with plastome comparison, phylogenetic analyses and morphological characteristics, we discussed the morphological delimitation of Pachypleurum genus. CONCLUSIONS: This study characterized six Pachypleurum plastomes and highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions. In conclusion, our study not only enriched the data on the plastomes of Pachypleurum, but also provided a framework for Pachypleurum and improved the taxonomic system of the Apiaceae family.