Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Six Polygonatum Species (Asparagaceae)

Abstract Background: Polygonatum Miller is the largest genus in the tribe Polygonateae of Asparagaceae, and the horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have been concerned mainly with the size and gene contents of the plastome, no intensive plastid genomic comparative analysis of this genus has been conducted, and there are still some species whose chloroplast genome information has not been reported. Results: In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among which, the chloroplast genome of P. campanulatum and P. franchetii were reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154, 565 bp ( P. multiflorum ) to 156, 028 bp ( P. stenophyllum ) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content, protein-coding genes and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were eight remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome illustrated that P. campanulatum with alternate leaves were strongly supported locating in sect. Verticillata , a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. Conclusions: This study revealed that the characters of plastomes in Polygonatum and Heteropolygonautm maintained a high similarity. Eight highly variable regions were found to be potential specific DNA barcodes in Polygonatum . Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.