1 | INTRODUCTION

Polygonatum Mill. is the largest genus in the Polygonateae tribe.Polygonatum Mill. comprises 70 species widely distributed across the temperate Northern Hemisphere (Gong et al., 2023). Of these, 37 species and one variety had records of medicinal use and the rhizome was the most commonly used part of the plant. Many Polygonatum plants are highly effective in treatment age-related diseases, diabetes, lung diseases, coughs, fatigue, and feebleness in clinical practice (Zhao et al., 2018). Polygonatum kingianum , P. sibiricum ,P. cyrtonema and P. odoratum contain various active ingredients, such as polysaccharides, steroidal saponins, and alkaloids which are collected from the Chinese Pharmacopoeia as the official source of Polygonati rhizoma and Polygonate odorati rhizome (Luo et al., 2022). Polysaccharides from P. filipes and P. zanlanscianense , as recorded by provincial standards, can significantly inhibit the formation of intermediate diabetes products (Zhao et al., 2020).Polygonatum is a diverse and widely distributed plant.Flora of China records that it is distributed in many provinces of China, including Heilongjiang, Jilin, Liaoning, Hebei, Shanxi, Shaanxi, Nei Mongol, Ningxia, Gansu, Henan, Shandong, Anhui, Zhejiang, and Sichuan. Among them, P. cyrtonema is mainly distributed in the Yangtze River Basin, whereas P. kingianum occurs in southwestern China (Guo et al., 2022). In addition, the presence of multiple medicinal plants of Polygonatum make it difficult to identify. The phyllotaxis is usually an important basis for distinguishing Polygonatum plants (Xia et al., 2022), which can be mainly classified into alternate leaf types and verticillate leaf types according to the phyllotaxis characteristics; for example,P. cyrtonema , P. filipes , and P. odoratum are alternate leaf types and P. sibiricum , P. kingianum , andP. zanlanscianense are verticillate leaf types. The rhizome morphology of Polygonatum plants is also diverse, with P. sibiricum having a “Jitou-type” and an atypical “Jitou-type”.P. cyrtonema have three types, “Jiang-type”, “Cylinder-type”, and “Baiji-type”, with variations in the composition of the rhizomes of the different types (Hu et al., 2022). The indiscriminate use of different species may cause crucial effects on the patient. Therefore, establishing an effective identification method to distinguish between the medicinal species of Polygonatum , is necessary. DNA barcoding and molecular markers have been used for accurate species delimitation and phylogenetic relationship inference inPolygonatum (Jiao et al., 2018; Lee et al., 2021). However, species identification using traditional DNA barcoding techniques is limited and does not allow for the accurate identification of closely related species (Newmaster et al., 2008). The chloroplast genome sequence has been proposed as a superbarcode for species authentication (Li et al., 2015). The chloroplast genomes of medicinal plants such asAtractylodes (Wang et al., 2021), Gentiana (Zhao et al., 2022), Peucedanum (Sun et al., 2023) and Tripterygium (Xu et al., 2024) have been studied one after another and their intragenus evolutionary relationships have been explored. Studies of the chloroplast genomes of Polygonatum spp. have also been reported. The genus Polygonatum is a monophyletic group comprising three sections (sect. Sibirica , sect. Polygonatum , andsect. Verticillata ) (Xia et al., 2022).Heteropolygonatum , Disporopsis , Maianthemum , andDisporum are sister groups to Polygonatum within Polygonateae (Wang et al., 2022). During the long evolutionary process of the genus, the leaf type of this group evolved from verticillate leaves to alternate leaves. The construction of a phylogenetic tree based on the chloroplast genome showed that P. kingianum can be clearly distinguished from other species in the verticillate leaf group, providing a reliable means for the accurate identification of P. kingianum (Shi et al., 2023). However, these studies did not focus on sequencing or analyzing the chloroplast genomes of medicinal plants of the genus Polygonatum . Consequently, we sequenced and analyzed the whole chloroplast genomes of six medicinal species of Polygonatum to enrich the understanding of genome characteristics, screen mutational hotspots, and SSRs for authentication of Polygonatum medicinal plants and elucidate the phylogenetic relationship of Polygonatum medicinal plants.