AUTHOR=Wang Jing , Qian Jun , Jiang Yuan , Chen Xiaochen , Zheng Baojiang , Chen Shilin , Yang Fajian , Xu Zhichao , Duan Baozhong 

TITLE=Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.882189

DOI=10.3389/fpls.2022.882189

ISSN=1664-462X

ABSTRACT=<p>Members of <italic>Polygonatum</italic> are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within <italic>Polygonatum</italic> have long been controversial because of the complexity of their morphological variations and lack of high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering phylogenetic relationships in related families. In the present study, the complete cp genome of 26 species of Trib. Polygonateae were <italic>de novo</italic> assembled and characterized; all species exhibited a conserved quadripartite structure, that is, two inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, large single sequence (LSC) and small single sequence (SSC). A total of 8 highly variable regions (<italic>rps16-trnQ-UUG, trnS-GCU-trnG-UCC</italic>, <italic>rpl32-trnL-UAG</italic>, <italic>matK-rps16</italic>, <italic>petA-psbJ, trnT-UGU-trnL-UAA</italic>, <italic>accD-psaI</italic>, and <italic>trnC-GCA-petN</italic>) that might be useful as potential molecular markers for identifying <italic>Polygonatum</italic> species were identified. The molecular clock analysis results showed that the divergence time of <italic>Polygonatum</italic> might occur at ∼14.71 Ma, and the verticillate leaf might be the ancestral state of this genus. Moreover, phylogenetic analysis based on 88 cp genomes strongly supported the monophyly of <italic>Polygonatum</italic>. The phylogenetic analysis also suggested that <italic>Heteropolygonatum</italic> may be the sister group of the <italic>Polygonatum</italic>, but the <italic>Disporopsis, Maianthemum</italic>, and <italic>Disporum</italic> may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of <italic>Polygonatum</italic>.</p>