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

Abstract

Members of Polygonatum 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 Polygonatum 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 de novo 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 (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, and trnC-GCA-petN) that might be useful as potential molecular markers for identifying Polygonatum species were identified. The molecular clock analysis results showed that the divergence time of Polygonatum 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 Polygonatum. The phylogenetic analysis also suggested that Heteropolygonatum may be the sister group of the Polygonatum, but the Disporopsis, Maianthemum, and Disporum may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of Polygonatum.

Comparative analysis of medicinal plant Isodon rubescens and its common adulterants based on chloroplast genome sequencing

“…Except for ndhF , ycf1 , and ycf2 genes, all protein-coding genes showed a highly conserved character ( Figure 6 ); the intergenic spacers (IGS) with the highest divergence were trnH-GUG-psbA , trnQ-UUG-psbK , trnS-GCU-trnT-CGU , atpH-atpI , trnE-UUC-trnT-GGU, psaA-ycf3, ndhC-trnM-CAU, psbH-petB, and rps15-ycf1 , as predicted. In addition, the sliding window analysis revealed that seven regions, including rps16-trnQ-UUG , ndhF , ndhB , ccsA-ndhD , ndhA , ndhH , and ycf1 genes, exhibited higher nucleotide diversity values (> 0.014, Figure 7 ); the IR regions exhibited lower sequence divergence than LSC and SSC regions, consistent with the previous comparisons of cp genomes ( Jiang et al., 2022 ; Wang et al., 2022 ). Among these 16 high polymorphic regions, 11 intergenic spacers were found in the trnH-GUG-psbA , trnQ-UUG-psbK , trnS-GCU-trnT-CGU , atpH-atpI , trnE-UUC-trnT-GGU, psaA-ycf3, ndhC-trnM-CAU, psbH-petB, rps15-ycf1 , rps16-trnQ-UUG , and ccsA-ndhD .…”

“…Furthermore, as illustrated in Figure 2 , higher RSCU values (≥1) were found for codons with A or T at the 3’ position, which showed high encoding efficacy. Similar findings were reported for codon usage and amino acid frequency in the cp genomes of other angiosperms, which may be attributable to the high overall AT content in the cp genome ( Kawabe and Miyashita, 2003 ; Jiang et al., 2022 ; Wang et al., 2022 ). In addition, the codon usage was similar in I. rubescens , I. lophanthoides , and I. japonicaus , whereas the codon usage of I. eriocalyx and I. excisus was relatively close to that of I. inflexus and I. coetsa ( Figure 2 ).…”

“…The chloroplast (cp) is an essential organelle that plays a crucial role in plant photosynthesis and biochemical processes ( Bendich, 2004 ). Compared with the gene fragments, the cp genome is relatively conserved and slightly varied ( Drouin et al., 2008 ; Ferrarini et al., 2013 ), which has been widely used for identifying Paris , Polygonatum , and its contaminants ( Kawabe and Miyashita, 2003 ; Jiang et al., 2022 ; Wang et al., 2022 ). Recently, although the complete plastid genomes of I. rubescens has reported by Lian et al.…”

Biosynthesized silver nanoparticles using Polygonatum geminiflorum efficiently control fusarium wilt disease of tomato

“…The genus is represented by about 75 species in the world, distributed primarily in the temperate and alpine regions of the northern hemisphere, extending into mountains in the subtropical region as well ( Chase et al, 2016 ; Floden and Schilling, 2018 ). Polygonatum species are characterized by sympodial rhizomes, and opposite to verticillate leaves and fleshy berries ( Wang et al, 2022 ). The subterranean rhizome in many species of the genus have been utilized in traditional as well as modern medicine for the cure of several diseases.…”

Comparative genomic analysis of five Coprinus species

“…With the in-depth development of sequencing technology and bioinformatics analysis tools, comparative genomics has been widely used in studies on species evolution and formation, ecological diffusion, habitat adaptation, and antibiotic resistance gene diffusion [22][23][24][25][26][27]. The core genome is generally considered as the minimum genome necessary for the survival of free-living organisms [28,29].…”