The complete chloroplast genome of the medicinal plant Polygonum cuspidatum (Polygonaceae) and its phylogenetic implications within the subfamily Polygonoideae

Abstract

Polygonum cuspidatum Siebold & Zucc. is a well-known and widely used medical plant to treat arthritis, gout and inflammation. In this study, we determined the complete chloroplast genome sequence of P. cuspidatum from Zhejiang Province. The assembled chloroplast (cp) genome was 163,183 bp in length, containing two inverted repeated (IR) regions of 30,859 bp each, a large single copy (LSC) region of 87,905 bp, and a small single copy (SSC) region of 13,560 bp. The genome encodes 131 genes, consisting of 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content of P. cuspidatum is 37.53%, with the highest GC content of 41.27% in the IR region. The 86 protein-coding genes encode 27,597 amino acids in total, most of which use the initiation codon ATG, except the ndhD gene which starts with ACG. The length of the tRNA genes range from 48 bp to 88 bp, with the highest GC content of 62.16% in tRNA-Arg (ACG) and tRNA-Asp (GUC). A total of 66 simple sequence repeats are identified in the cp of P. cuspidatum. Phylogenetic analysis indicated a sister relationship between P. cuspidatum and Fallopia sachalinensis, suggesting a close genetic relationship between the genera of Polygonum and Fallopia. This work provides basic genetic resources for investigating the evolutionary status and population genetics of this important medicinal species.

A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants

“…The raw reads were trimmed using Skewer v0.22 (skewer -q 20 -Q 30–l 100 -t 32) ( Jiang et al, 2014 ). BLAST was used to predict the chloroplast-like reads by cleaning the reads with the sequences of the reference P. cuspidatum (MW411186.1) ( Deng et al, 2015 ; Ye, Lin, Zhou, He, Yan and Cheng 2021 ). Generally, SOAPdenovo-2.…”

“…Studies ( Jansen, Saski, Lee, Hansen and Daniell 2011 ; Cheon, Kim, Kwak, Lee and Yoo 2019 ) have shown that changes in the IR region are the main reason for chloroplast genome changes. In the earlier reported cp genome in Polygonaceae, Yu and Ye ( Yu et al, 2020 ; Ye et al, 2021 ) studied the length of the cp genome of LSC, SSC, and IR region and classified the species of Polygonum chinense and P. cuspidatum . The result would be a valuable genetic resource for studying the genetics and evolutionary relationships between the Polygonaceae species.…”

“…Most of the Polygonum species have high financial and therapeutic values. Here, four Polygonum chloroplast genomes ( P. aviculare , P. bistorta , P. orientale , P. perfoliatum ) were identified and assembled, compared with other published Polygonum chloroplast genomes ( Yu, Liu, Liu, Lan and Qu 2020 ; Ye, Lin, Zhou, He, Yan and Cheng 2021 ), we got considerable biological evidence, with the cp genome structure, repeat sequences, and other characteristics. This work also provided an essential foundation of the Polygonum cp genome library, encouraging the progress of phylogenetics, DNA barcoding, and population ( Lee et al, 2019 ).…”

A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different Reynoutria japonica Populations

“…In this study, we sequenced and assembled three chloroplast genomes of R. japonica and performed a series of comprehensive comparative analyses with other published data. All the chloroplast genomes in R. japonica presented a typically quadripartite structure [ 22 , 23 ]. The chloroplast genome structure, codon bias, and gene order were conserved, consistent with buckwheat [ 20 ].…”

“…In Flora of China , R. japonica was separated from Polygonum and considered to belong to a new genus, Reynoutria Houtt. Several studies using chloroplast genomes revealed that R. japonica and F. multiflora had a close genetic relationship [ 22 , 23 ]. However, the intraspecific and population structure among R. japonica has not yet been clarified till now.…”