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

Abstract

Reynoutria japonica Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role in population diversity analysis. However, there are few studies on the chloroplast genome of R. japonica. In this study, the complete chloroplast genomes of three R. japonica from different regions were performed by next-generation sequencing technology. The results revealed that the lengths of the three chloroplast genomes are between 163,371~163,372 bp, and they have a highly conserved structure with a pair of inverted repeat (IR) regions (31,121 bp), a large single-copy (LSC) region (87,571~87,572 bp), and a small single-copy (SSC) region (13,558 bp). In total, 132 genes were annotated, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. The phylogenetic analysis strongly revealed that 13 populations of R. japonica form a monophyly, and Fallopia multiflora (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and R. japonica in China could be further divided into two major groups based on genetic structure analysis. In addition, several potential loci with suitable polymorphism were identified as molecular markers. Our study provides important genetic resources for further development and utilization of R. japonica germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

“…The chloroplast genomes of these six species exhibit a typical quadripartite structure, which is consistent with other plants of the Polygonaceae family, such as Calligonum L. 48 , Polygonum L. 23 , F. sachalinensis 49 , and Reynoutria japonica Houtt. 24 . This phenomenon is also widely observed in other angiosperm chloroplast genomes 50 – 52 .…”

“…Previous studies have utilized chloroplast genomic techniques to conduct phylogenetic analysis of Polygonaceae plants, shedding light on the issue of taxonomic confusion within this plant family 6 , 23 , 24 . In this study, we employed both CDS and whole genome data to reconstruct the phylogenetic relationships among 29 Polygonaceae plants.…”

“…Guo et al 23 sequenced and assembled the chloroplast genomes of four species from genus Polygonum , followed by phylogenetic analysis, revealing the relationships between them. Additionally, Chen et al 24 analyzed chloroplast genomes of Reynoutria japonica Houtt. from different regions, performing phylogenetic analyses that highlighted R. japonica 's close association with P. multiflorus .…”

De novo assembly and comparative analysis of the mitochondrial genome of Reynoutria japonica

“…Mitochondrial contigs were identified by the BLASTn program (Chen et al, 2015) with Fallopia multiflora (accession number: MF611850, MF611851) mitogenome as references. And the self-loop candidate contigs were found and polished by Pilon v1.23 (Walker et al, 2014) using Illumina Novaseq sequencing reads, which has been used to assemble the R. japonica chloroplast genome before (Chen et al, 2022). Finally, one circular structure of the R. japonica mitogenome was obtained.…”

“…The dried root of R. japonica in combination with other traditional Chinese medicine herbs have multiple therapeutic uses (Zhang et al, 2013). In this ancient traditional Chinese medicine plant, the chloroplast genome of different regions R. japonica has been systematically analyzed (Chen et al, 2022). But its nuclear genome or mitogenome has not been published yet.…”