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

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...

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Bibliographic Details
Published in:Genes 2022-10, Vol.13 (11), p.1979
Main Authors: Chen, Jianhui, Huang, Tiran, Fan, Haili, Lin, Fan, Ma, Hongping, Cao, Jie, Chai, Tuanyao, Ma, Lanqing, Wang, Hong
Format: Article
Language:English
Subjects:
Chloroplasts
Gene polymorphism
Genetic analysis
Genetic diversity
Genetic resources
Genetic structure
Genomes
Germplasm
Herbal medicine
Inverted repeat
Medicinal plants
Next-generation sequencing
Phylogenetics
Phylogeny
Polygonaceae
Proteins
Reynoutria japonica
rRNA
Trees
tRNA
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Summary: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.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes13111979