Genome structure and variation of <i>Reynoutria japonica</i> Houtt. chloroplast genome.

Mengtao Sun; Junxin Zhang; Tiran Huang; Mingfeng Yang; Lanqing MA; Liusheng Duan

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Genome structure and variation of Reynoutria japonica Houtt. chloroplast genome.

Author: Mengtao SUN ¹ ; Junxin ZHANG ¹ ; Tiran HUANG ¹ ; Mingfeng YANG ¹ ; Lanqing MA ¹ ; Liusheng DUAN ²
Author Information

1. Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China.
2. College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
Publication Type:Journal Article
Keywords: Chinese medicinal herb; circular tetrad structure; genomics analysis; whole chloroplast genome
MeSH: Base Composition; Genome, Chloroplast/genetics*; Open Reading Frames; Phylogeny; Reynoutria
From: Chinese Journal of Biotechnology 2022;38(5):1953-1964
CountryChina
Language:Chinese
Abstract: Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).