A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations
<i>Reynoutria japonica</i> 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, the...
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MDPI AG
2022-10-01
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| Series: | Genes |
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| author | Jianhui Chen Tiran Huang Haili Fan Fan Lin Hongping Ma Jie Cao Tuanyao Chai Lanqing Ma Hong Wang |
| author_facet | Jianhui Chen Tiran Huang Haili Fan Fan Lin Hongping Ma Jie Cao Tuanyao Chai Lanqing Ma Hong Wang |
| author_sort | Jianhui Chen |
| collection | DOAJ |
| description | <i>Reynoutria japonica</i> 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 <i>R</i><i>. japonica</i>. In this study, the complete chloroplast genomes of three <i>R. japonica</i> 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 <i>R. japonica</i> form a monophyly, and <i>Fallopia multiflora</i> (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and <i>R. japonica</i> 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 <i>R. japonica</i> germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant. |
| first_indexed | 2024-03-09T19:03:52Z |
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| language | English |
| last_indexed | 2024-03-09T19:03:52Z |
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| spelling | doaj.art-c151c94f26b74a539adafee7ffa4c9222023-11-24T04:47:53ZengMDPI AGGenes2073-44252022-10-011311197910.3390/genes13111979A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> PopulationsJianhui Chen0Tiran Huang1Haili Fan2Fan Lin3Hongping Ma4Jie Cao5Tuanyao Chai6Lanqing Ma7Hong Wang8College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China<i>Reynoutria japonica</i> 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 <i>R</i><i>. japonica</i>. In this study, the complete chloroplast genomes of three <i>R. japonica</i> 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 <i>R. japonica</i> form a monophyly, and <i>Fallopia multiflora</i> (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and <i>R. japonica</i> 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 <i>R. japonica</i> germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.https://www.mdpi.com/2073-4425/13/11/1979<i>Reynoutria japonica</i>chloroplast genomegenetic diversitymolecular markerphylogeographyphylogenomics |
| spellingShingle | Jianhui Chen Tiran Huang Haili Fan Fan Lin Hongping Ma Jie Cao Tuanyao Chai Lanqing Ma Hong Wang A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations Genes <i>Reynoutria japonica</i> chloroplast genome genetic diversity molecular marker phylogeography phylogenomics |
| title | A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations |
| title_full | A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations |
| title_fullStr | A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations |
| title_full_unstemmed | A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations |
| title_short | A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different <i>Reynoutria japonica</i> Populations |
| title_sort | comparative phylogenetic analysis on the chloroplast genome in different i reynoutria japonica i populations |
| topic | <i>Reynoutria japonica</i> chloroplast genome genetic diversity molecular marker phylogeography phylogenomics |
| url | https://www.mdpi.com/2073-4425/13/11/1979 |
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