RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limit...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1332460/full |
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| author | Cui Li Cui Li Cui Li Han Liu Han Liu Han Liu Mei Qin Mei Qin Mei Qin Yao-jing Tan Xia-lian Ou Xia-lian Ou Xia-lian Ou Xiao-ying Chen Xiao-ying Chen Xiao-ying Chen Ying Wei Ying Wei Zhan-jiang Zhang Zhan-jiang Zhang Ming Lei Ming Lei Ming Lei |
| author_facet | Cui Li Cui Li Cui Li Han Liu Han Liu Han Liu Mei Qin Mei Qin Mei Qin Yao-jing Tan Xia-lian Ou Xia-lian Ou Xia-lian Ou Xiao-ying Chen Xiao-ying Chen Xiao-ying Chen Ying Wei Ying Wei Zhan-jiang Zhang Zhan-jiang Zhang Ming Lei Ming Lei Ming Lei |
| author_sort | Cui Li |
| collection | DOAJ |
| description | Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis. |
| first_indexed | 2024-03-08T05:32:33Z |
| format | Article |
| id | doaj.art-f22d2d88a4064554ba6ae73a7aeeac91 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-08T05:32:33Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f22d2d88a4064554ba6ae73a7aeeac912024-02-06T04:48:12ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-02-011510.3389/fpls.2024.13324601332460RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicolaCui Li0Cui Li1Cui Li2Han Liu3Han Liu4Han Liu5Mei Qin6Mei Qin7Mei Qin8Yao-jing Tan9Xia-lian Ou10Xia-lian Ou11Xia-lian Ou12Xiao-ying Chen13Xiao-ying Chen14Xiao-ying Chen15Ying Wei16Ying Wei17Zhan-jiang Zhang18Zhan-jiang Zhang19Ming Lei20Ming Lei21Ming Lei22National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaSchool of Basic Medical Sciences, Guangxi Medical University, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaNational Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaGuangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, ChinaCorydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.https://www.frontiersin.org/articles/10.3389/fpls.2024.1332460/fullCorydalis saxicolamitochondrial genomeRNA editingmitochondrial plastid DNAsexpression profile |
| spellingShingle | Cui Li Cui Li Cui Li Han Liu Han Liu Han Liu Mei Qin Mei Qin Mei Qin Yao-jing Tan Xia-lian Ou Xia-lian Ou Xia-lian Ou Xiao-ying Chen Xiao-ying Chen Xiao-ying Chen Ying Wei Ying Wei Zhan-jiang Zhang Zhan-jiang Zhang Ming Lei Ming Lei Ming Lei RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola Frontiers in Plant Science Corydalis saxicola mitochondrial genome RNA editing mitochondrial plastid DNAs expression profile |
| title | RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola |
| title_full | RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola |
| title_fullStr | RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola |
| title_full_unstemmed | RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola |
| title_short | RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola |
| title_sort | rna editing events and expression profiles of mitochondrial protein coding genes in the endemic and endangered medicinal plant corydalis saxicola |
| topic | Corydalis saxicola mitochondrial genome RNA editing mitochondrial plastid DNAs expression profile |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1332460/full |
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