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Yao J, Zhao F, Xu Y, Zhao K, Quan H, Su Y, Hao P, Liu J, Yu B, Yao M, Ma X, Liao Z, Lan X. Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4374801. [PMID: 33457408 PMCID: PMC7787725 DOI: 10.1155/2020/4374801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022]
Abstract
Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene's lengths of 82,221 bp and 81,450 bp, large single-copy region's (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region's (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region's (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.
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Affiliation(s)
- Junjun Yao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Fangyu Zhao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Yuanjiang Xu
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, Tibet 860000, China
| | - Kaihui Zhao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Hong Quan
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, Tibet 860000, China
| | - Yanjie Su
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Peiyu Hao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Jiang Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Min Yao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaojing Ma
- Jiangxi Institute for Drug Control, NMPA Key Laboratory of Quality Evaluation of Traditional Chinese Patent Medicine, Nanchang, Jiangxi 330029, China
| | - Zhihua Liao
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Jiangxi Institute for Drug Control, NMPA Key Laboratory of Quality Evaluation of Traditional Chinese Patent Medicine, Nanchang, Jiangxi 330029, China
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing 400715, China
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Zhu X, Ze M, Yin J, Chern M, Wang M, Zhang X, Deng R, Li Y, Liao H, Wang L, Tu B, Song L, He M, Li S, Wang WM, Chen X, Wang J, Li W. A phosphofructokinase B-type carbohydrate kinase family protein, PFKB1, is essential for chloroplast development at early seedling stage in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110295. [PMID: 31779907 DOI: 10.1016/j.plantsci.2019.110295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Among the phosphofructokinase B-type carbohydrate kinase (PCK) family proteins, only few proteins, like the FRUCTOKINASE-LIKE 1 and 2, have been functionally characterized in regulation of chloroplast development. Here, we report the involvement of a PCK protein PFKB1 in chloroplast development by identification of a new rice mutant, revertible early yellowing Kitaake 2 [rey(k2)]. The mutant rey(k2) shows yellow leaf phenotype, reduced photosynthetic pigments, and retarded chloroplast development during early stages of seedlings, but gradually recovered at later stages. The phenotype of rey(k2) is resulted from the disruption of the PFKB1 protein. The Pfkb1 gene is ubiquitously expressed, and its protein is mainly targeted to the chloroplast and, in some cells, to the nucleus. In addition, the PFKB1 protein possesses phosphofructokinase activity in vitro. The rey(k2) mutant affects RNA levels of chloroplast-associated genes. In particular, the nuclear-encoded RNA polymerase (NEP)-dependent genes are expressed at a sustained high level in rey(k2) even after turning green, indicating that PFKB1 is essential for suppressing the expression of NEP-dependent genes. Taken together, our study suggests that PFKB1 functions as a novel regulator indispensable for early chloroplast development, at least partly by regulating chloroplast-associated genes.
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Affiliation(s)
- Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Mu Ze
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Mawsheng Chern
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Mingrui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiang Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Rui Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Yongzhen Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Haicheng Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Long Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Li Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China.
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China.
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