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Liu D, Zhang Z, Hao Y, Li M, Yu H, Zhang X, Mi H, Cheng L, Zhao Y. Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae. BMC Genomics 2024; 25:114. [PMID: 38273225 PMCID: PMC10811901 DOI: 10.1186/s12864-024-10016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. RESULT We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. CONCLUSIONS We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
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Affiliation(s)
- Daliang Liu
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Zhihan Zhang
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
- College of Engineering and Technology, Northeast Forestry University, Harbin, 150040, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xingruo Zhang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yiyong Zhao
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
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Liang YN, Li H, Huang XY, Bin YJ, Zhen YM, Qin XM. The complete chloroplast genome and phylogenomic analysis of Camellia sinensis var. sinensis cultivar 'Liupao', a landrace from Guangxi, China. Mitochondrial DNA B Resour 2023; 8:921-926. [PMID: 37645477 PMCID: PMC10461518 DOI: 10.1080/23802359.2023.2250072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Liupao tea is one of the well-known Chinese tea brands and a famous local specialty in Wuzhou, Guangxi, China. However, the genetic background and phylogenetic relationship of the native resource plants of Liupao tea need study, especially at the genomic level. In this study, we reported the complete chloroplast (cp) genome sequence of Camellia sinensis var. sinensis cultivar 'Liupao' (LP, Liupao tea population) and inferred its phylogenetic relationship to other tea plant variants or cultivars. The cp genome had a total length of 157,097 bp and the overall GC content was 37.3%. The cp genome contained one LSC region (86,641 bp) and one SSC region (18,276 bp), which were separated by two IR regions (26,090 bp, respectively). Moreover, the cp genomes were composed of 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that LP was closely related to C. sinensis var. pabilimba cv. 'Lingyunbaihao'. This study will provide useful information for further investigating the genetic background, evolution, and breeding of LP as well as other tea cultivars and varieties.
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Affiliation(s)
- Yan-Ni Liang
- Modern Industry College of Liupao Tea, Wuzhou University, Wuzhou, China
| | - Hong Li
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xi-Yang Huang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yue-Jing Bin
- Modern Industry College of Liupao Tea, Wuzhou University, Wuzhou, China
| | - Yu-Mei Zhen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xin-Mei Qin
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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Zhang ZB, Xiong T, Chen JH, Ye F, Cao JJ, Chen YR, Zhao ZW, Luo T. Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea. J Mol Evol 2023; 91:156-168. [PMID: 36859501 DOI: 10.1007/s00239-023-10099-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023]
Abstract
Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.
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Affiliation(s)
- Zai-Bao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China.
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Jia-Hui Chen
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Jia-Jia Cao
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Zi-Wei Zhao
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Tian Luo
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
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4
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Liu H, Qin L, Chen Y, Xu S, Zhou X, Zhu Y, Li B. The complete mitochondrial genome of Camellia nitidissima (Theaceae). Mitochondrial DNA B Resour 2023; 8:565-569. [PMID: 37200681 PMCID: PMC10187084 DOI: 10.1080/23802359.2023.2209211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
The mitochondrial genome of Camellia nitidissima was sequenced by Illumina and Pacbio sequencing. The results of sequences showed that a total length was 949,915 bp, and the GC content was 45.7% in assembled mitochondrial genome of C. nitidissima. 71 unigenes had been found, including 36 coding proteins and 35 non-coding proteins. Subsequently, the phylogenetic tree was built on 24 plants with the maximum-likelihood method, which had high bootstrap value and fited to the angiosperm phylogeny group classification (APG IV). The study's findings unravel the taxonomic status of C. nitidissima and benefit the evolution study.
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Affiliation(s)
- Hexia Liu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Liu Qin
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
| | - Yuling Chen
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Saiying Xu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Xingwen Zhou
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Yulin Zhu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
- Yulin Zhu College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Bo Li
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
- CONTACT Bo Li
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5
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Yang J, Ling C, Zhang H, Hussain Q, Lyu S, Zheng G, Liu Y. A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants. Genes (Basel) 2022; 13:genes13101827. [PMID: 36292711 PMCID: PMC9601400 DOI: 10.3390/genes13101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/01/2022] [Accepted: 10/01/2022] [Indexed: 11/04/2022] Open
Abstract
Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.
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Affiliation(s)
- Jun Yang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Chengcheng Ling
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Huamin Zhang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Shiheng Lyu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Guohua Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (G.Z.); (Y.L.)
| | - Yongsheng Liu
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
- Correspondence: (G.Z.); (Y.L.)
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Xu Y, Dong Y, Cheng W, Wu K, Gao H, Liu L, Xu L, Gong B. Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae. Heliyon 2022; 8:e09870. [PMID: 35847622 PMCID: PMC9283892 DOI: 10.1016/j.heliyon.2022.e09870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/18/2022] [Accepted: 06/30/2022] [Indexed: 01/30/2023] Open
Abstract
Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.
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Affiliation(s)
- Yang Xu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Yi Dong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Wenqiang Cheng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Kaiyun Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Haidong Gao
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Liu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Xu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Bangchu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
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7
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Yuan F, Lan X. Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae). BMC Genom Data 2022; 23:28. [PMID: 35418016 PMCID: PMC9008926 DOI: 10.1186/s12863-022-01042-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/08/2022] [Indexed: 11/26/2022] Open
Abstract
Objectives Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms. Data description Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746 bp and 267,334 bp, respectively) and chloroplast genomes of B. spectabilis (154,520 bp) and M. jalapa (154,532 bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.
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Affiliation(s)
- Fang Yuan
- Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, TAAHC-SWU Medicinal Plant Joint R&D Center, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China
| | - Xiaozhong Lan
- Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, TAAHC-SWU Medicinal Plant Joint R&D Center, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China.
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Wang Z, Cai Q, Wang Y, Li M, Wang C, Wang Z, Jiao C, Xu C, Wang H, Zhang Z. Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species. Front Genet 2022; 13:824610. [PMID: 35360853 PMCID: PMC8961065 DOI: 10.3389/fgene.2022.824610] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Theaceae species are dicotyledonous angiosperms with extremely high ornamental and economic value. The chloroplast genome is traditionally used to study species evolution, expression of chloroplast genes and chloroplast transformation. Codon usage bias (CUB) analysis is beneficial for investigations of evolutionary relationships and can be used to improve gene expression efficiency in genetic transformation research. However, there are relatively few systematic studies of the CUB in the chloroplast genomes of Theaceae species. In this study, CUB and nucleotide compositions parameters were determined by the scripts written in the Perl language, CodonW 1.4.2, CU.Win2000, RStudio and SPSS 23.0. The chloroplast genome data of 40 Theaceae species were obtained to analyse the codon usage (CU) characteristics of the coding regions and the influence of the source of variation on CUB. To explore the relationship between the CUB and gene expression levels in these 40 Theaceae plastomes, the synonymous codon usage order (SCUO) and measure independent of length and composition (MILC) values were determined. Finally, phylogenetic analysis revealed the genetic evolutionary relationships among these Theaceae species. Our results showed that based on the chloroplast genomes of these 40 Theaceae species, the CUB was for codons containing A/T bases and those that ended with A/T bases. Moreover, there was great commonality in the CUB of the Theaceae species according to comparative analysis of relative synonymous codon usage (RSCU) and relative frequency of synonymous codon (RFSC): these species had 29 identical codons with bias (RSCU > 1), and there were 19 identical high-frequency codons. The CUB of Theaceae species is mainly affected by natural selection. The SCUO value of the 40 Theaceae species was 0.23 or 0.24, and the chloroplast gene expression level was moderate, according to MILC values. Additionally, we observed a positive correlation between the SCUO and MILC values, which indicated that CUB might affect gene expression. Furthermore, the phylogenetic analysis showed that the evolutionary relationships in these 40 Theaceae species were relatively conserved. A systematic study on the CUB and expression of Theaceae species provides further evidence for their evolution and phylogeny.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Yue Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Li
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chenchen Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhaoxia Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Congcong Xu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Hongyan Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Zhaoliang Zhang,
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Wang C, Zhang Y, Ding H, Song M, Yin J, Yu H, Li Z, Han L, Zhang Z. Authentication of Zingiber Species Based on Analysis of Metabolite Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:705446. [PMID: 34880881 PMCID: PMC8647842 DOI: 10.3389/fpls.2021.705446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/11/2021] [Indexed: 05/10/2023]
Abstract
Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.
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Affiliation(s)
- Chenxi Wang
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yue Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Hui Ding
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Meifang Song
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Jiaxin Yin
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Heshui Yu
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zheng Li
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lifeng Han
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhonglian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
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10
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Wambulwa MC, Meegahakumbura MK, Kamunya S, Wachira FN. From the Wild to the Cup: Tracking Footprints of the Tea Species in Time and Space. Front Nutr 2021; 8:706770. [PMID: 34422884 PMCID: PMC8377202 DOI: 10.3389/fnut.2021.706770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/15/2021] [Indexed: 01/22/2023] Open
Abstract
Tea is one of the world's most popular beverages, known for its cultural significance and numerous health benefits. A clear understanding of the origin and history of domestication of the tea species is a fundamental pre-requisite for effective germplasm conservation and improvement. Though there is a general consensus about the center of origin of the tea plant, the evolutionary origin and expansion history of the species remain shrouded in controversy, with studies often reporting conflicting findings. This mini review provides a concise summary of the current state of knowledge regarding the origin, domestication, and dissemination of the species around the world. We note that tea was domesticated around 3000 B.C. either from non-tea wild relatives (probably Camellia grandibracteata and/or C. leptophylla) or intra-specifically from the wild Camellia sinensis var. assamica trees, and that the genetic origins of the various tea varieties may need further inquiry. Moreover, we found that lineage divergence within the tea family was apparently largely driven by a combination of orogenic, climatic, and human-related forces, a fact that could have important implications for conservation of the contemporary tea germplasm. Finally, we demonstrate the robustness of an integrative approach involving linguistics, historical records, and genetics to identify the center of origin of the tea species, and to infer its history of expansion. Throughout the review, we identify areas of debate, and highlight potential research gaps, which lay a foundation for future explorations of the topic.
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Affiliation(s)
- Moses C. Wambulwa
- Department of Life Sciences, South Eastern Kenya University, Kitui, Kenya
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Samson Kamunya
- Kenya Agricultural and Livestock Research Organization, Tea Research Institute (KALRO-TRI), Kericho, Kenya
| | - Francis N. Wachira
- Department of Life Sciences, South Eastern Kenya University, Kitui, Kenya
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11
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Li L, Hu Y, He M, Zhang B, Wu W, Cai P, Huo D, Hong Y. Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. BMC Genomics 2021; 22:138. [PMID: 33637038 PMCID: PMC7912895 DOI: 10.1186/s12864-021-07427-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/05/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea ('Wuyi narcissus' cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed. RESULTS Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4-8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4-1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. CONCLUSIONS The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
| | - Yunfei Hu
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Min He
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Bo Zhang
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Wei Wu
- College of Mathematics and Computer Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Pumo Cai
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Da Huo
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Yongcong Hong
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
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12
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Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea. Sci Rep 2021; 11:110. [PMID: 33420248 PMCID: PMC7794434 DOI: 10.1038/s41598-020-80431-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/09/2020] [Indexed: 11/08/2022] Open
Abstract
Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.
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13
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Tyagi S, Jung JA, Kim JS, Won SY. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E568. [PMID: 32365609 PMCID: PMC7285121 DOI: 10.3390/plants9050568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
Aster spathulifolius, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland A. spathulifolius and compared it with those of the island type and other Aster species. The chloroplast genome of mainland A. spathulifolius is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two A. spathulifolius lines and the other Aster species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All Aster species clustered into a monophyletic group, but the chloroplast genome of mainland A. spathulifolius was more similar to the other Aster species than to that of the island A. spathulifolius. The accD and ndhF genes were detected to be under positive selection within the Aster lineage compared to other related taxa. The complete chloroplast genome of mainland A. spathulifolius presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the Aster genus and the Asteraceae.
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Affiliation(s)
- Swati Tyagi
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
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Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database (Oxford) 2020; 2020:baaa013. [PMID: 32159215 PMCID: PMC7065459 DOI: 10.1093/database/baaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/05/2020] [Accepted: 01/25/2020] [Indexed: 12/05/2022]
Abstract
Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.
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Affiliation(s)
- Himanshu Dubey
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Hukam C Rawal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Megha Rohilla
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Urvashi Lama
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - P Mohan Kumar
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - Tanoy Bandyopadhyay
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Madhurjya Gogoi
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Nagendra Kumar Singh
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
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