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Ju Z, Liang L, Zheng Y, Shi H, Zhao W, Sun W, Pang Y. Full-Length Transcriptome Sequencing and RNA-Seq Analysis Offer Insights into Terpenoid Biosynthesis in Blumea balsamifera (L.) DC. Genes (Basel) 2024; 15:285. [PMID: 38540346 PMCID: PMC10970515 DOI: 10.3390/genes15030285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
Blumea balsamifera (L.) DC., an important economic and medicinal herb, has a long history of being used as a traditional Chinese medicine. Its leaves have always been used as a raw material for the extraction of essential oils, comprising large amounts of terpenoids, which have good therapeutic effects on many diseases, such as eczema, bacterial infection, and hypertension. However, the genetic basis of terpenoid biosynthesis in this plant is virtually unknown on account of the lack of genomic data. Here, a combination of next-generation sequencing (NGS) and full-length transcriptome sequencing was applied to identify genes involved in terpenoid biosynthesis at five developmental stages. Then, the main components of essential oils in B. balsamifera were identified using GC-MS. Overall, 16 monoterpenoids and 20 sesquiterpenoids were identified and 333,860 CCS reads were generated, yielding 65,045 non-redundant transcripts. Among these highly accurate transcripts, 59,958 (92.18%) transcripts were successfully annotated using NR, eggNOG, Swissprot, KEGG, KOG, COG, Pfam, and GO databases. Finally, a total of 56 differently expressed genes (DEGs) involved in terpenoid biosynthesis were identified, including 38 terpenoid backbone genes and 18 TPSs, which provide a significant amount of genetic information for B. balsamifera. These results build a basis for resource protection, molecular breeding, and the metabolic engineering of this plant.
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Affiliation(s)
- Zhigang Ju
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
| | - Lin Liang
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
| | - Yaqiang Zheng
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
| | - Hongxi Shi
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
| | - Wenxuan Zhao
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
| | - Wei Sun
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountain Area of Southwest of China, School of Life Science, Guizhou Normal University, Guiyang 550025, China
| | - Yuxin Pang
- Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (Z.J.); (L.L.); (Y.Z.); (H.S.); (W.Z.)
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
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Yao S, Tan X, Huang D, Li L, Chen J, Ming R, Huang R, Yao C. Integrated transcriptomics and metabolomics analysis provides insights into aromatic volatiles formation in Cinnamomum cassia bark at different harvesting times. BMC PLANT BIOLOGY 2024; 24:84. [PMID: 38308239 PMCID: PMC10835945 DOI: 10.1186/s12870-024-04754-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Cinnamomum cassia Presl, classified in the Lauraceae family, is widely used as a spice, but also in medicine, cosmetics, and food. Aroma is an important factor affecting the medicinal and flavoring properties of C. cassia, and is mainly determined by volatile organic compounds (VOCs); however, little is known about the composition of aromatic VOCs in C. cassia and their potential molecular regulatory mechanisms. Here, integrated transcriptomic and volatile metabolomic analyses were employed to provide insights into the formation regularity of aromatic VOCs in C. cassia bark at five different harvesting times. RESULTS The bark thickness and volatile oil content were significantly increased along with the development of the bark. A total of 724 differentially accumulated volatiles (DAVs) were identified in the bark samples, most of which were terpenoids. Venn analysis of the top 100 VOCs in each period showed that twenty-eight aromatic VOCs were significantly accumulated in different harvesting times. The most abundant VOC, cinnamaldehyde, peaked at 120 months after planting (MAP) and dominated the aroma qualities. Five terpenoids, α-copaene, β-bourbonene, α-cubebene, α-funebrene, and δ-cadinene, that peaked at 240 MAP could also be important in creating C. cassia's characteristic aroma. A list of 43,412 differentially expressed genes (DEGs) involved in the biosynthetic pathways of aromatic VOCs were identified, including phenylpropanoids, mevalonic acid (MVA) and methylerythritol phosphate (MEP). A gene-metabolite regulatory network for terpenoid and phenylpropanoid metabolism was constructed to show the key candidate structural genes and transcription factors involved in the biosynthesis of terpenoids and phenylpropanoids. CONCLUSIONS The results of our research revealed the composition and changes of aromatic VOCs in C. cassia bark at different harvesting stages, differentiated the characteristic aroma components of cinnamon, and illuminated the molecular mechanism of aroma formation. These foundational results will provide technical guidance for the quality breeding of C. cassia.
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Affiliation(s)
- Shaochang Yao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China
| | - Xiaoming Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China
| | - Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China
| | - Linshuang Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jianhua Chen
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China
| | - Ruhong Ming
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China
| | - Rongshao Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China.
- Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China.
| | - Chun Yao
- Guangxi Scientific Experimental Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China.
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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Liao H, Quan H, Huang B, Ji H, Zhang T, Chen J, Zhou J. Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata. PHYTOCHEMISTRY 2023; 214:113831. [PMID: 37598994 DOI: 10.1016/j.phytochem.2023.113831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Fritillaria unibracteata is an endangered medicinal plant whose bulb has been used as a Chinese herb to suppress cough, asthma and excessive phlegm for centuries. Steroidal alkaloids, which are synthesized via the steroid synthesis pathways, are their significant bioactive constituents. However, few studies on genes involved in steroidal alkaloid biosynthesis in F. unibracteata have been reported, mainly due to the lack of the F. unibracteata genome. In this paper, comparative transcriptomic and metabolomic analyses of four different tissues of F. unibracteata (leaves, flowers, stems, and bulbs) were performed. Imperialine, peiminine, and peimisine were among the significant bioactive compounds that were considerably abundant in bulb tissue, according to the metabolomic findings. Then, 83.60 Gb transcriptome sequencing of four different tissues was performed, of which one gene encoding phosphomevalonate kinase was directly functionally characterized to verify the accuracy of sequences obtained from the transcriptome. A total of 9217 differentially expressed unigenes (DEGs) were identified in four different tissues of F. unibracteata. GO and KEGG enrichments revealed that phenylpropanoid biosynthesis, MVA-mediated terpenoid backbone biosynthesis, and steroid biosynthesis were enriched in bulb tissue, whereas enrichment of MEP-mediated terpenoid backbone biosynthesis, photosynthesis, photosynthesis-antenna protein and carotenoid biosynthesis was observed in aerial tissues. Moreover, clustering analysis indicated that the downstream steroid biosynthesis pathway was more important in steroidal alkaloid biosynthesis compared to the upstream terpenoid backbone biosynthesis pathway. Hence, MVA-mediated biosynthesis of steroidal alkaloids was proposed, in which 15 bulb-clustered DEGs were positively correlated with a high accumulation of bioactive steroid alkaloids, further validating our proposal. In addition, 36 CYP450s showing a positive correlation with bioactive steroidal alkaloids provided candidate enzymes to catalyze the subsequent steps of steroidal alkaloid biosynthesis. In addition, the transcription factors and ABC transporters clustered in bulb tissue might be responsible for the regulation and transportation of steroidal alkaloid biosynthesis. Protein-protein interaction analysis implied a highly complex steroid alkaloid biosynthesis network in which delta (24)-sterol reductase might be one of the central catalysts. Based on the integrated transcriptome and metabolome, this current study is a first step in understanding the tissue-specific biosynthesis of steroidal alkaloids in F. unibracteata. Furthermore, key genes and regulators identified herein could facilitate metabolic engineering to improve steroidal alkaloids in F. unibracteata.
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Affiliation(s)
- Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Huige Quan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Binhan Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Huiyue Ji
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Tian Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Jiao Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
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Claude SJ, Raman G, Park SJ. Comparative Analysis and Identification of Terpene Synthase Genes in Convallaria keiskei Leaf, Flower and Root Using RNA-Sequencing Profiling. PLANTS (BASEL, SWITZERLAND) 2023; 12:2797. [PMID: 37570951 PMCID: PMC10421360 DOI: 10.3390/plants12152797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
The 'Lilly of the Valley' species, Convallaria, is renowned for its fragrant white flowers and distinctive fresh and green floral scent, attributed to a rich composition of volatile organic compounds (VOCs). However, the molecular mechanisms underlying the biosynthesis of this floral scent remain poorly understood due to a lack of transcriptomic data. In this study, we conducted the first comparative transcriptome analysis of C. keiskei, encompassing the leaf, flower, and root tissues. Our aim was to investigate the terpene synthase (TPS) genes and differential gene expression (DEG) patterns associated with essential oil biosynthesis. Through de novo assembly, we generated a substantial number of unigenes, with the highest count in the root (146,550), followed by the flower (116,434) and the leaf (72,044). Among the identified unigenes, we focused on fifteen putative ckTPS genes, which are involved in the synthesis of mono- and sesquiterpenes, the key aromatic compounds responsible for the essential oil biosynthesis in C. keiskei. The expression of these genes was validated using quantitative PCR analysis. Both DEG and qPCR analyses revealed the presence of ckTPS genes in the flower transcriptome, responsible for the synthesis of various compounds such as geraniol, germacrene, kaurene, linalool, nerolidol, trans-ocimene and valencene. The leaf transcriptome exhibited genes related to the biosynthesis of kaurene and trans-ocimene. In the root, the identified unigenes were associated with synthesizing kaurene, trans-ocimene and valencene. Both analyses indicated that the genes involved in mono- and sesquiterpene biosynthesis are more highly expressed in the flower compared to the leaf and root. This comprehensive study provides valuable resources for future investigations aiming to unravel the essential oil-biosynthesis-related genes in the Convallaria genus.
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Affiliation(s)
| | | | - Seon-Joo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
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Wei J, Yang Y, Peng Y, Wang S, Zhang J, Liu X, Liu J, Wen B, Li M. Biosynthesis and the Transcriptional Regulation of Terpenoids in Tea Plants ( Camellia sinensis). Int J Mol Sci 2023; 24:ijms24086937. [PMID: 37108101 PMCID: PMC10138656 DOI: 10.3390/ijms24086937] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Terpenes, especially volatile terpenes, are important components of tea aroma due to their unique scents. They are also widely used in the cosmetic and medical industries. In addition, terpene emission can be induced by herbivory, wounding, light, low temperature, and other stress conditions, leading to plant defense responses and plant-plant interactions. The transcriptional levels of important core genes (including HMGR, DXS, and TPS) involved in terpenoid biosynthesis are up- or downregulated by the MYB, MYC, NAC, ERF, WRKY, and bHLH transcription factors. These regulators can bind to corresponding cis-elements in the promoter regions of the corresponding genes, and some of them interact with other transcription factors to form a complex. Recently, several key terpene synthesis genes and important transcription factors involved in terpene biosynthesis have been isolated and functionally identified from tea plants. In this work, we focus on the research progress on the transcriptional regulation of terpenes in tea plants (Camellia sinensis) and thoroughly detail the biosynthesis of terpene compounds, the terpene biosynthesis-related genes, the transcription factors involved in terpene biosynthesis, and their importance. Furthermore, we review the potential strategies used in studying the specific transcriptional regulation functions of candidate transcription factors that have been discriminated to date.
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Affiliation(s)
- Junchi Wei
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Yun Yang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Ye Peng
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Shaoying Wang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Jing Zhang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Xiaobo Liu
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Jianjun Liu
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Beibei Wen
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Meifeng Li
- College of Tea Science, Guizhou University, Guiyang 550025, China
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