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Mi X, Tang M, Zhu J, Shu M, Wen H, Zhu J, Wei C. Alternative splicing of CsWRKY21 positively regulates cold response in tea plant. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108473. [PMID: 38430784 DOI: 10.1016/j.plaphy.2024.108473] [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: 12/05/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Alternative splicing (AS) was an important post-transcriptional mechanism that involved in plant resistance to adversity stress. WRKY transcription factors function as transcriptional activators or repressors to modulate plant growth, development and stress response. However, the role of alternate splicing of WRKY in cold tolerance is poorly understood in tea plants. In this study, we found that the CsWRKY21 transcription factor, a member of the WRKY IId subfamily, was induced by low temperature. Subcellular localization and transcriptional activity assays showed that CsWRKY21 localized to the nucleus and had no transcriptional activation activity. Y1H and dual-luciferase reporter assays showed that CsWRKY21 suppressed expression of CsABA8H and CsUGT by binding with their promoters. Transient overexpression of CsABA8H and CsUGT reduced abscisic acid (ABA) content in tobacco leaves. Furthermore, we discovered that CsWRKY21 undergoes AS in the 5'UTR region. The AS transcript CsWRKY21-b was induced at low temperature, up to 6 folds compared to the control, while the full-length CsWRKY21-a transcript did not significantly change. Western blot analysis showed that the retention of introns in the 5'UTR region of CsWRKY21-b led to higher CsWRKY21 protein content. These results revealed that alternative splicing of CsWRKY21 involved in cold tolerance of tea plant by regulating the protein expression level and then regulating the content of ABA, and provide insights into molecular mechanisms of low temperature defense mediated by AS in tea plant.
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Affiliation(s)
- Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China; Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang, Guizhou, 550006, People's Republic of China
| | - Mengsha Tang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China; Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang, Guizhou, 550006, People's Republic of China
| | - Jiaxin Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Mingtao Shu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Huilin Wen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
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Zhang Y, Van de Peer Y, Lu B, Zhang S, Che J, Chen J, Marchal K, Yang X. Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii. BMC Biol 2023; 21:244. [PMID: 37926805 PMCID: PMC10626718 DOI: 10.1186/s12915-023-01743-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Sterile-fertile heteroblasty is a common phenomenon observed in ferns, where the leaf shape of a fern sporophyll, responsible for sporangium production, differs from that of a regular trophophyll. However, due to the large size and complexity of most fern genomes, the molecular mechanisms that regulate the formation of these functionally different heteroblasty have remained elusive. To shed light on these mechanisms, we generated a full-length transcriptome of Ceratopteris chingii with PacBio Iso-Seq from five tissue samples. By integrating Illumina-based sequencing short reads, we identified the genes exhibiting the most significant differential expression between sporophylls and trophophylls. RESULTS The long reads were assembled, resulting in a total of 24,024 gene models. The differential expressed genes between heteroblasty primarily involved reproduction and cell wall composition, with a particular focus on expansin genes. Reconstructing the phylogeny of expansin genes across 19 plant species, ranging from green algae to seed plants, we identified four ortholog groups for expansins. The observed high expression of expansin genes in the young sporophylls of C. chingii emphasizes their role in the development of heteroblastic leaves. Through gene coexpression analysis, we identified highly divergent expressions of expansin genes both within and between species. CONCLUSIONS The specific regulatory interactions and accompanying expression patterns of expansin genes are associated with variations in leaf shapes between sporophylls and trophophylls.
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Affiliation(s)
- Yue Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bei Lu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Jingru Che
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Department of Information Technology, IDLab, IMEC, Ghent University, 9052, Ghent, Belgium.
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China.
- Hubei Ecology Polytechnic College, Wuhan, 430200, China.
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Zhu C, Zhang S, Zhou C, Tian C, Shi B, Xu K, Huang L, Sun Y, Lin Y, Lai Z, Guo Y. RNA Methylome Reveals the m 6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:769-787. [PMID: 36791953 PMCID: PMC10787128 DOI: 10.1016/j.gpb.2023.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/20/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
The epitranscriptomic mark N6-methyladenosine (m6A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m6A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized. We performed an integrated RNA methylome and transcriptome analysis to explore the m6A-mediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea (Camellia sinensis) leaves under solar-withering conditions. Dynamic changes in global m6A level in tea leaves were mainly controlled by two m6A erasers (CsALKBH4A and CsALKBH4B) during solar-withering treatments. Differentially methylated peak-associated genes following solar-withering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid, catechin, and theaflavin contents by triggering alternative splicing-mediated regulation. Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m6A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Biying Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Linjie Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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An Y, Mi X, Xia X, Qiao D, Yu S, Zheng H, Jing T, Zhang F. Genome-wide identification of the PYL gene family of tea plants (Camellia sinensis) revealed its expression profiles under different stress and tissues. BMC Genomics 2023; 24:362. [PMID: 37380940 DOI: 10.1186/s12864-023-09464-5] [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: 02/21/2023] [Accepted: 06/17/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND PYL (Pyrabactin resistance 1-like) protein is a receptor of abscisic acid (ABA), which plays an important role in ABA signaling and influences plant growth and development and stress response. However, studies on PYL gene family in tea plants have not been reported. RESULTS In this study, we identified 20 PYL genes from the reference genome of tea plant ('Shuchazao'). Phylogeny analysis indicated that PYLs from tea and other plant species were clustered into seven groups. The promoter region of PYL genes contains a large number of cis-elements related to hormones and stresses. A large number of PYL genes responding to stress were found by analyzing the expression levels of abiotic stress and biotic stress transcriptome data. For example, CSS0047272.1 were up-regulated by drought stress, and CSS0027597.1 could respond to both anthracnose disease and geometrid feeding treatments. In addition, 10 PYL genes related to growth and development were verified by RT-qPCR and their tissue expression characteristics were revealed. CONCLUSIONS Our results provided a comprehensive characteristic of the PYL gene family in tea plants and provided an important clue for further exploring its functions in the growth and development, and resistance to stress of tea plants.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, P.R. China
| | - Xiaozeng Mi
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jinxin Community, Guiyang, 550025, Guizhou, China
| | - Xiaobo Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dahe Qiao
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jinxin Community, Guiyang, 550025, Guizhou, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, P.R. China
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, P.R. China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, P.R. China.
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Bi C, Han W, Yu J, Zhang H, Xing G, Liu Z. Insights into the pharmacological and therapeutic effects of apigenin in liver injuries and diseases. Heliyon 2023; 9:e15609. [PMID: 37144193 PMCID: PMC10151377 DOI: 10.1016/j.heliyon.2023.e15609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
Background Liver diseases are a spectrum of diseases that include hepatic steatosis, nonalcoholic fatty liver disease, hepatitis, liver fibrosis, cirrhosis, and hepatic cancer. These diseases not only severely decrease the quality of life for patients, but also cause financial burden. Although apigenin (APG) has recently become the primary treatment for liver injuries and diseases (LIADs), there has been no systematic review of its use. Purpose To review the existing literature and put forward novel strategies for future APG research on LIADs. Methods A search was conducted in PubMed, Science Direct, Research Gate, Web of Science, VIP, Wanfang, and CNKI, and 809 articles were obtained. After applying inclusion and exclusion criteria, 135 articles were included. Results APG is promising in treating LIADs via various mechanisms arising from its anti-inflammation, anti-proliferation, anti-infection, anti-oxidation, and anti-cancer properties. Conclusion This review summarizes the evidence supporting the use of APG as a treatment for LIADs and provides an insight into the intestinal microbiota, which may have important implications in its future clinical use.
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Affiliation(s)
- Chenchen Bi
- Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
- Department of Clinical Medicine, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
| | - Wenwen Han
- Department of Clinical Medicine, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
| | - Jingru Yu
- Department of Clinical Medicine, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
| | - Huafang Zhang
- Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
| | - Guiying Xing
- Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
- Corresponding author.
| | - Zheng Liu
- Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, P. R. China
- Corresponding author.
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Mi X, Yang C, Qiao D, Tang M, Guo Y, Liang S, Li Y, Chen Z, Chen J. De novo full length transcriptome analysis of a naturally caffeine-free tea plant reveals specificity in secondary metabolic regulation. Sci Rep 2023; 13:6015. [PMID: 37045909 PMCID: PMC10097665 DOI: 10.1038/s41598-023-32435-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Tea plants are crops with economic, health and cultural value. Catechin, caffeine and theanine are the main secondary metabolites of taste. In the process of germplasm collection, we found a resource in the Sandu Aquatic Autonomous County of Guizhou (SDT) that possessed significantly different characteristic metabolites compared with the cultivar 'Qiancha 1'. SDT is rich in theobromine and theophylline, possesses low levels of (-)-epicatechin-3-gallate, (-)-epigallocatechin-3-gallate, and theanine content, and is almost free of caffeine. However, research on this tea resource is limited. Full-length transcriptome analysis was performed to investigate the transcriptome and gene expression of these metabolites. In total, 78,809 unique transcripts were obtained, of which 65,263 were complete coding sequences. RNA-seq revealed 3415 differentially expressed transcripts in the tender leaves of 'Qiancha 1' and 'SDT'. Furthermore, 2665, 6231, and 2687 differentially expressed transcripts were found in different SDT tissues. These differentially expressed transcripts were enriched in flavonoid and amino acid metabolism processes. Co-expression network analysis identified five modules associated with metabolites and found that genes of caffeine synthase (TCS) may be responsible for the low caffeine content in SDT. Phenylalanine ammonia lyase (PAL), glutamine synthetase (GS), glutamate synthase (GOGAT), and arginine decarboxylase (ADC) play important roles in the synthesis of catechin and theanine. In addition, we identified that ethylene resposive factor (ERF) and WRKY transcription factors may be involved in theanine biosynthesis. Overall, our study provides candidate genes to improve understanding of the synthesis mechanisms of these metabolites and provides a basis for molecular breeding of tea plant.
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Affiliation(s)
- Xiaozeng Mi
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Chun Yang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Dahe Qiao
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Mengsha Tang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Yan Guo
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Sihui Liang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Yan Li
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Zhengwu Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Juan Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China.
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Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
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Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
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Guo P, Huang Z, Li X, Zhao W, Wang Y. Transcriptome Sequencing of Broussonetia papyrifera Leaves Reveals Key Genes Involved in Flavonoids Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:563. [PMID: 36771647 PMCID: PMC9920218 DOI: 10.3390/plants12030563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Broussonetia papyrifera is rich in flavonoids, which have significant antioxidant, antibacterial, and anti-inflammatory activities and certain pharmacological activities. Nevertheless, scarce transcriptome resources of B. papyrifera have impeded further study regarding the process of its production and accumulation. In this study, RNA-seq was utilized to evaluate the gene expression of B. papyrifera leaves at three distinct developmental phases (T1: young leaves, T3: immature leaves, T4: matured leaves). We obtained 2447 upregulated and 2960 downregulated DEGs, 4657 upregulated and 4804 downregulated DEGs, and 805 upregulated and 484 downregulated DEGs from T1 vs. T3, T1 vs. T4, and T3 vs. T4, respectively. Further research found that the following variables contributed to the formation of flavonoids in the leaves of B. papyrifera: Several important enzyme genes involved in flavonoid production pathways have been discovered. The results demonstrated that the dynamic changing trend of flavonoid contents is related to the expression pattern of the vast majority of essential genes in the biosynthetic pathway. Genes associated in energy and glucose metabolism, polysaccharide, cell wall and cytoskeleton metabolism, signal transduction, and protein and amino acid metabolism may affect the growth and development of B. papyrifera leaves, and eventually their flavonoid content. This study's results offer a strong platform for future research into the metabolic pathways of B. papyrifera.
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Affiliation(s)
- Peng Guo
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Zhengzhou 450046, China
| | - Ziqi Huang
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Zhengzhou 450046, China
| | - Xinke Li
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Zhengzhou 450046, China
| | - Wei Zhao
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Zhengzhou 450046, China
| | - Yihan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Zhengzhou 450046, China
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Nelson TM, Ghosh S, Postler TS. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int J Mol Sci 2022; 23:ijms232415851. [PMID: 36555493 PMCID: PMC9781625 DOI: 10.3390/ijms232415851] [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: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Long-read sequencing (LRS) has been adopted to meet a wide variety of research needs, ranging from the construction of novel transcriptome annotations to the rapid identification of emerging virus variants. Amongst other advantages, LRS preserves more information about RNA at the transcript level than conventional high-throughput sequencing, including far more accurate and quantitative records of splicing patterns. New studies with LRS datasets are being published at an exponential rate, generating a vast reservoir of information that can be leveraged to address a host of different research questions. However, mining such publicly available data in a tailored fashion is currently not easy, as the available software tools typically require familiarity with the command-line interface, which constitutes a significant obstacle to many researchers. Additionally, different research groups utilize different software packages to perform LRS analysis, which often prevents a direct comparison of published results across different studies. To address these challenges, we have developed the Long-Read Analysis Pipeline for Transcriptomics (L-RAPiT), a user-friendly, free pipeline requiring no dedicated computational resources or bioinformatics expertise. L-RAPiT can be implemented directly through Google Colaboratory, a system based on the open-source Jupyter notebook environment, and allows for the direct analysis of transcriptomic reads from Oxford Nanopore and PacBio LRS machines. This new pipeline enables the rapid, convenient, and standardized analysis of publicly available or newly generated LRS datasets.
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Liu H, Liu Q, Chen Y, Zhu Y, Zhou X, Li B. Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Camellia nitidissima Petals. Gene 2022; 850:146924. [PMID: 36191826 DOI: 10.1016/j.gene.2022.146924] [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: 06/08/2022] [Revised: 09/01/2022] [Accepted: 09/25/2022] [Indexed: 10/06/2022]
Abstract
Flavonoids are the main medicinal ingredients in Camellia nitidissima, but the regulatory mechanism of flavonoid biosynthesis in flowers is unclear; therefore, the flavonoids in C. nitidissima have not been effectively used. The present study performed full-length transcriptome sequencing of C. nitidissima flower. Furthermore, the reported RNA-sequencing data of C. nitidissima petals were reanalyzed using the full-length transcriptome as a reference, and the regulatory mechanism of flavonoid synthesis in petals was elucidated. The analysis identified 43,350 isoforms annotated in non-redundant protein (Nr), Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups (KOG), and Swiss-Prot databases, among which 34,602 aligned to Camellia sinensis genes. A total of 11,857 differentially expressed genes (DEGs), including 112 related to flavonoid synthesis, were identified by pairwise comparison. Subsequently, analysis of the phylogeny and the conserved motifs of R2R3-MYB using the proteins sequences identified three R2R3-MYB transcription factors that regulated flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified phenylalanine ammonia-lyase (PAL) and 4-coumarate: CoA ligase(4CL) as the hub genes and showed that bHLH79 interacted with PAL. Finally, validated the expression of seven DEGs involved in flavonoid biosynthesis using real-time quantitative PCR (qRT-PCR). Thus, the present study generated and used the full-length transcriptome as the reference to analyze the transcriptome of petals and proposed a possible regulatory mechanism of flavonoid synthesis in C. nitidissima. The study's findings unravel the genetic mechanisms underlying flavonoid synthesis and suggest candidate genes for the genetic improvement of C. nitidissima.
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Affiliation(s)
- Hexia Liu
- College of Biology and Pharmacy, Yulin Normal University, Yulin 537000, China
| | - Qin Liu
- College of Biology and Pharmacy, Yulin Normal University, Yulin 537000, China
| | - Yuling Chen
- College of Biology and Pharmacy, Yulin Normal University, Yulin 537000, China
| | - Yulin Zhu
- College of Biology and Pharmacy, Yulin Normal University, Yulin 537000, China.
| | - Xingwen Zhou
- College of Architecture and Planning, FuJian University of Technology, Fuzhou 350108, China.
| | - Bo Li
- College of Biology and Pharmacy, Yulin Normal University, Yulin 537000, China.
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11
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D’Auria JC, Cohen SP, Leung J, Glockzin K, Glockzin KM, Gervay-Hague J, Zhang D, Meinhardt LW. United States tea: A synopsis of ongoing tea research and solutions to United States tea production issues. FRONTIERS IN PLANT SCIENCE 2022; 13:934651. [PMID: 36212324 PMCID: PMC9538180 DOI: 10.3389/fpls.2022.934651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/25/2022] [Indexed: 06/01/2023]
Abstract
Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States.
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Affiliation(s)
- John C. D’Auria
- Metabolic Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stephen P. Cohen
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Jason Leung
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Kyle Mark Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jacquelyn Gervay-Hague
- Department of Chemistry, University of California, University of California, Davis, Davis, CA, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
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12
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Hao DC, Chen H, Xiao PG, Jiang T. A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales. Curr Genomics 2022; 23:207-216. [PMID: 36777007 PMCID: PMC9878827 DOI: 10.2174/1389202923666220527112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The multiple isoforms are often generated from a single gene via Alternative Splicing (AS) in plants, and the functional diversity of the plant genome is significantly increased. Despite well-studied gene functions, the specific functions of isoforms are little known, therefore, the accurate prediction of isoform functions is exceedingly wanted. Methods: Here we perform the first global analysis of AS of Dichocarpum, a medicinal genus of Ranunculales, by utilizing full-length transcriptome datasets of five Chinese endemic Dichocarpum taxa. Multiple software were used to identify AS events, the gene function was annotated based on seven databases, and the protein-coding sequence of each AS isoform was translated into an amino acid sequence. The self-developed software DIFFUSE was used to predict the functions of AS isoforms. Results: Among 8,485 genes with AS events, the genes with two isoforms were the most (6,038), followed by those with three isoforms and four isoforms. Retained intron (RI, 551) was predominant among 1,037 AS events, and alternative 3' splice sites and alternative 5' splice sites were second. The software DIFFUSE was effective in predicting functions of Dichocarpum isoforms, which have not been unearthed. When compared with the sequence alignment-based database annotations, DIFFUSE performed better in differentiating isoform functions. The DIFFUSE predictions on the terms GO:0003677 (DNA binding) and GO: 0010333 (terpene synthase activity) agreed with the biological features of transcript isoforms. Conclusion: Numerous AS events were for the first time identified from full-length transcriptome datasets of five Dichocarpum taxa, and functions of AS isoforms were successfully predicted by the self-developed software DIFFUSE. The global analysis of Dichocarpum AS events and predicting isoform functions can help understand the metabolic regulations of medicinal taxa and their pharmaceutical explorations.
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Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China;,Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;,Address correspondence to these authors at the School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China; Tel: 0086-411-84572552; E-mail: ; and Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Tel/Fax: 001-951-827-2991; E-mail:
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA;,Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA;,These authors contributed equally to this work.
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA;,Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China,Address correspondence to these authors at the School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China; Tel: 0086-411-84572552; E-mail: ; and Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Tel/Fax: 001-951-827-2991; E-mail:
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13
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Zhao S, Cheng H, Xu P, Wang Y. Regulation of biosynthesis of the main flavor-contributing metabolites in tea plant ( Camellia sinensis): A review. Crit Rev Food Sci Nutr 2022; 63:10520-10535. [PMID: 35608014 DOI: 10.1080/10408398.2022.2078787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the process of adapting to the environment, tea plants (Camellia sinensis) endow tea with unique flavor and health functions, which should be attributed to secondary metabolites, including catechins, L-theanine, caffeine and terpene volatiles. Since the content of these flavor-contributing metabolites are mainly determined by the growth of tea plant, it is very important to understand their alteration and regulation mechanisms. In the present work, we first summarize the distribution, change characteristics of the main flavor-contributing metabolites in different cultivars, organs and under environmental stresses of tea plant. Subsequently, we discuss the regulating mechanisms involved in the biosynthesis of these metabolites based on the existing evidence. Finally, we propose the remarks and perspectives on the future study relating flavor-contributing metabolites. This review would contribute to the acceleration of research on the characteristic secondary metabolites and the breeding programs in tea plants.
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Affiliation(s)
- Shiqi Zhao
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Haiyan Cheng
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Ping Xu
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Yuefei Wang
- Tea Research Institute, Zhejiang University, Hangzhou, China
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14
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Multi-omics approach in tea polyphenol research regarding tea plant growth, development and tea processing: current technologies and perspectives. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Li P, Xia E, Fu J, Xu Y, Zhao X, Tong W, Tang Q, Tadege M, Fernie AR, Zhao J. Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1144-1165. [PMID: 35277905 DOI: 10.1111/tpj.15729] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 05/20/2023]
Abstract
Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.
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Affiliation(s)
- Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jiamin Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xuecheng Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, Oklahoma, 73401, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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16
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Ding YQ, Fan K, Wang Y, Fang WP, Zhu XJ, Chen L, Sun LT, Qiu C, Ding ZT. Drought and Heat Stress-Mediated Modulation of Alternative Splicing in the Genes Involved in Biosynthesis of Metabolites Related to Tea Quality. Mol Biol 2022. [DOI: 10.1134/s0026893322020042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Mao L, Jin B, Chen L, Tian M, Ma R, Yin B, Zhang H, Guo J, Tang J, Chen T, Lai C, Cui G, Huang L. Functional identification of the terpene synthase family involved in diterpenoid alkaloids biosynthesis in Aconitum carmichaelii. Acta Pharm Sin B 2021; 11:3310-3321. [PMID: 34729318 PMCID: PMC8546855 DOI: 10.1016/j.apsb.2021.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Aconitum carmichaelii is a high-value medicinal herb widely used across China, Japan, and other Asian countries. Aconitine-type diterpene alkaloids (DAs) are the characteristic compounds in Aconitum. Although six transcriptomes, based on short-read next generation sequencing technology, have been reported from the Aconitum species, the terpene synthase (TPS) corresponding to DAs biosynthesis remains unidentified. We apply a combination of Pacbio isoform sequencing and RNA sequencing to provide a comprehensive view of the A. carmichaelii transcriptome. Nineteen TPSs and five alternative splicing isoforms belonging to TPS-b, TPS-c, and TPS-e/f subfamilies were identified. In vitro enzyme reaction analysis functional identified two sesqui-TPSs and twelve diTPSs. Seven of the TPS-c subfamily genes reacted with GGPP to produce the intermediate ent-copalyl diphosphate. Five AcKSLs separately reacted with ent-CPP to produce ent-kaurene, ent-atiserene, and ent-13-epi-sandaracopimaradie: a new diterpene found in Aconitum. AcTPSs gene expression in conjunction DAs content analysis in different tissues validated that ent-CPP is the sole precursor to all DAs biosynthesis, with AcKSL1, AcKSL2s and AcKSL3-1 responsible for C20 atisine and napelline type DAs biosynthesis, respectively. These data clarified the molecular basis for the C20-DAs biosynthetic pathway in A. carmichaelii and pave the way for further exploration of C19-DAs biosynthesis in the Aconitum species.
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Affiliation(s)
- Liuying Mao
- College of Pharmacy, Shandong University of Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baolong Jin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lingli Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mei Tian
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Rui Ma
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Biwei Yin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Haiyan Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jinfu Tang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Tong Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Changjiangsheng Lai
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guanghong Cui
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luqi Huang
- College of Pharmacy, Shandong University of Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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18
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Fan M, Yang K, Zhou R, Liu Q, Guo X, Sun Y. Temporal transcriptome profiling reveals candidate genes involved in cold acclimation of Camellia japonica (Naidong). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:795-805. [PMID: 34530324 DOI: 10.1016/j.plaphy.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 05/15/2023]
Abstract
Cold is a common problem that limits the distribution of Camellia. Camellia japonica (Naidong) is the northernmost species of camellia in China, which is a Tertiary remnant species that can adapt to large changes in temperature. An analysis of the transcriptional response of C. japonica (Naidong) to cold is very important for the planting and distribution of camellia. In this study, the rate of H₂O₂ levels, electrolyte leakage, chlorophyll and sugar content had a higher degree of cold response during 12-72 h period, than other periods (0-12h, 72h-120h) in C. japonica (Naidong) response to cold treatment. We constructed the first full-length C. japonica (Naidong) transcriptome and identified 4544 significantly differentially expressed genes (DEGs). A weighted gene coexpression network analysis showed that carbon metabolism, lipid metabolism, and transcription factors played important roles in the resistance of C. japonica (Naidong) to cold stress, and three hub transcription factor regulatory networks were constructed. In addition, overexpressing CjRAV1 led to cold sensitivity in Arabidopsis thaliana, thus CjRAV1 likely plays a negative regulatory role during cold stress in Camellia japonica. This study deepens our understanding of the regulatory mechanism of C. japonica (Naidong) under cold stress and will benefit genetic improvement of camellia.
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Affiliation(s)
- MengLong Fan
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kai Yang
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China; College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Rui Zhou
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - QingHua Liu
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao Guo
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - YingKun Sun
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao, 266109, China.
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19
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Zhang C, Ren H, Yao X, Wang K, Chang J. Full-length transcriptome analysis of pecan ( Carya illinoinensis) kernels. G3 GENES|GENOMES|GENETICS 2021; 11:6288450. [PMID: 34849807 PMCID: PMC8496322 DOI: 10.1093/g3journal/jkab182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022]
Abstract
Abstract
Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.
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Affiliation(s)
- Chengcai Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jun Chang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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20
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Li X, Wu J, Xiao X, Rong Y, Yang H, Li J, Zhou Q, Zhou W, Shi J, Qi H, Du H. Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq. DNA Res 2021; 28:6275749. [PMID: 33989386 PMCID: PMC8320875 DOI: 10.1093/dnares/dsab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 bp with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT–PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.
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Affiliation(s)
- Xindan Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jinming Wu
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Xinping Xiao
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yifeng Rong
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Haile Yang
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Junyi Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Qiong Zhou
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Weiguo Zhou
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Jianquan Shi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hongfang Qi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hao Du
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China.,The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
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21
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Mei M, Wei J, Ai W, Zhang L, Lu XJ. Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination. Sci Rep 2021; 11:10842. [PMID: 34035372 PMCID: PMC8149418 DOI: 10.1038/s41598-021-90270-y] [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: 09/03/2020] [Accepted: 04/20/2021] [Indexed: 02/04/2023] Open
Abstract
Magnolia sieboldii K. Koch (M. sieboldii) is a deciduous Chinese tree species of the Magnoliaceae family with high ornamental, medicinal, and economic benefits. The germination of M. sieboldii seeds under natural conditions is extremely difficult, thereby hindering the cultivation and breeding of this important species. The molecular mechanisms underlying M. sieboldii seed germination remain unclear due to the lack of genomic and transcriptomic resources. Here, we integrated both mRNA and miRNA sequencing to identify the genes and pathways related to M. sieboldii germination. A comprehensive full-length transcriptome containing 158,083 high-quality unigenes was obtained by single-molecule real-time (SMRT) sequencing technology. We identified a total of 13,877 genes that were differentially expressed between non-germinated and germinated seeds. These genes were mainly involved in plant hormone signal transduction and diverse metabolic pathways such as those involving lipids, sugars, and amino acids. Our results also identified a complex regulatory network between miRNAs and their target genes. Taken together, we present the first transcriptome of M. sieboldii and provide key genes and pathways associated with seed germination for further characterization. Future studies of the molecular basis of seed germination will facilitate the genetic improvement M. sieboldii.
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Affiliation(s)
- Mei Mei
- grid.412557.00000 0000 9886 8131Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jun Wei
- grid.9227.e0000000119573309Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wanfeng Ai
- grid.412557.00000 0000 9886 8131Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Lijie Zhang
- grid.412557.00000 0000 9886 8131Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiu-jun Lu
- grid.412557.00000 0000 9886 8131Department of Forestry, Shenyang Agricultural University, Shenyang, China
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22
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SMRT sequencing of full-length transcriptome of birch-leaf pear (Pyrus betulifolia Bunge) under drought stress. J Genet 2021. [DOI: 10.1007/s12041-021-01272-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Zhang Y, Li P, She G, Xu Y, Peng A, Wan X, Zhao J. Molecular Basis of the Distinct Metabolic Features in Shoot Tips and Roots of Tea Plants ( Camellia sinensis): Characterization of MYB Regulator for Root Theanine Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3415-3429. [PMID: 33719427 DOI: 10.1021/acs.jafc.0c07572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The physiological and metabolic differences between shoot tips and roots of tea plants are significant, and understanding them is required for improvement of tea quality and plant growth. A high-quality full-length transcriptome sequencing on tea plant roots and shoot tips by PacBio SMRT technology was done to gain a further understanding. Approximately 160699 and 166120 full-length transcripts were recovered in roots and shoots, respectively, including 31232 and 41068 novel isoforms and 16960 and 26029 alternative splicing (AS) isoforms. These supported 21699 full-length reads and 31232 and 41068 novel transcripts from root and shoot, respectively, including 1679 long noncoding RNAs (lncRNAs) and 2772 fusion transcripts, which significantly upgrade the Camellia sinensis genome annotation. The respective 6475 and 6981 transcripts in roots and shoots differ in 3'-untranslated regions. Meanwhile, extensive analyses of novel transcripts, ASs, and lncRNAs also revealed a large number of ASs and lincRNAs closely related to the regulation of characteristic secondary metabolites including catechins, theanine, and caffeine. Finally, a root-specific CsMYB6 was characterized to regulate theanine biosynthesis by genetic and molecular analyses. CsMYB6 directly bound to and activate the promoter of theanine synthetase gene (CsTSI). The study lays a foundation for the further investigation of metabolic genomics and regulation in tea plants.
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Affiliation(s)
- Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Anqi Peng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
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24
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Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021; 10:62438. [PMID: 33460557 PMCID: PMC7815308 DOI: 10.7554/elife.62438] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. In most organisms, specific segments of a cell’s genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are ‘non-coding’ and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.
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Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, United States
| | - Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kavya Chegireddy
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Molly Monge
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, United States.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
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25
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Zhu C, Zhang S, Zhou C, Xie S, Chen G, Tian C, Xu K, Lin Y, Lai Z, Guo Y. Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea ( Camellia sinensis) Leaves During Withering Process. FRONTIERS IN PLANT SCIENCE 2021; 12:702303. [PMID: 34211493 PMCID: PMC8240813 DOI: 10.3389/fpls.2021.702303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/24/2021] [Indexed: 05/12/2023]
Abstract
N6-methyladenosine (m6A), one of the internal modifications of RNA molecules, can directly influence RNA abundance and function without altering the nucleotide sequence, and plays a pivotal role in response to diverse environmental stresses. The precise m6A regulatory mechanism comprises three types of components, namely, m6A writers, erasers, and readers. To date, the research focusing on m6A regulatory genes in plant kingdom is still in its infancy. Here, a total of 34 m6A regulatory genes were identified from the chromosome-scale genome of tea plants. The expansion of m6A regulatory genes was driven mainly by whole-genome duplication (WGD) and segmental duplication, and the duplicated gene pairs evolved through purifying selection. Gene structure analysis revealed that the sequence variation contributed to the functional diversification of m6A regulatory genes. Expression pattern analysis showed that most m6A regulatory genes were differentially expressed under environmental stresses and tea-withering stage. These observations indicated that m6A regulatory genes play essential roles in response to environmental stresses and tea-withering stage. We also found that RNA methylation and DNA methylation formed a negative feedback by interacting with each other's methylation regulatory genes. This study provided a foundation for understanding the m6A-mediated regulatory mechanism in tea plants under environmental stresses and tea-withering stage.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siyi Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangwu Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Zhongxiong Lai,
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
- Yuqiong Guo,
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26
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An Y, Chen L, Tao L, Liu S, Wei C. QTL Mapping for Leaf Area of Tea Plants ( Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:705285. [PMID: 34394160 PMCID: PMC8358608 DOI: 10.3389/fpls.2021.705285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 05/08/2023]
Abstract
High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.
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Affiliation(s)
- Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Linbo Chen
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Lingling Tao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Chaoling Wei,
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27
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Chen C, Shi X, Zhou T, Li W, Li S, Bai G. Full-length transcriptome analysis and identification of genes involved in asarinin and aristolochic acid biosynthesis in medicinal plant Asarum sieboldii. Genome 2020; 64:639-653. [PMID: 33320770 DOI: 10.1139/gen-2020-0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asarum sieboldii, a well-known traditional Chinese medicinal herb, is used for curing inflammation and ache. It contains both the bioactive ingredient asarinin and the toxic compound aristolochic acid. To address further breeding demand, genes involved in the biosynthetic pathways of asarinin and aristolochic acid should be explored. Therefore, the full-length transcriptome of A. sieboldii was sequenced using PacBio Iso-Seq to determine the candidate transcripts that encode the biosynthetic enzymes of asarinin and aristolochic acid. In this study, 63 023 full-length transcripts were generated with an average length of 1371 bp from roots, stems, and leaves, of which 49 593 transcripts (78.69%) were annotated against public databases. Furthermore, 555 alternative splicing (AS) events, 10 869 long noncoding RNAs (lncRNAs) as well as their 11 291 target genes, and 17 909 simple sequence repeats (SSRs) were identified. The data also revealed 97 candidate transcripts related to asarinin metabolism, of which six novel genes that encoded enzymes involved in asarinin biosynthesis were initially reported. In addition, 56 transcripts related to aristolochic acid biosynthesis were also identified, including CYP81B. In summary, these transcriptome data provide a useful resource to study gene function and genetic engineering in A. sieboldii.
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Affiliation(s)
- Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Xinwei Shi
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Tao Zhou
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76 Yanta West Road, 710061, Xi'an City, Shaanxi Province, China
| | - Weimin Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Sifeng Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
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28
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Zhang S, Liu Q, Lyu C, Chen J, Xiao R, Chen J, Yang Y, Zhang H, Hou K, Wu W. Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana. BMC Genomics 2020; 21:794. [PMID: 33187479 PMCID: PMC7664074 DOI: 10.1186/s12864-020-07195-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/27/2020] [Indexed: 01/21/2023] Open
Abstract
Background Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides. Results Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a full-length transcriptome of S. rebaudiana. Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2, SrUGT74G1, SrUGT76G1 and SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results. Conclusion Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07195-5.
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Affiliation(s)
- Shaoshan Zhang
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China.,Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Qiong Liu
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chengcheng Lyu
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinsong Chen
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Renfeng Xiao
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingtian Chen
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunshu Yang
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huihui Zhang
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Hou
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Wu
- Agronomy College, Sichuan Agricultural University, Chengdu, 611130, China.
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29
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Wang F, Chen Z, Pei H, Guo Z, Wen D, Liu R, Song B. Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology. Gene 2020; 769:145247. [PMID: 33096183 DOI: 10.1016/j.gene.2020.145247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/16/2020] [Accepted: 10/15/2020] [Indexed: 01/22/2023]
Abstract
Transcriptome profiles have been widely captured using short-read sequencing technology, but there are still limitations partially due to the read length. Here, we generated long reads using Oxford Nanopore PromethION™ technology and short reads using the Illumina sequencing platform to study the transcriptome of root, stem, and leaf of Camellia sinensis cv. Fudingdabai. We mapped the Nanopore reads to the Shuchazao of C. sinensis genome sequence, and the mapping rates ranged from 82.63% to 90.59% (average 86.44%); this is lower than that of the Illumina reads which was 87.83% to 91.14% (average 90.12%). Gene expression level was quantified using the Nanopore and Illumina data and we observed a good agreement. The same tea leaf flavor synthesis pathways were highlighted using both sequencing technologies when analyzing the differentially expressed genes between leaf and root. Alternative splicing was then analyzed, and the intron-retention was observed as the most common alternative splicing. Moreover Nanopore long reads could correct transcript isoform annotation for differential expression investigation purposes. Nanopore sequencing techniques can provide a novel reference basis for molecular analysis of tea plants.
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Affiliation(s)
- Fen Wang
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China.
| | - Zhi Chen
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Huimin Pei
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Zhiyou Guo
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Di Wen
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Rong Liu
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Baoxing Song
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China.
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30
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Wu Q, Zang F, Xie X, Ma Y, Zheng Y, Zang D. Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. Sci Rep 2020; 10:16249. [PMID: 33004908 PMCID: PMC7530656 DOI: 10.1038/s41598-020-73289-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
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Affiliation(s)
- Qichao Wu
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Fengqi Zang
- Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Xiaoman Xie
- Center for Forest Genetic Resources of Shandong Province, Jinan, 250014, People's Republic of China
| | - Yan Ma
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Yongqi Zheng
- Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Dekui Zang
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
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31
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Alternative Splicing Regulation of Anthocyanin Biosynthesis in Camellia sinensis var. assamica Unveiled by PacBio Iso-Seq. G3-GENES GENOMES GENETICS 2020; 10:2713-2723. [PMID: 32518082 PMCID: PMC7407465 DOI: 10.1534/g3.120.401451] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although the pathway and transcription factor regulation of anthocyanin biosynthesis in tea plants [Camellia sinensis (L.) O. Ktze] are known, post-transcriptional regulation mechanisms involved in anthocyanin accumulation have not been comprehensively studied. We obtained the full-length transcriptome of a purple cultivar (‘Zijuan’) and a normal green cultivar (‘Yunkang 10#) of C. sinensis var. asssamica (Masters) showing different accumulation of anthocyanins and catechins through PacBio isoform sequencing (Iso-Seq). In total, 577,557 mapped full-length cDNAs were obtained, and 2,600 average-length gene isoforms were identified in both cultivars. After gene annotations and pathway predictions, we found that 98 key genes in anthocyanin biosynthesis pathways could have undergone alternative splicing (AS) events, and identified a total of 238 isoforms involved in anthocyanin biosynthesis. We verified expression of the C4H, CHS, FLS, CCOM, F3′5’H, LAR, PAL, CCR, CYP73A13, UDP75L12, UDP78A15/UFGT, UDP94P1, GL3, MYB113, ANR, ANS, F3H, 4CL1, CYP98A3/C3H, CHI, DFR genes and their AS transcripts using qRT-PCR. Correlation analysis of anthocyanin biosynthesis and gene expression results revealed that C4H1, FLS1, PAL2, CCR2, UDP75L122 and MYB113-1 are crucial AS transcripts for regulating anthocyanin biosynthesis in C. sinensis var. assamica. Our results reveal post-transcriptional regulation of anthocyanin biosynthesis in tea plants, and provide more new insights into the regulation of secondary metabolism.
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Sun S, Li Y, Chu L, Kuang X, Song J, Sun C. Full-length sequencing of ginkgo transcriptomes for an in-depth understanding of flavonoid and terpenoid trilactone biosynthesis. Gene 2020; 758:144961. [PMID: 32693148 DOI: 10.1016/j.gene.2020.144961] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Ginkgo biloba L. is regarded as the most ancient living tree, and its kernel has been used as a traditional Chinese medicine for more than 2,000 years. The leaf extracts of this tree have been among the bestselling herbal remedies in Western countries since the last century. To understand the biosynthesis of the pharmacologically active ingredients in G. biloba, flavonoids and terpenoid trilactones (TTLs), we sequenced the transcriptomes of G. biloba leaves, kernels and testae with Iso-Seq and RNA-Seq technologies and obtained 152,524 clean consensus reads. When these reads were used to improve the annotation of the G. biloba genome, 4,856 novel genes, 25,583 new isoforms of previously annotated genes and 4,363 lncRNAs were discovered. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that genes involved in growth, regulation and response to stress were more likely to be regulated by alternative splicing (AS) or alternative polyadenylation (APA), which represent the two most important posttranscriptional regulation mechanisms. It was found that some of the characterized genes involved in the biosynthesis of flavonoids and TTLs were also possibly regulated by AS and APA. Using phylogenetic and gene expression pattern analyses, some candidate genes for the biosynthesis of flavonoids and TTLs were screened. After qRT-PCR validation, the final candidate genes for flavonoid biosynthesis included three UDP-glycosyltransferases and one MYB transcription factor, while the candidate genes for TTL biosynthesis included two cytochrome P450 and one WRKY transcription factor. Our study suggested that Iso-Seq may play an important role in improving genome annotation, elucidating AS and APA mechanisms and discovering candidate genes involved in the biosynthesis of some secondary metabolites.
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Affiliation(s)
- Sijie Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Lihua Chu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xuejun Kuang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Chao Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China.
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Yang Y, Zhou Z, Li Y, Lv Y, Yang D, Yang S, Wu J, Li X, Gu Z, Sun X, Yang Y. Uncovering the role of a positive selection site of wax ester synthase/diacylglycerol acyltransferase in two closely related Stipa species in wax ester synthesis under drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4159-4170. [PMID: 32309855 PMCID: PMC7475244 DOI: 10.1093/jxb/eraa194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/17/2020] [Indexed: 06/02/2023]
Abstract
Natural selection drives local adaptations of species to biotic or abiotic environmental stresses. As a result, adaptive phenotypic divergence can evolve among related species living in different habitats. However, the genetic foundation of this divergence process remains largely unknown. Two closely related alpine grass species, Stipa capillacea and Stipa purpurea, are distributed in different rainfall regions of northern Tibet. Here, we analyzed the drought tolerance of these two closely related Stipa species, and found that S. purpurea was more resistance to drought stress than S. capillacea. To further understand the genetic diversity behind their adaptation to drought environments, a comprehensive gene repertoire was generated using PacBio isoform and Illumina RNA sequencing technologies. Bioinformatics analyses revealed that differential transcripts were mainly enriched in the wax synthetic pathway, and a threonine residue at position 239 of WSD1 was identified as having undergone positive selection in S. purpurea. Using heterologous expression in the Saccharomyces cerevisiae mutant H1246, site-directed mutagenesis studies demonstrated that a positive selection site results in changes to the wax esters profile. This difference may play an important role in S. purpurea in response to drought conditions, indicating that S. purpurea has evolved specific strategies involving its wax biosynthetic pathway as part of its long-term adaptation to the Qinghai-Tibet Plateau.
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Affiliation(s)
- Yunqiang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhili Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanqiu Lv
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Danni Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shihai Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianshuang Wu
- Functional Biodiversity, Dahlem Center of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Xiong Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhijia Gu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
| | - Xudong Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yongping Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Lyu JI, Ramekar R, Kim DG, Kim JM, Lee MK, Hung NN, Kim JB, Ahn JW, Kang SY, Choi IY, Park KC, Kwon SJ. Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf ( Hibiscus cannabinus L.) Mutant. PLANTS 2020; 9:plants9050631. [PMID: 32423146 PMCID: PMC7285769 DOI: 10.3390/plants9050631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/12/2023]
Abstract
Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the wild type. We sequenced and analyzed the transcriptome of apical leaf and stem using Pacific Biosciences single-molecule long-read isoform sequencing platform. De novo assembly yielded 26,822 full-length transcripts with a total length of 59 Mbp. Sequence similarity against protein sequence allowed the functional annotation of 11,370 unigenes. Among them, 10,100 unigenes were assigned gene ontology terms, the majority of which were associated with the metabolic and cellular process. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 8875 of the annotated unigenes to 149 metabolic pathways. We also identified the majority of putative genes involved in cellulose and lignin-biosynthesis. We further evaluated the expression pattern in eight gene families involved in lignin-biosynthesis at different growth stages. In this study, appropriate biotechnological approaches using the information obtained for these putative genes will help to modify the desirable content traits in mutants. The transcriptome data can be used as a reference dataset and provide a resource for molecular genetic studies in kenaf.
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Affiliation(s)
- Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Rahul Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Min-Kyu Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
| | - Kyoung-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
- Correspondence: (K.-C.P.); (S.-J.K.)
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
- Correspondence: (K.-C.P.); (S.-J.K.)
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Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
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Yue J, Wang R, Ma X, Liu J, Lu X, Balaso Thakar S, An N, Liu J, Xia E, Liu Y. Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. Comput Struct Biotechnol J 2020; 18:774-783. [PMID: 32280432 PMCID: PMC7132054 DOI: 10.1016/j.csbj.2020.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 12/31/2022] Open
Abstract
Crocus sativus, containing remarkably amounts of crocin, picrocrocin and safranal, is the source of saffron with tremendous medicinal, economic and cultural importance. Here, we present a high-quality full-length transcriptome of the sterile triploid C. sativus, using the PacBio SMRT sequencing technology. This yields 31,755 high-confidence predictions of protein-coding genes, with 50.1% forming paralogous gene pairs. Analysis on distribution of Ks values suggests that the current genome of C. sativus is probably a product resulting from at least two rounds of whole-genome duplication (WGD) events occurred at ~28 and ~114 million years ago (Mya), respectively. We provide evidence demonstrating that the recent β WGD event confers a major impact on family expansion of secondary metabolite genes, possibly leading to an enhanced accumulation of three distinct compounds: crocin, picrocrocin and safranal. Phylogenetic analysis unravels that the founding member (CCD2) of CCD enzymes necessary for the biosynthesis of apocarotenoids in C. sativus might be evolved from the CCD1 family via the β WGD event. Based on the gene expression profiling, CCD2 is found to be expressed at an extremely high level in the stigma. These findings may shed lights on further genomic refinement of the characteristic biosynthesis pathways and promote germplasm utilization for the improvement of saffron quality.
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Affiliation(s)
- Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,School of Computer and Information, Hefei University of Technology, Hefei 230009, China.,State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Ran Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaojing Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jiayi Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaohui Lu
- College of Information Technology, Jiaxing Vocational Technical College, Jiaxing 314000, China
| | - Sambhaji Balaso Thakar
- State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China.,Department of Biotechnology, Shivaji University, Kolhapur 416003, India
| | - Ning An
- School of Computer and Information, Hefei University of Technology, Hefei 230009, China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yongsheng Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China.,Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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Xue T, Zhang H, Zhang Y, Wei S, Chao Q, Zhu Y, Teng J, Zhang A, Sheng W, Duan Y, Xue J. Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata. BMC PLANT BIOLOGY 2019; 19:565. [PMID: 31852442 PMCID: PMC6921527 DOI: 10.1186/s12870-019-2197-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as "sprout tumble", which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata. RESULTS Compared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production. CONCLUSION The full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.
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Affiliation(s)
- Tao Xue
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Han Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yuanyuan Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Shuqin Wei
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Qiujie Chao
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yanfang Zhu
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Jingtong Teng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Aimin Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Wei Sheng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yongbo Duan
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Jianping Xue
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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Tang Q, Xu Y, Deng C, Cheng C, Dai Z, Yang Z, Liu C, Su J. A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy. Int J Genomics 2019; 2019:4025747. [PMID: 31950027 PMCID: PMC6948294 DOI: 10.1155/2019/4025747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/21/2019] [Indexed: 01/27/2023] Open
Abstract
Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to "cell differentiation" and "cell cycle process," as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
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Zhou T, Luo X, Zhang C, Xu X, Yu C, Jiang Z, Zhang L, Yuan H, Zheng B, Pi E, Shen C. Comparative metabolomic analysis reveals the variations in taxoids and flavonoids among three Taxus species. BMC PLANT BIOLOGY 2019; 19:529. [PMID: 31783790 PMCID: PMC6884900 DOI: 10.1186/s12870-019-2146-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/18/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Trees of the genus Taxus are highly valuable medicinal plants with multiple pharmacological effects on various cancer treatments. Paclitaxel from Taxus trees is an efficient and widely used anticancer drug, however, the accumulation of taxoids and other active ingredients can vary greatly among Taxus species. In our study, the metabolomes of three Taxus species have been investigated. RESULTS A total of 2246 metabolites assigned to various primary and secondary metabolic pathways were identified using an untargeted approach. Analysis of differentially accumulated metabolites identified 358 T. media-, 220 T. cuspidata-, and 169 T. mairei-specific accumulated metabolites, respectively. By searching the metabolite pool, 7 MEP pathway precursors, 11 intermediates, side chain products and derivatives of paclitaxel, and paclitaxel itself were detected. Most precursors, initiated intermediates were highly accumulated in T. mairei, and most intermediate products approaching the end point of taxol biosynthesis pathway were primarily accumulated in T. cuspidata and T. media. Our data suggested that there were higher-efficiency pathways to paclitaxel in T. cuspidata and T. media compared with in T. mairei. As an important class of active ingredients in Taxus trees, a majority of flavonoids were predominantly accumulated in T. mairei rather than T. media and T. cuspidata. The variations in several selected taxoids and flavonoids were confirmed using a targeted approach. CONCLUSIONS Systematic correlativity analysis identifies a number of metabolites associated with paclitaxel biosynthesis, suggesting a potential negative correlation between flavonoid metabolism and taxoid accumulation. Investigation of the variations in taxoids and other active ingredients will provide us with a deeper understanding of the interspecific differential accumulation of taxoids and an opportunity to accelerate the highest-yielding species breeding and resource utilization.
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Affiliation(s)
- Ting Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036 China
| | - Xiujun Luo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Chengchao Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Xinyun Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Chunna Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Zhifang Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
| | - Lei Zhang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Hangzhou, 311300 People’s Republic of China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Hangzhou, 311300 People’s Republic of China
| | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036 China
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Xu Q, Cheng L, Mei Y, Huang L, Zhu J, Mi X, Yu Y, Wei C. Alternative Splicing of Key Genes in LOX Pathway Involves Biosynthesis of Volatile Fatty Acid Derivatives in Tea Plant ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13021-13032. [PMID: 31693357 DOI: 10.1021/acs.jafc.9b05925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Volatile fatty acid derivatives (VFADs) produced in tea plants (Camellia sinensis) not only have been shown to function as defense compounds but also impart a "fresh green" odor to green tea products; however, little is known about alternative splicing (AS) of genes in regulating the production of VFADs in plants. In this study, the contents of VFADs and corresponding transcriptome profiles were obtained in five different months (April, June, August, September, and October). Correlation analysis identified seven unique transcripts of enzyme-coding genes (CsLOX2, CsLOX4, CsADH4, CsADH8, and CsADH10), which are responsible for regulating VFAD biosynthesis; four AS transcripts of these genes (CsLOX2, CsLOX4, CsADH4, and CsADH8) were validated by RT-PCR. By employing the gene-specific antisense oligodeoxynucleotide-mediated reduction method, we found the expression levels of alternatively spliced transcripts of CsLOX4-iso1, CsLOX4-iso2, and CsADH4-iso3 were lower, and the contents of cis-3-hexenol were correspondingly reduced in the leaves of tea plant; this result suggested that the AS play important roles in regulating biosynthesis of VFADs in C. sinensis. Our results provide new insights into the important contribution of AS events in regulating the VFAD biosynthesis in tea plant.
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Affiliation(s)
- Qingshan Xu
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Long Cheng
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Yu Mei
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Linli Huang
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Youben Yu
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
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Vilperte V, Lucaciu CR, Halbwirth H, Boehm R, Rattei T, Debener T. Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. BMC Genomics 2019; 20:900. [PMID: 31775622 PMCID: PMC6882326 DOI: 10.1186/s12864-019-6247-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species. RESULTS The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration. CONCLUSIONS In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.
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Affiliation(s)
- Vinicius Vilperte
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.,Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Calin Rares Lucaciu
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060, Vienna, Austria
| | - Robert Boehm
- Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria.
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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Li FD, Tong W, Xia EH, Wei CL. Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. BMC Bioinformatics 2019; 20:553. [PMID: 31694521 PMCID: PMC6836513 DOI: 10.1186/s12859-019-3166-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. Results We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS. Conclusions The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.
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Affiliation(s)
- Fang-Dong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.,School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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45
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Xia E, Li F, Tong W, Li P, Wu Q, Zhao H, Ge R, Li R, Li Y, Zhang Z, Wei C, Wan X. Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1938-1953. [PMID: 30913342 PMCID: PMC6737018 DOI: 10.1111/pbi.13111] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 05/05/2023]
Abstract
Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large-scale omics-data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web-accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well-organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well-resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.
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Affiliation(s)
- En‐Hua Xia
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Fang‐Dong Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Peng‐Hui Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Hui‐Juan Zhao
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Ruo‐Heng Ge
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Ruo‐Pei Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Ye‐Yun Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Zheng‐Zhu Zhang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Chao‐Ling Wei
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
| | - Xiao‐Chun Wan
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036China
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Gao Y, Xi F, zhang H, Liu X, Wang H, zhao L, Reddy AS, Gu L. Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190204151746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing
(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found to
be much superior in identifying full-length splice variants and other post-transcriptional events as
compared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).
Several different bioinformatics tools to analyze the Iso-Seq data have been developed and some
of them are still being refined to address different aspects of transcriptome complexity. However, a
comprehensive summary of the available tools and their utility is still lacking.
Objective:
Here, we summarized the existing Iso-Seq analysis tools and presented an integrated
bioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generates
long contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptional
events.
Results:
In this review, we summarized recent applications of Iso-Seq in plants, which include improved
genome annotations, identification of novel genes and lncRNAs, identification of fulllength
splice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation
(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensive
Iso-Seq data analysis, including how to reduce the error rate in the reads and how to identify and
quantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussed
as well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptome
quantification.
Conclusion:
Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptome
complexity and this new method offers unprecedented opportunities to comprehensively understand
transcripts diversity.
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Affiliation(s)
- Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangzhen zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado ( Persea americana). Int J Mol Sci 2019; 20:ijms20174117. [PMID: 31450745 PMCID: PMC6747375 DOI: 10.3390/ijms20174117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/17/2022] Open
Abstract
Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.
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Xia E, Li F, Tong W, Yang H, Wang S, Zhao J, Liu C, Gao L, Tai Y, She G, Sun J, Cao H, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Wu Q, Ge R, Zhao H, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Zhao S, Bennetzen JL, Wei C, Wan X. The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. Sci Data 2019; 6:122. [PMID: 31308375 PMCID: PMC6629666 DOI: 10.1038/s41597-019-0127-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/25/2019] [Indexed: 11/25/2022] Open
Abstract
Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.
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Affiliation(s)
- Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chun Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Liping Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yuling Tai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Sun
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Haisheng Cao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiang Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenzhao Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Shihua Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Haijing Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Junlan Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chengying Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | | | - Bei Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Dai Shan
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Congbing Fang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Yue
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Daxiang Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Changjun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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49
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Zhao L, Zhang H, Kohnen MV, Prasad KVSK, Gu L, Reddy ASN. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Front Genet 2019; 10:253. [PMID: 30949200 PMCID: PMC6438080 DOI: 10.3389/fgene.2019.00253] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
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Affiliation(s)
- Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Markus V. Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kasavajhala V. S. K. Prasad
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
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50
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Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis). Sci Rep 2019; 9:2709. [PMID: 30804390 PMCID: PMC6389920 DOI: 10.1038/s41598-019-39286-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/22/2019] [Indexed: 11/08/2022] Open
Abstract
Flavonoids, theanine and caffeine are the main secondary metabolites of the tea plant (Camellia sinensis), which account for the tea's unique flavor quality and health benefits. The biosynthesis pathways of these metabolites have been extensively studied at the transcriptional level, but the regulatory mechanisms are still unclear. In this study, to explore the transcriptome diversity and complexity of tea plant, PacBio Iso-Seq and RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression during the leaf development. A total of 1,388,066 reads of insert (ROI) were generated with an average length of 1,762 bp, and more than 54% (755,716) of the ROIs were full-length non-chimeric (FLNC) reads. The Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness was 92.7%. A total of 93,883 non-redundant transcripts were obtained, and 87,395 (93.1%) were new alternatively spliced isoforms. Meanwhile, 7,650 differential expression transcripts (DETs) were identified. A total of 28,980 alternative splicing (AS) events were predicted, including 1,297 differential AS (DAS) events. The transcript isoforms of the key genes involved in the flavonoid, theanine and caffeine biosynthesis pathways were characterized. Additionally, 5,777 fusion transcripts and 9,052 long non-coding RNAs (lncRNAs) were also predicted. Our results revealed that AS potentially plays a crucial role in the regulation of the secondary metabolism of the tea plant. These findings enhanced our understanding of the complexity of the secondary metabolic regulation of tea plants and provided a basis for the subsequent exploration of the regulatory mechanisms of flavonoid, theanine and caffeine biosynthesis in tea plants.
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