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Pham MP, Vu DD, Bei C, Bui TTX, Vu DG, Shah SNM. Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics. Biodivers Data J 2024; 12:e123405. [PMID: 38919771 PMCID: PMC11196892 DOI: 10.3897/bdj.12.e123405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.
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Affiliation(s)
- Mai-Phuong Pham
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology, Hanoi, VietnamGraduate University of Science and Technology (GUST), Vietnam Academy of Science and TechnologyHanoiVietnam
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Dinh Duy Vu
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Cui Bei
- Jiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100, Jiangsu, ChinaJiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100JiangsuChina
| | - Thi Tuyet Xuan Bui
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology, Hanoi, VietnamInstitute of Ecology and Biological Resource, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Dinh Giap Vu
- Institute of Technology, Hanoi University of Industry (HaUI), Hanoi, VietnamInstitute of Technology, Hanoi University of Industry (HaUI)HanoiVietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail Khan, PakistanDepartment of Horticulture, Faculty of Agriculture, Gomal UniversityDera Ismail KhanPakistan
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Yu JJ, Cui J, Huang H, Cen DC, Liu F, Xu ZF, Wang Y. Identification of flowering genes in Camellia perpetua by comparative transcriptome analysis. Funct Integr Genomics 2023; 24:2. [PMID: 38066213 DOI: 10.1007/s10142-023-01267-x] [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] [Received: 06/09/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]
Abstract
Camellia perpetua has the excellent characteristic of flowering multiple times throughout the year, which is of great importance to solve the problem of "short flowering period" and "low fresh flower yield" in the yellow Camellia industry at present. Observations of flowering phenology have demonstrated that most floral buds of C. perpetua were formed by the differentiation of axillary buds in the scales at the base of the terminal buds of annual branches. However, the molecular mechanism of flowering in C. perpetua is still unclear. In this study, we conducted a comparative transcriptomic study of the terminal buds and their basal flower buds in March (spring) and September (autumn) using RNA-seq and found that a total of 11,067 genes were significantly differentially expressed in these two periods. We identified 27 genes related to gibberellin acid (GA) synthesis, catabolism, and signal transduction during floral bud differentiation. However, treatment of the terminal buds and axillary buds of C. perpetua on annual branch with GA3 did not induce floral buds at the reproductive growth season (in August) but promoted shoot sprouting. Moreover, 203 flowering genes were identified from the C. perpetua transcriptome library through homology alignment, including flowering integrators LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO), as well as MADS-box, SQUAMOSA PROMOTER BINDING PROTEIN-box (SBP-box), and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) genes, which were specifically upregulated in floral buds and were likely involved in flowering in C. perpetua. The floral inhibitor CperTFL1b was identified and cloned from C. perpetua, and its expression level was specifically regulated in terminal buds in autumn. Ectopic overexpression of CperTFL1b delayed flowering time and produced abnormal inflorescence and floral organs in Arabidopsis, suggesting that CperTFL1b inhibits flowering. In conclusion, this study deepens our understanding of the molecular mechanism of blooms throughout the year in C. perpetua and provides a helpful reference for cultivating new varieties of yellow Camellia with improved flowering traits.
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Affiliation(s)
- Jing-Jing Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530000, China
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530000, China
| | - Jia Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530000, China
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530000, China
| | - Han Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530000, China
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530000, China
| | - Dong-Can Cen
- Guangxi Yuanzhiyuan Ecological Agriculture Investment Co., Ltd., Nanning, 530212, China
| | - Fang Liu
- Nanning Tree Garden, Nanning, 530031, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530000, China.
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530000, China.
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530000, China.
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530000, China.
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Wang Y, Pang D, Ruan L, Liang J, Zhang Q, Qian Y, Zhang Y, Bai P, Wu L, Cheng H, Cui Q, Wang L, Wei K. Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis). BMC PLANT BIOLOGY 2022; 22:319. [PMID: 35787241 PMCID: PMC9251942 DOI: 10.1186/s12870-022-03701-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Tea plant breeding or cultivation mainly involves propagation via cuttings, which not only ensures the inheritance of the excellent characteristics of the mother plant but also facilitates mechanized management. The formation of adventitious root (AR) determines the success of cutting-based propagation, and auxin is an essential factor involved in this process. To understand the molecular mechanism underlying AR formation in nodal tea cuttings, transcriptome and endogenous hormone analysis was performed on the stem bases of red (mature)- and green (immature)-stem cuttings of 'Echa 1 hao' tea plant as affected by a pulse treatment with naphthalene acetic acid (NAA). RESULTS In this study, NAA significantly promoted AR formation in both red- and green-stem cuttings but slightly reduced callus formation. External application of NAA reduced the levels of endogenous indole-3-acetic acid (IAA) and cytokinin (TZR, trans-zeatin riboside). The number of DEGs (NAA vs. CK) identified in the green-stem cuttings was significantly higher than that in the red-stem cuttings, which corresponded to a higher rooting rate of green-stem cuttings under the NAA treatment. A total of 82 common DEGs were identified as being hormone-related and involved in the auxin, cytokinin, abscisic acid, ethylene, salicylic acid, brassinosteroid, and jasmonic acid pathways. The negative regulation of NAA-induced IAA and GH3 genes may explain the decrease of endogenous IAA. NAA reduced endogenous cytokinin levels and further downregulated the expression of cytokinin signalling-related genes. By the use of weighted gene co-expression network analysis (WGCNA), several hub genes, including three [cellulose synthase (CSLD2), SHAVEN3-like 1 (SVL1), SMALL AUXIN UP RNA (SAUR21)] that are highly related to root development in other crops, were identified that might play important roles in AR formation in tea cuttings. CONCLUSIONS NAA promotes the formation of AR of tea cuttings in coordination with endogenous hormones. The most important endogenous AR inductor, IAA, was reduced in response to NAA. DEGs potentially involved in NAA-mediated AR formation of tea plant stem cuttings were identified via comparative transcriptome analysis. Several hub genes, such as CSLD2, SVL1 and SAUR21, were identified that might play important roles in AR formation in tea cuttings.
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Affiliation(s)
- Yongxin Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Dandan Pang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, 666201, China
| | - Li Ruan
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Jinbo Liang
- Tea Research Institute of Enshi Academy of Agricultural Sciences, Enshi, 445000, China
| | - Qiang Zhang
- Tea Research Institute of Enshi Academy of Agricultural Sciences, Enshi, 445000, China
| | - Yinhong Qian
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Yazhen Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Peixian Bai
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Liyun Wu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Hao Cheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Qingmei Cui
- Tea Research Institute of Enshi Academy of Agricultural Sciences, Enshi, 445000, China.
| | - Liyuan Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
| | - Kang Wei
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:406-421. [PMID: 35510493 DOI: 10.1111/tpj.15799] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- 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
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- 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
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- 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
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- 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
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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5
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Chen N, Zhang H, Zang E, Liu ZX, Lan YF, Hao WL, He S, Fan X, Sun GL, Wang YL. Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains. BMC Genomics 2022; 23:466. [PMID: 35751010 PMCID: PMC9233376 DOI: 10.1186/s12864-022-08703-5] [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: 10/27/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.
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Affiliation(s)
- Ning Chen
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Hao Zhang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - En Zang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Zhi-Xia Liu
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Ya-Fei Lan
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Wei-Li Hao
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Shan He
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gen-Lou Sun
- Department of Biology, Saint Mary's University, Halifax, B3H3C3, Canada.
| | - Yi-Ling Wang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
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Collings ER, Alamar MC, Márquez MB, Kourmpetli S, Kevei Z, Thompson AJ, Mohareb F, Terry LA. Improving the Tea Withering Process Using Ethylene or UV-C. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13596-13607. [PMID: 34739246 DOI: 10.1021/acs.jafc.1c02876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using a combination of biochemical, transcriptomic, and physiological analyses, we elucidated the mechanisms of physical and chemical withering of tea shoots subjected to UV-C and ethylene treatments. UV-C irradiation (15 kJ m-2) initiated oxidation of catechins into theaflavins, increasing theaflavin-3-monogallate and theaflavin digallate by 5- and 13.2-4.4-fold, respectively, at the end of withering. Concomitantly, a rapid change to brown/red, an increase in electrolyte leakage, and the upregulation of peroxidases (viz. Px2, Px4, and Px6) and polyphenol oxidases (PPO-1) occurred. Exogenous ethylene significantly increased the metabolic rate (40%) and moisture loss (30%) compared to control during simulated withering (12 h at 25 °C) and upregulated transcripts associated with responses to dehydration and abiotic stress, such as those in the ethylene signaling pathway (viz. EIN4-like, EIN3-FBox1, and ERFs). Incorporating ethylene during withering could shorten the tea manufacturing process, while UV-C could enhance the accumulation of flavor-related compounds.
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Affiliation(s)
- Emma R Collings
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | - M Carmen Alamar
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | | | - Sofia Kourmpetli
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | - Zoltan Kevei
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | - Andrew J Thompson
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
| | - Leon A Terry
- Plant Science Laboratory, Cranfield University, Cranfield, Bedfordshire MK43 0AL, U.K
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Jiang CK, Liu ZL, Li XY, Ercisli S, Ma JQ, Chen L. Non-Volatile Metabolic Profiling and Regulatory Network Analysis in Fresh Shoots of Tea Plant and Its Wild Relatives. FRONTIERS IN PLANT SCIENCE 2021; 12:746972. [PMID: 34659317 PMCID: PMC8519607 DOI: 10.3389/fpls.2021.746972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
There are numerous non-volatile metabolites in the fresh shoots of tea plants. However, we know little about the complex relationship between the content of these metabolites and their gene expression levels. In investigating this, this study involved non-volatile metabolites from 68 accessions of tea plants that were detected and identified using untargeted metabolomics. The tea accessions were divided into three groups from the results of a principal component analysis based on the relative content of the metabolites. There were differences in variability between the primary and secondary metabolites. Furthermore, correlations among genes, gene metabolites, and metabolites were conducted based on Pearson's correlation coefficient (PCC) values. This study offered several significant insights into the co-current network of genes and metabolites in the global genetic background. Thus, the study is useful for providing insights into the regulatory relationship of the genetic basis for predominant metabolites in fresh tea shoots.
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Affiliation(s)
- Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhi-Long Liu
- Lishui Academy of Agricultural and Forestry Sciences, Lishui, China
| | - Xuan-Ye Li
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, China
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8
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Sharma B, Seth R, Thakur S, Parmar R, Masand M, Devi A, Singh G, Dhyani P, Choudhary S, Sharma RK. Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook. PHYTOCHEMISTRY 2021; 187:112772. [PMID: 33873018 DOI: 10.1016/j.phytochem.2021.112772] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Fritillaria roylei Hook. is a critically endangered high altitude Himalayan medicinal plant species with rich source of pharmaceutically active structurally diverse steroidal alkaloids. Nevertheless, except few marker compounds, the chemistry of the plant remains unexplored. Therefore, in the current study, transcriptome sequencing efforts were made to elucidate isosteroidal alkaloids biosynthesis by creating first organ-specific genomic resource using bulb, stem, and leaf tissues derived from natural populations of Indian Himalayan region. Overall, 349.9 million high quality paired-end reads obtained using NovaSeq 6000 platform were assembled (de novo) into 82,848 unigenes and 31,061 isoforms. Functional annotation and organ specific differential expression (DE) analysis identified 2488 significant DE transcripts, grouped into three potential sub-clusters (sub-cluster I: 728 transcripts; sub-cluster II: 446 transcripts and Sub-cluster III: 1314 transcripts). Subsequently, pathway enrichment (GO, KEGG) and protein-protein network analysis revealed significantly higher enrichment of phenyl-propanoid and steroid backbone including terpenoid, sesquiterpenoid and triterpenoid biosynthesis in bulb. Additionally, upregulated expression of cytochrome P450, UDP-dependent Glucuronosyltransferase families and key transcription factor families (FAR1, bHLH, GRAS, C2H2, TCP and MYB) suggests 'bulb' as a primary site of MVA mediated isosteroidal alkaloids biosynthesis. The comprehensive elucidation of molecular insights in this study is a first step towards the understanding of isosteroidal alkaloid biosynthesis pathway in F. roylei. Furthermore, key genes and regulators identified here can facilitate metabolic engineering of potential bioactive compounds at industrial scale.
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Affiliation(s)
- Balraj Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.
| | - Sapna Thakur
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Praveen Dhyani
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Shruti Choudhary
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India.
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9
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Rubel Mozumder NHM, Hwang KH, Lee MS, Kim EH, Hong YS. Metabolomic understanding of the difference between unpruning and pruning cultivation of tea (Camellia sinensis) plants. Food Res Int 2021; 140:109978. [PMID: 33648213 DOI: 10.1016/j.foodres.2020.109978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022]
Abstract
Tea (Camellia sinensis) leaf quality depends on several factors such as plucking seasons, cultivation practices, and climatic conditions, which affect the chemical compositions of tea leaves. Pruning has been practiced as one of the common cultivation managements in tea cultivation and is hypothesized to exhibit metabolic differences from unpruned tea plants. Although metabolomics studies provide immense information about production of distinct tea products, the metabolic physiology of the plants cultivated under unpruning conditions is poorly understood. Therefore, in the present study, we explored the metabolic characteristics of tea leaves obtained from unpruned tea plants collected at different plucking seasons in a single year and in a given plucking time in the three successive years, through 1H NMR-based metabolomics approach. Seasonal variations in diverse tea leaf metabolites both in pruned and unpruned tea plants were observed along with marked metabolic differences in tea leaves collected from pruned and unpruned tea plants in a given plucking time. Particularly, in abnormal year of vintage with high rainfall in 2018, high synthesis of glucose followed by high accumulations of catechin, including its derivatives, in unpruned tea, demonstrated intense active photosynthesis compared to pruned tea plants, indicating different metabolic responses of pruned and unpruned tea plants to similar climatic conditions. The current study highlights the important role of tea cultivation practices in tea plants for better management of leaf quality and the strong metabolic dependence on climatic conditions in a given vintage.
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Affiliation(s)
- N H M Rubel Mozumder
- Division of Food and Nutrition, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Kyeong Hwan Hwang
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Kyeonggi-do 17074, Republic of Korea
| | - Min-Seuk Lee
- Osulloc Tea R&D Center, Osulloc Farm Corporation, Jeju 63521, Republic of Korea
| | - Eun-Hee Kim
- Center for Research Equipment, Korea Basic Science Institute, Cheongwon-Gu, Cheongju-Si, Chungbuk 28119, Republic of Korea
| | - Young-Shick Hong
- Division of Food and Nutrition, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
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10
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Zheng C, Ma JQ, Ma CL, Yao MZ, Chen JD, Chen L. Identifying Conserved Functional Gene Modules Underlying the Dynamic Regulation of Tea Plant Development and Secondary Metabolism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11026-11037. [PMID: 32902975 DOI: 10.1021/acs.jafc.0c04744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tea plants adjust development and metabolism by integrating environmental and endogenous signals in complex but poorly defined gene networks. Here, we present an integrative analysis framework for the identification of conserved modules controlling important agronomic traits using a comprehensive collection of RNA-seq datasets in Camellia plants including 189 samples. In total, 212 secondary metabolism-, 182 stress response-, and 182 tissue development-related coexpressed modules were revealed. Functional modules (e.g., drought response, theobromine biosynthesis, and new shoot development-related modules) and potential regulators that were highly conserved across diverse genetic backgrounds and/or environmental conditions were then identified by cross-experiment comparisons and consensus clustering. Moreover, we investigate the preservation of gene networks between Camellia sinensis and other Camellia species. This revealed that the coexpression patterns of several recently evolved modules related to secondary metabolism and environmental adaptation were rewired and showed higher connectivity in tea plants. These conserved modules are excellent candidates for modeling the core mechanism of tea plant development and secondary metabolism and should serve as a great resource for hypothesis generation and tea quality improvement.
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Affiliation(s)
- Chao Zheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Chun-Lei Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
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11
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Deng H, Chen S, Zhou Z, Li X, Chen S, Hu J, Lai Z, Sun Y. Transcriptome analysis reveals the effect of short-term sunlight on aroma metabolism in postharvest leaves of oolong tea(Camellia sinensis). Food Res Int 2020; 137:109347. [PMID: 33233053 DOI: 10.1016/j.foodres.2020.109347] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 11/25/2022]
Abstract
Tea (Camellia sinensis (L.)) is an important economic plant. Light is the earliest external signal factor during the postharvest processing of oolong tea, and the solar withering is an indispensable process for aroma formation. In this study, Tieguanyin was used to analyze the effect of sunlight on aroma metabolism, which indicated that the main aroma compounds were significantly increased during solar withering for 15 min compared to the indoor withering. In addition, differentially expressed genes related to aroma metabolism were identified and quantified using the high-throughput Illumina RNA-Seq technology. The expression levels of key regulatory genes were consistent with the results from the gas chromatography-time of flight mass spectrometry (GC-TOF-MS) analysis, especially in terpenoid metabolic pathway, which showed that aroma metabolism could significantly respond to the short-term light, while its expression level was easily inhibited by the up-regulation of heat shock protein. Taken together, those data provides further insights into the mechanisms, contributing to aroma metabolism of tea plant.
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Affiliation(s)
- Huili Deng
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, PR China; Public Basic Department, Minjiang Teachers College, Fuzhou, PR China
| | - Shousong Chen
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Ziwei Zhou
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Xinlei Li
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Si Chen
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China; FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Juan Hu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, PR China.
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12
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Liu ZW, Li H, Liu JX, Wang Y, Zhuang J. Integrative transcriptome, proteome, and microRNA analysis reveals the effects of nitrogen sufficiency and deficiency conditions on theanine metabolism in the tea plant ( Camellia sinensis). HORTICULTURE RESEARCH 2020; 7:65. [PMID: 32377356 PMCID: PMC7192918 DOI: 10.1038/s41438-020-0290-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/13/2020] [Accepted: 03/02/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is associated with amino acid metabolism in higher plants. Theanine is an important amino acid in tea plants. To explore the relationship between theanine metabolism and N conditions, we examined the differentially expressed genes (DEGs), proteins (DEPs), and microRNAs (DEMs) involved in theanine metabolism in tea plant shoots and roots under N sufficiency and deficiency conditions. Transcriptome, proteome, and microRNA analyses were performed on tea plant shoots and roots under N sufficiency and deficiency conditions. The contents of theanine, expression levels of genes involved in theanine metabolism, contents of proteinogenic amino acids, and activity of enzymes were analyzed. The DEP-DEG correlation pairs and negative DEM-DEG interactions related to theanine metabolism were identified based on correlation analyses. The expression profiles of DEGs and negative DEM-DEG pairs related to theanine biosynthesis were consistent with the sequencing results. Our results suggest that the molecular and physiological mechanism of theanine accumulation is significantly affected by N sufficiency and deficiency conditions. The DEGs, DEPs, and DEMs and the activity of the enzymes involved in theanine biosynthesis might play vital roles in theanine accumulation under N sufficiency and deficiency conditions in the shoots and roots of tea plants.
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Affiliation(s)
- Zhi-Wei Liu
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Hui Li
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yu Wang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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13
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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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14
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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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15
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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: 154] [Impact Index Per Article: 30.8] [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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16
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Szeliga M, Ciura J, Grzesik M, Tyrka M. Identification of candidate genes involved in steroidal alkaloids biosynthesis in organ-specific transcriptomes of Veratrum nigrum L. Gene 2019; 712:143962. [PMID: 31288057 DOI: 10.1016/j.gene.2019.143962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/10/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
Veratrum nigrum is protected plant of Melanthiaceae family, able to synthetize unique steroidal alkaloids important for pharmacy. Transcriptomes from leaves, stems and rhizomes of in vitro maintained V. nigrum plants were sequenced and annotated for genes and markers discovery. Sequencing of samples derived from the different organs resulted in a total of 108,511 contigs with a mean length of 596 bp. Transcripts derived from leaf and stalk were annotated at 28%, and 38% in Nr nucleotide database, respectively. The sequencing revealed 949 unigenes related with lipid metabolism, including 73 transcripts involved in steroids and genus-specific steroid alkaloids biosynthesis. Additionally, 3203 candidate SSRs markers we identified in unigenes with average density of one SSR locus every 6.2 kb sequence. Unraveling of biochemical machinery of the pathway responsible for steroidal alkaloids will open possibility to design and optimize biotechnological process. The transcriptomic data provide valuable resources for biochemical, molecular genetics, comparative transcriptomics, functional genomics, ecological and evolutionary studies of V. nigrum.
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Affiliation(s)
- Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland.
| | - Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland; Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Michalina Grzesik
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland; Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Ćwiklińskiej 1, 35-601 Rzeszów, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland
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17
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Koech RK, Malebe PM, Nyarukowa C, Mose R, Kamunya SM, Joubert F, Apostolides Z. Functional annotation of putative QTL associated with black tea quality and drought tolerance traits. Sci Rep 2019; 9:1465. [PMID: 30728388 PMCID: PMC6365519 DOI: 10.1038/s41598-018-37688-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022] Open
Abstract
The understanding of black tea quality and percent relative water content (%RWC) traits in tea (Camellia sinensis) by a quantitative trait loci (QTL) approach can be useful in elucidation and identification of candidate genes underlying the QTL which has remained to be difficult. The objective of the study was to identify putative QTL controlling black tea quality and percent relative water traits in two tea populations and their F1 progeny. A total of 1,421 DArTseq markers derived from the linkage map identified 53 DArTseq markers to be linked to black tea quality and %RWC. All 53 DArTseq markers with unique best hits were identified in the tea genome. A total of 5,592 unigenes were assigned gene ontology (GO) terms, 56% comprised biological processes, cellular component (29%) and molecular functions (15%), respectively. A total of 84 unigenes in 15 LGs were assigned to 25 different Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways based on categories of secondary metabolite biosynthesis. The three major enzymes identified were transferases (38.9%), hydrolases (29%) and oxidoreductases (18.3%). The putative candidate proteins identified were involved in flavonoid biosynthesis, alkaloid biosynthesis, ATPase family proteins related to abiotic/biotic stress response. The functional annotation of putative QTL identified in this current study will shed more light on the proteins associated with caffeine and catechins biosynthesis and % RWC. This study may help breeders in selection of parents with desirable DArTseq markers for development of new tea cultivars with desirable traits.
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Affiliation(s)
- Robert K Koech
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.,Kenya Agriculture and Livestock Research Organization, Tea Research Institute, P.O. Box 820, Kericho, 20200, Kenya
| | - Pelly M Malebe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Christopher Nyarukowa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Richard Mose
- James Finlay (Kenya) Limited, P.O. Box 223, Kericho, 20200, Kenya
| | - Samson M Kamunya
- Kenya Agriculture and Livestock Research Organization, Tea Research Institute, P.O. Box 820, Kericho, 20200, Kenya
| | - Fourie Joubert
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Zeno Apostolides
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
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18
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Identification of a Novel Gene Encoding the Specialized Alanine Decarboxylase in Tea ( Camellia sinensis) Plants. Molecules 2019; 24:molecules24030540. [PMID: 30717241 PMCID: PMC6384637 DOI: 10.3390/molecules24030540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/18/2019] [Accepted: 01/27/2019] [Indexed: 11/17/2022] Open
Abstract
Theanine, a unique amino acid in Camellia sinensis, accounts for more than 50% of total free amino acids in tea and has a significant contribution to the quality of green tea. Previous research indicated that theanine is synthesized from glutamic acid (Glu) and ethylamine mainly in roots, and that theanine accumulation depends on the availability of ethylamine which is derived from alanine (Ala) decarboxylation catalyzed by alanine decarboxylase (AlaDC). However, the specific gene encoding AlaDC protein remains to be discovered in tea plants or in other species. To explore the gene of AlaDC in tea plants, the differences in theanine contents and gene expressions between pretreatment and posttreatment of long-time nitrogen starvation were analyzed in young roots of two tea cultivars. A novel gene annotated as serine decarboxylase (SDC) was noted for its expression levels, which showed high consistency with theanine content, and the expression was remarkably high in young roots under sufficient nitrogen condition. To verify its function, full-length complementary DNA (cDNA) of this candidate gene was cloned from young roots of tea seedlings, and the target protein was expressed and purified from Escherichia coli (E. coli). The enzymatic activity of the protein for Ala and Ser was measured in vitro using ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS). The results illustrated that the target protein could catalyze the decarboxylation of Ala despite of its high similarity with SDC from other species. Therefore, this novel gene was identified as AlaDC and named CsAlaDC. Furthermore, the gene expression levels of CsAlaDC in different tissues of tea plants were also quantified with quantitative real-time PCR (qRT-PCR). The results suggest that transcription levels of CsAlaDC in root tissues are significantly higher than those in leaf tissues. That may explain why theanine biosynthesis preferentially occurs in the roots of tea plants. The expression of the gene was upregulated when nitrogen was present, suggesting that theanine biosynthesis is regulated by nitrogen supply and closely related to nitrogen metabolism for C. sinensis. The results of this study are significant supplements to the theanine biosynthetic pathway and provide evidence for the differential accumulation of theanine between C. sinensis and other species.
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19
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Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics. Genes (Basel) 2018; 9:genes9100488. [PMID: 30308953 PMCID: PMC6211025 DOI: 10.3390/genes9100488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.
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Li X, Fan Z, Guo H, Ye N, Lyu T, Yang W, Wang J, Wang JT, Wu B, Li J, Yin H. Comparative genomics analysis reveals gene family expansion and changes of expression patterns associated with natural adaptations of flowering time and secondary metabolism in yellow Camellia. Funct Integr Genomics 2018; 18:659-671. [PMID: 29948459 DOI: 10.1007/s10142-018-0617-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/12/2018] [Accepted: 05/31/2018] [Indexed: 11/27/2022]
Abstract
Yellow-flowering species are unique in the genus Camellia not only for their bright yellow pigments but also the health-improving substances in petals. However, little is known regarding the biosynthesis pathways of pigments and secondary metabolites. Here, we performed comparative genomics studies in two yellow-flowered species of the genus Camellia with distinctive flowering periods. We obtained 112,190 and 89,609 unigenes from Camellia nitidissima and Camellia chuongtsoensis, respectively, and identified 9547 gene family clusters shared with various plant species and 3414 single-copy gene families. Global gene expression analysis revealed six comparisons of differentially expressed gene sets in different developmental stages of floral bud. Through the identification of orthologous pairs, conserved and specific differentially expressed genes (DEGs) between species were compared. Functional enrichment analysis suggested that the gibberellin (GA) biosynthesis pathway might be related to the alteration of flowering responses. Furthermore, the expression patterns of secondary metabolism pathway genes were analyzed between yellow- and red-flowered Camellias. We showed that the key enzymes involved in glycosylation of flavonoids displayed differential expression patterns, indicating that the direct glycosylation of flavonols rather than anthocyanins was pivotal to coloration and health-improving metabolites in the yellow Camellia petals. Finally, the gene family analysis of UDP-glycosyltransferases revealed an expansion of group C members in C. nitidissima. Through comparative genomics analysis, we demonstrate that changes of gene expression and gene family members are critical to the variation of natural traits. This work provides valuable insights into the molecular regulation of trait adaptations of floral pigmentation and flowering timing.
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Affiliation(s)
- Xinlei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Haobo Guo
- Colleges of Engineering and Computer Science, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN, 37403, USA
| | - Ning Ye
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China
| | - Tao Lyu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- College of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wen Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Jie Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Jia-Tong Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Bin Wu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China.
- Key Laboratory of Forest Genetics and Breeding, Chinese Academy of Forestry, Fuyang, Zhejiang, 311400, China.
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Choudhary S, Thakur S, Najar RA, Majeed A, Singh A, Bhardwaj P. Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum). Genome 2018; 61:417-428. [DOI: 10.1139/gen-2017-0143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
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Affiliation(s)
- Shruti Choudhary
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Sapna Thakur
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Raoof Ahmad Najar
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Aasim Majeed
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Amandeep Singh
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
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22
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Zhang M, Liu XK, Fan W, Yan DF, Zhong NS, Gao JY, Zhang WJ. Transcriptome analysis reveals hybridization-induced genome shock in an interspecific F 1 hybrid from Camellia. Genome 2018; 61:477-485. [PMID: 29718690 DOI: 10.1139/gen-2017-0105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The combination of two divergent genomes during hybridization can result in "genome shock". Although genome shock has been reported in the hybrids of some herbaceous plants, the pattern and the principle it follows are far from understood, especially in woody plants. Here, the gene expression patterns were remodeled in the F1 hybrid from the crossing of Camellia azalea × Camellia amplexicaulis compared with the parents as revealed by RNA-seq. About 54.5% of all unigenes were differentially expressed between the F1 hybrid and at least one of the parents, including 6404 unigenes with the highest expression level in the F1 hybrid. A series of genes, related to flower development, essential for RNA-directed DNA methylation and histone methylation, as well as 223 transposable elements, were enriched; and most of them exhibited a higher level of expression in the F1 hybrid. These results indicated that the genome shock induced by interspecific hybridization in Camellia could indeed result in changes of gene expression patterns, potentially through regulating DNA methylation and histone methylation which may be helpful for the maintaining of genome stability and even related to the unique phenotype of the F1 hybrid.
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Affiliation(s)
- Min Zhang
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Kai Liu
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Wen Fan
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dan-Feng Yan
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Nai-Sheng Zhong
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China
| | - Ji-Yin Gao
- b Palm Eco-Town Development Co., Ltd., Guangzhou, Guangdong 510627, China.,c Research Institute of Subtropical Forest, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Wen-Ju Zhang
- a Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
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Huang H, Xia EH, Zhang HB, Yao QY, Gao LZ. De novo transcriptome sequencing of Camellia sasanqua and the analysis of major candidate genes related to floral traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:103-111. [PMID: 28992542 DOI: 10.1016/j.plaphy.2017.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Camellia sasanqua is one of the most famous horticultural plants in Camellia (Theaceae) due to its aesthetic appeal as landscape plant. Knowledge regarding the genetic basis of flowering time, floral aroma and color in C. sasanqua is limited, but is essential to breed new varieties with desired floral traits. Here, we described the de novo transcriptome of young leaves, flower buds and flowers of C. sasanqua. A total of 60,127 unigenes were functionally annotated based on the sequence similarity. After analysis, we found that two floral integrator genes, SOC1 and AP1, in flowering time pathway showed evidence of gene family expansion. Compared with 1-deoxy-D-xylulose-5-phosphate pathway, some genes in the mevalonate pathway were most highly expressed, suggesting that this might represent the major pathway for terpenoid biosynthesis related to floral aroma in C. sasanqua. In flavonoid biosynthesis pathway, PAL, CHI, DFR and ANS showing significantly higher expression levels in flowers and flower buds might have important role in regulation of floral color. The top five most transcription factors (TFs) families in C. sasanqua transcriptome were MYB, MIKC, C3H, FAR1 and HD-ZIP, many of which have a direct relationship with floral traits. In addition, we also identified 33,540 simple sequence repeats (SSRs) in the C. sasanqua transcriptome. Collectively, the C. sasanqua transcriptome dataset generated from this study along with the SSR markers provide a new resource for the identification of novel regulatory transcripts and will accelerate the genetic improvement of C. sasanqua breeding programs.
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Affiliation(s)
- Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qiu-Yang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
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24
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Ciura J, Szeliga M, Grzesik M, Tyrka M. Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum). PLANTA 2017; 245:977-991. [PMID: 28161815 PMCID: PMC5393294 DOI: 10.1007/s00425-017-2657-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/30/2017] [Indexed: 05/21/2023]
Abstract
Representational difference analysis of cDNA was performed and differential products were sequenced and annotated. Candidate genes involved in biosynthesis of diosgenin in fenugreek were identified. Detailed mechanism of diosgenin synthesis was proposed. Fenugreek (Trigonella foenum-graecum L.) is a valuable medicinal and crop plant. It belongs to Fabaceae family and has a unique potential to synthesize valuable steroidal saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were used to enhance the content of sterols and steroidal sapogenins in in vitro grown plants for representational difference analysis of cDNA (cDNA-RDA). To identify candidate genes involved in diosgenin biosynthesis, differential, factor-specific libraries were subject to the next-generation sequencing. Approximately 9.9 million reads were obtained, trimmed, and assembled into 31,491 unigenes with an average length of 291 bp. Then, functional annotation and gene ontogeny enrichment analysis was performed by aligning all-unigenes with public databases. Within the transcripts related to sterol and steroidal saponin biosynthesis, we discovered novel candidate genes of diosgenin biosynthesis and validated their expression using quantitative RT-PCR analysis. Based on these findings, we supported the idea that diosgenin is biosynthesized from cycloartenol via cholesterol. This is the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes enriched in low copy sequences contributed substantially to our understanding of the biochemical pathways of steroid synthesis in fenugreek.
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Affiliation(s)
- Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Michalina Grzesik
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland.
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De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes. Int J Mol Sci 2017; 18:ijms18040712. [PMID: 28346370 PMCID: PMC5412298 DOI: 10.3390/ijms18040712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/11/2023] Open
Abstract
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome. De novo assembly of the reads resulted in approximately 130,000 unigenes. Based on bioinformatic analysis, 71,825 (52.3%) caladium unigenes were annotated for putative functions, 48,417 (67.4%) and 31,417 (72.7%) were assigned to Gene Ontology (GO) and Clusters of Orthologous Groups (COG), respectively, and 46,406 (64.6%) unigenes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 4518 distinct unigenes were observed only in Pythium-resistant "Candidum" roots, of which 98 seemed to be involved in disease resistance and defense responses. In addition, 28,837 simple sequence repeat sites and 44,628 single nucleotide polymorphism sites were identified among the three caladium cultivars. These root transcriptome data will be valuable for further genetic improvement of caladium and related aroids.
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Liu ZW, Wu ZJ, Li H, Wang YX, Zhuang J. L-Theanine Content and Related Gene Expression: Novel Insights into Theanine Biosynthesis and Hydrolysis among Different Tea Plant ( Camellia sinensis L.) Tissues and Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:498. [PMID: 28439281 PMCID: PMC5383724 DOI: 10.3389/fpls.2017.00498] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/22/2017] [Indexed: 05/18/2023]
Abstract
L-Theanine content has tissues and cultivars specificity in tea plant (Camellia sinensis L.), the correlations of theanine metabolic related genes expression profiles with theanine contents were explored in this study. L-theanine contents in the bud and 1st leaf, 2nd leaf, 3rd leaf, old leaf, stem, and lateral root were determined by HPLC from three C. sinensis cultivars, namely 'Huangjinya', 'Anjibaicha', and 'Yingshuang', respectively. The theanine contents in leaves and root of 'Huangjinya' were the highest, followed by 'Anjibaicha', and 'Yingshuang'. The theanine contents in the leaves reduced as the leaf mature gradually, and in stem were the least. Seventeen genes encoding enzymes involved in theanine metabolism were identified from GenBank and our tea transcriptome database, including CsTS1, CsTS2, CsGS1, CsGS2, CsGOGAT-Fe, CsGOGAT-NAD(P)H, CsGDH1, CsGDH2, CsALT, CsSAMDC, CsADC, CsCuAO, CsPAO, CsNiR, CsNR, CsGGT1, and CsGGT3. The transcript profiles of those seventeen genes in the different tissues of three tea plant cultivars were analyzed comparatively. Among the different cultivars, the transcript levels of most selected genes in 'Huangjinya' were significantly higher than that in the 'Anjibaicha' and 'Yingshuang'. Among the different tissues, the transcript levels of CsTS2, CsGS1, and CsGDH2 almost showed positive correlation with the theanine contents, while the other genes showed negative correlation with the theanine contents in most cases. The theanine contents showed correlations with related genes expression levels among cultivars and tissues of tea plant, and were determined by the integrated effect of the metabolic related genes.
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Xu Q, Zhu J, Zhao S, Hou Y, Li F, Tai Y, Wan X, Wei C. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis. FRONTIERS IN PLANT SCIENCE 2017; 8:1205. [PMID: 28744294 PMCID: PMC5504172 DOI: 10.3389/fpls.2017.01205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/26/2017] [Indexed: 05/22/2023]
Abstract
Characteristic secondary metabolites, including flavonoids, theanine and caffeine, are important components of Camellia sinensis, and their biosynthesis has attracted widespread interest. Previous studies on the biosynthesis of these major secondary metabolites using next-generation sequencing technologies limited the accurately prediction of full-length (FL) splice isoforms. Herein, we applied single-molecule sequencing to pooled tea plant tissues, to provide a more complete transcriptome of C. sinensis. Moreover, we identified 94 FL transcripts and four alternative splicing events for enzyme-coding genes involved in the biosynthesis of flavonoids, theanine and caffeine. According to the comparison between long-read isoforms and assemble transcripts, we improved the quality and accuracy of genes sequenced by short-read next-generation sequencing technology. The resulting FL transcripts, together with the improved assembled transcripts and identified alternative splicing events, enhance our understanding of genes involved in the biosynthesis of characteristic secondary metabolites in C. sinensis.
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28
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De novo transcriptome sequencing of marine-derived Aspergillus glaucus and comparative analysis of metabolic and developmental variations in response to salt stress. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0497-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jia S, Wang Y, Hu J, Ding Z, Liang Q, Zhang Y, Wang H. Mineral and metabolic profiles in tea leaves and flowers during flower development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:316-326. [PMID: 27372442 DOI: 10.1016/j.plaphy.2016.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/04/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
Tea [Camellia sinensis (L.) O. Kuntze] is one of the most popular non-alcoholic beverage crops in the world, and the physiological processes and gene regulations involved in development in tea plants have been well characterized. However, relatively little is known about the metabolic changes combined with mineral distributions that occur during flower development. Here we detected the contents of 11 elements in tea leaves and flowers and found that, some of them, especially phosphorus, sulfur and copper, showed significant changes during tea flowering. We also detected 122 metabolites in tea leaves and flowers and found that, 72 of them showed significant differences between flowers and leaves, of which sugars, organic acids, and flavonoids dominated. The sugars, such as trehalose and galactose, all accumulated in tea flowers, and the organic acids, such as malic acid, citric acid and fumaric acid involved in TCA cycle. The flavonoids, like epicatechin, catechin gallate and epigallocatechin, were more abundant in leaves. Furthermore, we found that the contents of 33 metabolites changed during the development of flowers. Especially, citric acid, phenylalanine and most flavonoids decreased while fructose and galactose increased during flowering stages in flowers. We also analyzed the correlations between the ions and metabolites and found that, some mineral nutrients including phosphorus, sulfur, manganese and zinc had close relations to organic acids, flavonoids, sugars and several amino acids during flowering. We mapped the metabolic pathway according to the KEGG database. This work will serve as the foundation for a systems biology approach to the understanding of mineral metabolism.
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Affiliation(s)
- Sisi Jia
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianhui Hu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Qing Liang
- Rizhao Vocational and Technical College, Rizhao, Shandong, 276826, China
| | - Yinfei Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hui Wang
- Rizhao Tea Research Institute of Shandong, Rizhao, Shandong, 276800, China
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30
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Ip JCH, Leung PTY, Ho KKY, Qiu JW, Leung KMY. De novo transcriptome assembly of the marine gastropod Reishia clavigera for supporting toxic mechanism studies. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 178:39-48. [PMID: 27450239 DOI: 10.1016/j.aquatox.2016.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/06/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709bp with N50 of 2,236bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.
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Affiliation(s)
- Jack C H Ip
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Priscilla T Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kevin K Y Ho
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - J W Qiu
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Biology, Hong Kong Baptist University, Waterloo Road, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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31
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Yao QY, Huang H, Tong Y, Xia EH, Gao LZ. Transcriptome Analysis Identifies Candidate Genes Related to Triacylglycerol and Pigment Biosynthesis and Photoperiodic Flowering in the Ornamental and Oil-Producing Plant, Camellia reticulata (Theaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:163. [PMID: 26941748 PMCID: PMC4763035 DOI: 10.3389/fpls.2016.00163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/30/2016] [Indexed: 05/19/2023]
Abstract
Camellia reticulata, which is native to Southwest China, is famous for its ornamental flowers and high-quality seed oil. However, the lack of genomic information for this species has largely hampered our understanding of its key pathways related to oil production, photoperiodic flowering process and pigment biosynthesis. Here, we first sequenced and characterized the transcriptome of a diploid C. reticulata in an attempt to identify genes potentially involved in triacylglycerol biosynthesis (TAGBS), photoperiodic flowering, flavonoid biosynthesis (FlaBS), carotenoid biosynthesis (CrtBS) pathways. De novo assembly of the transcriptome provided a catalog of 141,460 unigenes with a total length of ~96.1 million nucleotides (Mnt) and an N50 of 1080 nt. Of them, 22,229 unigenes were defined as differentially expressed genes (DEGs) across five sequenced tissues. A large number of annotated genes in C. reticulata were found to have been duplicated, and differential expression patterns of these duplicated genes were commonly observed across tissues, such as the differential expression of SOC1_a, SOC1_b, and SOC1_c in the photoperiodic flowering pathway. Up-regulation of SAD_a and FATA genes and down-regulation of FAD2_a gene in the TAGBS pathway in seeds may be relevant to the ratio of monounsaturated fatty acid (MUFAs) to polyunsaturated fatty acid (PUFAs) in seed oil. MYBF1, a transcription regulator gene of the FlaBS pathway, was found with great sequence variation and alteration of expression patterns, probably resulting in functionally evolutionary differentiation in C. reticulata. MYBA1_a and some anthocyanin-specific biosynthetic genes in the FlaBS pathway were highly expressed in both flower buds and flowers, suggesting important roles of anthocyanin biosynthesis in flower development. Besides, a total of 40,823 expressed sequence tag simple sequence repeats (EST-SSRs) were identified in the C. reticulata transcriptome, providing valuable marker resources for further basic and applied researches on this economically important Camellia plant.
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Affiliation(s)
- Qiu-Yang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- *Correspondence: Li-Zhi Gao
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De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes. Int J Mol Sci 2015; 16:29482-95. [PMID: 26690414 PMCID: PMC4691121 DOI: 10.3390/ijms161226178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/02/2015] [Accepted: 12/03/2015] [Indexed: 01/08/2023] Open
Abstract
Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant–pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future.
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Xia EH, Yao QY, Zhang HB, Jiang JJ, Zhang LP, Gao LZ. CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences. FRONTIERS IN PLANT SCIENCE 2015; 6:1171. [PMID: 26779212 PMCID: PMC4703815 DOI: 10.3389/fpls.2015.01171] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/07/2015] [Indexed: 05/02/2023]
Abstract
Simple sequence repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs (PolySSRs) based on the multiple assembled sequences. The pipeline allows users to identify putative PolySSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation and missing rate of the SSR repetitions are provided to systematically assess the feasibility of the detected PolySSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified PolySSR are also automatically designed and further evaluated by the global sequence similarities of the primer-binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of PolySSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the PolySSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html.
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Affiliation(s)
- En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Qiu-Yang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian-Jun Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Li-Ping Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- *Correspondence: Li-Zhi Gao,
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