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Chen C, Shi L, Bin Y, Liu C, Tian M, Jiang A. Integration of transcriptome, miRNA and degradome sequencing reveals the early browning response in fresh-cut apple. Food Chem 2023; 406:134663. [PMID: 36459799 DOI: 10.1016/j.foodchem.2022.134663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 10/15/2022] [Indexed: 12/27/2022]
Abstract
Surface browning negatively impacts the shelf-life of fresh-cut apple. Herein, we found that the browning of fresh-cut apple aggravated rapidly after 24 h post-cutting, then the transcriptomic and miRNA expression profiles of fresh-cut apple immediately after cutting (T0) and 24 h post-cutting (T24) were analyzed to explore the molecular mechanism of early browning response. A total of 3156 differentially expressed mRNAs (DEGs) and 23 differentially expressed miRNAs (DEmiRNAs) were identified in T24 vs T0. Most DEGs related to respiratory, energy, antioxidant, lipid and secondary metabolism were activated in the early stage of browning. There were 63 target genes of 10 DEmiRNAs validated by degradome sequencing and among them, mdm-miR156aa_L + 1_1 targets 12-oxophytodienoate reductase, ptc-miR6478_R-1 targets patatin-like protein, mdm-miR156aa_L + 1_1 and mdm-miR156aa_L + 1_2 co-target SPLs might participate in the early browning response through regulating antioxidant, lipid and secondary metabolism. Our results will be beneficial for the technological innovation of browning amelioration for fresh-cut apple.
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Affiliation(s)
- Chen Chen
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Lijia Shi
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Yuqi Bin
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Chenghui Liu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Mixia Tian
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Aili Jiang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China.
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2
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Ghai D, Kaur A, Kahlon PS, Pawar SV, Sembi JK. A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:837563. [PMID: 35574139 PMCID: PMC9100589 DOI: 10.3389/fpls.2022.837563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.
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Affiliation(s)
- Devina Ghai
- Department of Botany, Panjab University, Chandigarh, India
| | - Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, India
| | - Parvinderdeep S. Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sandip V. Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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Zeng D, Que C, Teixeira da Silva JA, Xu S, Li D. Comparative Transcriptomic and Metabolic Analyses Reveal the Molecular Mechanism of Ovule Development in the Orchid, Cymbidium sinense. FRONTIERS IN PLANT SCIENCE 2021; 12:814275. [PMID: 35126436 PMCID: PMC8813969 DOI: 10.3389/fpls.2021.814275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/27/2021] [Indexed: 05/04/2023]
Abstract
Ovule development is pivotal to plant reproduction and seed development. Cymbidium sinense (Orchidaceae) has high ornamental value due to its pleasant aroma and elegant floral morphology. The regulatory mechanism underlying ovule development in orchids, especially C. sinense, is largely unknown and information on the C. sinense genome is very scarce. In this study, a combined analysis was performed on the transcriptome and non-targeted metabolomes of 18 C. sinense 'Qi Jian Hei Mo' ovule samples. Transcriptome analysis assembled gene-related information related to six growth stages of C. sinense ovules (S1-S6, equivalent to 30, 35, 42, 46, 53, and 60 days after pollination). Illumina sequencing technology was used to obtain the complete set of transcriptome sequences of the 18 samples. A total of 81,585 unigene sequences were obtained after assembly, 24,860 (30.47%) of which were functionally annotated. Using transcriptome sequencing technology, a total of 9845 differentially expressed unigenes (DEUs) were identified in C. sinense ovules that were assigned to specific metabolic pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). DEUs associated with transcription factors (TFs) and phytohormones were identified and analyzed. The TFs homeobox and MADS-box were associated with C. sinense ovule development. In particular, the phytohormones associated with DEUs such as indole-3-acetic acid (IAA), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), brassinosteroid (BR), and jasmonate (JA), may have important regulatory effects on C. sinense ovule development. Metabolomic analysis showed an inconsistent number of KEGG annotations of differential metabolites across comparisons (S2_vs_S4, S2_vs_S5, and S4_vs_S5 contained 23, 26, and 3 annotations, respectively) in C. sinense ovules. This study provides a valuable foundation for further understanding the regulation of orchid ovule development and formation, and establishes a theoretical background for future practical applications during orchid cultivation.
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Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Caixia Que
- Guangdong Provincial Research Center for Standardization of Production Engineering Technology of Orchids, Shunde Polytechnic, Foshan, China
| | | | - Shutao Xu
- College of Innovative Design, City University of Macau, Taipa, Macao SAR, China
| | - Dongmei Li
- Guangdong Provincial Research Center for Standardization of Production Engineering Technology of Orchids, Shunde Polytechnic, Foshan, China
- *Correspondence: Dongmei Li,
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Cheng N, Xiao J, Ge S, Li J, Huang J, Wu X, Zhang S, Xiang T. High-Throughput Sequencing Strategy for miR-146b-regulated circRNA Expression in Hepatic Stellate Cells. Med Sci Monit 2018; 24:8699-8706. [PMID: 30504757 PMCID: PMC6286633 DOI: 10.12659/msm.910807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study was designed to detect and analyze miR-146b-mediated circular RNA (circRNA) expression in hepatic stellate cells. MATERIAL AND METHODS The experiment was divided into a control group and a siRNA-miR-146b group. The interference efficiency of siRNA-miR-146b was confirmed by real-time quantitative reverse transcription PCR (qRT-PCR) and the cells were collected, and total RNA was collected for high flux sequencing. The miRNA-targeted carcass were predicted. Finally, the expression of 5 circRNAs was verified by qRT-PCR. RESULTS miR-146b expression in the siRNA-miR-146b group was significantly lower than that in the control group. The quality of the original sequencing data and the processed data satisfied with the analysis, and the expression of circRNAs was modulated after the reduction of miR-146b. Among them, 18 circRNAs were upregulated, while 77 circRNAs were downregulated in the miR-146b group compared with the control group. The gene prediction showed that hsa_circ1887 was the largest contact point in miRNA and circRNA regulatory networks. qRT-PCR showed that rno-circRNA-469, rno-circRNA-1138, rno-circRNA-2168 and rno-circRAN-1907 were significantly reduced, while circRNA-1984 was significantly promoted in the siRNA-miR-146b group compared with the control group, which were consistent with the measurements by high-throughput sequencing technique. CONCLUSIONS miR-146b could regulate the expression of circRNAs in HSCs, which might take part in the formation and development of hepatic fibrosis.
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Affiliation(s)
- Na Cheng
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Juhua Xiao
- Department of Ultrasound, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China (mainland)
| | - Shanfei Ge
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Juntao Li
- Department of General Surgery, GanZhou People's Hospital, Ganzhou, Jiangxi, China (mainland)
| | - Jiansheng Huang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Xiaoping Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Shouhua Zhang
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China (mainland)
| | - Tianxin Xiang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China (mainland)
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Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:11640. [PMID: 30076357 PMCID: PMC6076244 DOI: 10.1038/s41598-018-30147-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/24/2018] [Indexed: 11/15/2022] Open
Abstract
Deceptive pollination is key to the species richness of Orchidaceae. However, the genetic basis of species diversification is still under study. Section Trigonopedia is a monophyletic clade of genus Cypripedium distributed in the southwest of China. The species of this section are pollinated by different flies. Pollinator differentiation makes section Trigonopedia an ideal group for studying the genetic basis underlying species diversification. Here, we sequenced the transcriptomes of eight species of the genus Cypripedium, including six co-flowering species of section Trigonopedia and two species outside this section as an outgroup. We reconstructed the phylogeny of the section with the combined 1572 single-copy genes extracted from the eight species and produced a highly resolved tree of the section. Furthermore, we combined substitution rate estimation and differential expression analysis to identify candidate genes, including genes related to floral scent synthesis and environmental adaptation, involved in species differentiation. Field investigations showed that these species have adapted to different habitats. We propose that the species diversification in this section is initiated by floral scent differentiation, followed by habitat differentiation, finally leading to speciation. This study sheds novel light on the diversification of closely related orchid species in the Qinghai-Tibetan region.
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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7
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Zhu H, Liu J, Wen Q, Chen M, Wang B, Zhang Q, Xue Z. De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits. PLoS One 2017; 12:e0187117. [PMID: 29145430 PMCID: PMC5690621 DOI: 10.1371/journal.pone.0187117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022] Open
Abstract
Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1-6 h). Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism.
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Affiliation(s)
- Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Jianting Liu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Mindong Chen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Bin Wang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qianrong Zhang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Zhuzheng Xue
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
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8
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Wang Y, Wang Y, Li K, Song X, Chen J. Characterization and Comparative Expression Profiling of Browning Response in Medinilla formosana after Cutting. FRONTIERS IN PLANT SCIENCE 2016; 7:1897. [PMID: 28066460 PMCID: PMC5178855 DOI: 10.3389/fpls.2016.01897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Plant browning is a recalcitrant problem for in vitro culture and often leads to poor growth of explants and even failure of tissue culture. However, the molecular mechanisms underlying browning-induced physiological processes remain unclear. Medinilla is considered one of the most difficult genera for tissue culture owning to its severe browning. In the present study, intact aseptic plantlets of Medinilla formosana Hayata previously obtained by ovary culture, were used to explore the characteristics and molecular mechanism of the browning response. Successive morphological and anatomical observations after cutting showed that the browning of M. formosana was not lethal but adaptive. De novo transcriptome and digital gene expression (DGE) profiling using Illumina high-throughput sequencing were then used to explore molecular regulation after cutting. About 7.5 million tags of de novo transcriptome were obtained and 58,073 unigenes were assembled and annotated. A total of 6,431 differentially expressed genes (DEGs) at three stages after cutting were identified, and the expression patterns of these browning-related genes were clustered and analyzed. A number of putative DEGs involved in signal transduction and secondary metabolism were particularly studied and the potential roles of these cutting-responsive mRNAs in plant defense to diverse abiotic stresses are discussed. The DGE profiling data were also validated by quantitative RT-PCR analysis. The data obtained in this study provide an excellent resource for unraveling the molecular mechanisms of browning processes during in vitro tissue culture, and lay a foundation for future studies to inhibit and eliminate browning damage.
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Affiliation(s)
- Yan Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yiting Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Kunfeng Li
- Agriculture Experiment Station, Zhejiang UniversityHangzhou, China
| | - Xijiao Song
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
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9
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Niu SC, Xu Q, Zhang GQ, Zhang YQ, Tsai WC, Hsu JL, Liang CK, Luo YB, Liu ZJ. De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. Sci Data 2016; 3:160083. [PMID: 27673730 PMCID: PMC5037975 DOI: 10.1038/sdata.2016.83] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/24/2016] [Indexed: 01/19/2023] Open
Abstract
Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search.
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Affiliation(s)
- Shan-Ce Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Jui-Ling Hsu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Chieh-Kai Liang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China.,The Centre for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510640, China.,College of Arts, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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