1
|
Li C, Krishnan S, Zhang M, Hu D, Meng D, Riedelsberger J, Dougherty L, Xu K, Piñeros MA, Cheng L. Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310159. [PMID: 38514904 PMCID: PMC11165477 DOI: 10.1002/advs.202310159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Vacuolar malic acid accumulation largely determines fruit acidity, a key trait for the taste and flavor of apple and other fleshy fruits. Aluminum-activated malate transporter 9 (ALMT9/Ma1) underlies a major genetic locus, Ma, for fruit acidity in apple, but how the protein transports malate across the tonoplast is unclear. Here, it is shown that overexpression of the coding sequence of Ma1 (Ma1α) drastically decreases fruit acidity in "Royal Gala" apple, leading to uncovering alternative splicing underpins Ma1's function. Alternative splicing generates two isoforms: Ma1β is 68 amino acids shorter with much lower expression than the full-length protein Ma1α. Ma1β does not transport malate itself but interacts with the functional Ma1α to form heterodimers, creating synergy with Ma1α for malate transport in a threshold manner (When Ma1β/Ma1α ≥ 1/8). Overexpression of Ma1α triggers feedback inhibition on the native Ma1 expression via transcription factor MYB73, decreasing the Ma1β level well below the threshold that leads to significant reductions in Ma1 function and malic acid accumulation in fruit. Overexpression of Ma1α and Ma1β or genomic Ma1 increases both isoforms proportionally and enhances fruit malic acid accumulation. These findings reveal an essential role of alternative splicing in ALMT9-mediated malate transport underlying apple fruit acidity.
Collapse
Affiliation(s)
- Chunlong Li
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China
| | | | - Mengxia Zhang
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dagang Hu
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dong Meng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Janin Riedelsberger
- Center for Bioinformatics, Simulation and Modeling, Department of Bioinformatics, Faculty of EngineeringUniversity of TalcaTalca3460000Chile
| | - Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Miguel A. Piñeros
- Plant Biology Section, School of Integrative Plant Science and Robert W. Holley Center for Agriculture and HealthUSDA‐ARS Cornell UniversityIthacaNY14853USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| |
Collapse
|
2
|
Zeng X, Wu C, Zhang L, Lan L, Fu W, Wang S. Molecular Mechanism of Resistance to Alternaria alternata Apple Pathotype in Apple by Alternative Splicing of Transcription Factor MdMYB6-like. Int J Mol Sci 2024; 25:4353. [PMID: 38673937 PMCID: PMC11050356 DOI: 10.3390/ijms25084353] [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: 02/22/2024] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
As a fruit tree with great economic value, apple is widely cultivated in China. However, apple leaf spot disease causes significant damage to apple quality and economic value. In our study, we found that MdMYB6-like is a transcription factor without auto-activation activity and with three alternative spliced variants. Among them, MdMYB6-like-β responded positively to the pathogen infection. Overexpression of MdMYB6-like-β increased the lignin content of leaves and improved the pathogenic resistance of apple flesh callus. In addition, all three alternative spliced variants of MdMYB6-like could bind to the promoter of MdBGLU H. Therefore, we believe that MdMYB6-like plays an important role in the infection process of the pathogen and lays a solid foundation for breeding disease-resistant cultivars of apple in the future.
Collapse
Affiliation(s)
| | | | | | | | | | - Sanhong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.Z.); (C.W.); (L.Z.); (L.L.); (W.F.)
| |
Collapse
|
3
|
Zuo H, Chen J, Lv Z, Shao C, Chen Z, Zhou Y, Shen C. Tea-Derived Polyphenols Enhance Drought Resistance of Tea Plants ( Camellia sinensis) by Alleviating Jasmonate-Isoleucine Pathway and Flavonoid Metabolism Flow. Int J Mol Sci 2024; 25:3817. [PMID: 38612625 PMCID: PMC11011871 DOI: 10.3390/ijms25073817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Extreme drought weather has occurred frequently in recent years, resulting in serious yield loss in tea plantations. The study of drought in tea plantations is becoming more and more intensive, but there are fewer studies on drought-resistant measures applied in actual production. Therefore, in this study, we investigated the effect of exogenous tea polyphenols on the drought resistance of tea plant by pouring 100 mg·L-1 of exogenous tea polyphenols into the root under drought. The exogenous tea polyphenols were able to promote the closure of stomata and reduce water loss from leaves under drought stress. Drought-induced malondialdehyde (MDA) accumulation in tea leaves and roots was also significantly reduced by exogenous tea polyphenols. Combined transcriptomic and metabolomic analyses showed that exogenous tea polyphenols regulated the abnormal responses of photosynthetic and energy metabolism in leaves under drought conditions and alleviated sphingolipid metabolism, arginine metabolism, and glutathione metabolism in the root system, which enhanced the drought resistance of tea seedlings. Exogenous tea polyphenols induced jasmonic acid-isoleucine (JA-ILE) accumulation in the root system, and the jasmonic acid-isoleucine synthetase gene (TEA028623), jasmonic acid ZIM structural domain proteins (JAMs) synthesis genes (novel.22237, TEA001821), and the transcription factor MYC2 (TEA014288, TEA005840) were significantly up-regulated. Meanwhile, the flavonoid metabolic flow was significantly altered in the root; for example, the content of EGCG, ECG, and EGC was significantly increased. Thus, exogenous tea polyphenols enhance the drought resistance of tea plants through multiple pathways.
Collapse
Affiliation(s)
- Haoming Zuo
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Jiahao Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Zhidong Lv
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Chenyu Shao
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Yuebin Zhou
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Chengwen Shen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
4
|
Mi X, Tang M, Zhu J, Shu M, Wen H, Zhu J, Wei C. Alternative splicing of CsWRKY21 positively regulates cold response in tea plant. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108473. [PMID: 38430784 DOI: 10.1016/j.plaphy.2024.108473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Alternative splicing (AS) was an important post-transcriptional mechanism that involved in plant resistance to adversity stress. WRKY transcription factors function as transcriptional activators or repressors to modulate plant growth, development and stress response. However, the role of alternate splicing of WRKY in cold tolerance is poorly understood in tea plants. In this study, we found that the CsWRKY21 transcription factor, a member of the WRKY IId subfamily, was induced by low temperature. Subcellular localization and transcriptional activity assays showed that CsWRKY21 localized to the nucleus and had no transcriptional activation activity. Y1H and dual-luciferase reporter assays showed that CsWRKY21 suppressed expression of CsABA8H and CsUGT by binding with their promoters. Transient overexpression of CsABA8H and CsUGT reduced abscisic acid (ABA) content in tobacco leaves. Furthermore, we discovered that CsWRKY21 undergoes AS in the 5'UTR region. The AS transcript CsWRKY21-b was induced at low temperature, up to 6 folds compared to the control, while the full-length CsWRKY21-a transcript did not significantly change. Western blot analysis showed that the retention of introns in the 5'UTR region of CsWRKY21-b led to higher CsWRKY21 protein content. These results revealed that alternative splicing of CsWRKY21 involved in cold tolerance of tea plant by regulating the protein expression level and then regulating the content of ABA, and provide insights into molecular mechanisms of low temperature defense mediated by AS in tea plant.
Collapse
Affiliation(s)
- Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China; Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang, Guizhou, 550006, People's Republic of China
| | - Mengsha Tang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China; Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang, Guizhou, 550006, People's Republic of China
| | - Jiaxin Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Mingtao Shu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Huilin Wen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
| |
Collapse
|
5
|
Song X, Zhang M, Shahzad K, Zhang X, Guo L, Qi T, Tang H, Wang H, Qiao X, Feng J, Han Y, Xing C, Wu J. Comparative Transcriptome Profiling of CMS-D2 and CMS-D8 Systems Characterizes Fertility Restoration Genes Network in Upland Cotton. Int J Mol Sci 2023; 24:10759. [PMID: 37445936 DOI: 10.3390/ijms241310759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Resolving the genetic basis of fertility restoration for cytoplasmic male sterility (CMS) can improve the efficiency of three-line hybrid breeding. However, the genetic determinants of male fertility restoration in cotton are still largely unknown. This study comprehensively compared the full-length transcripts of CMS-D2 and CMS-D8 systems to identify potential genes linked with fertility restorer genes Rf1 or Rf2. Target comparative analysis revealed a higher percentage of differential genes in each restorer line as compared to their corresponding sterile and maintainer lines. An array of genes with specific expression in the restorer line of CMS-D2 had functional annotations related to floral development and pathway enrichments in various secondary metabolites, while specifically expressed genes in the CMS-D8 restorer line showed functional annotations related to anther development and pathway enrichment in the biosynthesis of secondary metabolites. Further analysis identified potentially key genes located in the target region of fertility restorer genes Rf1 or Rf2. In particular, Ghir_D05G032450 can be the candidate gene related to restorer gene Rf1, and Ghir_D05G035690 can be the candidate gene associated with restorer gene Rf2. Further gene expression validation with qRT-PCR confirmed the accuracy of our results. Our findings provide useful insights into decoding the potential regulatory network that retrieves pollen fertility in cotton and will help to further reveal the differences in the genetic basis of fertility restoration for two CMS systems.
Collapse
Affiliation(s)
- Xiatong Song
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juanjuan Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yang Han
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jianyong Wu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| |
Collapse
|
6
|
Sybilska E, Daszkowska-Golec A. Alternative splicing in ABA signaling during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1144990. [PMID: 37008485 PMCID: PMC10060653 DOI: 10.3389/fpls.2023.1144990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is an essential step in a plant's life cycle. It is controlled by complex physiological, biochemical, and molecular mechanisms and external factors. Alternative splicing (AS) is a co-transcriptional mechanism that regulates gene expression and produces multiple mRNA variants from a single gene to modulate transcriptome diversity. However, little is known about the effect of AS on the function of generated protein isoforms. The latest reports indicate that alternative splicing (AS), the relevant mechanism controlling gene expression, plays a significant role in abscisic acid (ABA) signaling. In this review, we present the current state of the art about the identified AS regulators and the ABA-related changes in AS during seed germination. We show how they are connected with the ABA signaling and the seed germination process. We also discuss changes in the structure of the generated AS isoforms and their impact on the functionality of the generated proteins. Also, we point out that the advances in sequencing technology allow for a better explanation of the role of AS in gene regulation by more accurate detection of AS events and identification of full-length splicing isoforms.
Collapse
|
7
|
Hou L, Wang M, Zhu L, Ning M, Bi J, Du J, Kong X, Gu W, Meng Q. Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir. Front Cell Infect Microbiol 2022; 12:997574. [PMID: 36530442 PMCID: PMC9754153 DOI: 10.3389/fcimb.2022.997574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.
Collapse
Affiliation(s)
- Libo Hou
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Mengdi Wang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Lei Zhu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Mingxiao Ning
- Institution of Quality Standard and Testing Technology for Agro-product, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Jingxiu Bi
- Institution of Quality Standard and Testing Technology for Agro-product, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Jie Du
- Animal Husbandry and Veterinary College, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, China
| | - Xianghui Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu, China,*Correspondence: Qingguo Meng,
| |
Collapse
|
8
|
Kishi-Kaboshi M, Tanaka T, Sasaki K, Noda N, Aida R. Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization. Sci Rep 2022; 12:17874. [PMID: 36284128 PMCID: PMC9596691 DOI: 10.1038/s41598-022-22589-z] [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: 06/19/2022] [Accepted: 10/17/2022] [Indexed: 01/20/2023] Open
Abstract
Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained 'Sei Arabella' transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome.
Collapse
Affiliation(s)
- Mitsuko Kishi-Kaboshi
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan ,grid.416835.d0000 0001 2222 0432Present Address: Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Tsuyoshi Tanaka
- grid.416835.d0000 0001 2222 0432Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Katsutomo Sasaki
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Naonobu Noda
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Ryutaro Aida
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| |
Collapse
|
9
|
D’Auria JC, Cohen SP, Leung J, Glockzin K, Glockzin KM, Gervay-Hague J, Zhang D, Meinhardt LW. United States tea: A synopsis of ongoing tea research and solutions to United States tea production issues. FRONTIERS IN PLANT SCIENCE 2022; 13:934651. [PMID: 36212324 PMCID: PMC9538180 DOI: 10.3389/fpls.2022.934651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/25/2022] [Indexed: 06/01/2023]
Abstract
Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States.
Collapse
Affiliation(s)
- John C. D’Auria
- Metabolic Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stephen P. Cohen
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Jason Leung
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Kyle Mark Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jacquelyn Gervay-Hague
- Department of Chemistry, University of California, University of California, Davis, Davis, CA, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| |
Collapse
|
10
|
Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol 2022; 23:149. [PMID: 35799267 PMCID: PMC9264592 DOI: 10.1186/s13059-022-02711-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/15/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. RESULTS We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. CONCLUSIONS AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
Collapse
Affiliation(s)
- Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Max Coulter
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Present address: Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Yamile Marquez
- Centre for Genomic Regulation, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Linda Milne
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Stefan Riegler
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Present address: Institute of Science and Technology Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sarah Harvey
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Yubang Gao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Theresa Wießner-Kroh
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Martin Crespi
- French National Centre for Scientific Research | CNRS INRAE-Universities of Paris Saclay and Paris, Institute of Plant Sciences Paris Saclay IPS2, Rue de Noetzlin, 91192, Gif sur Yvette, France
| | - Katherine Denby
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Asa Ben Hur
- Department of Computer Science, Colorado State University, 1873 Campus Delivery, Fort Collins, CO, 80523-1873, USA
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, 100 East 24th St., Austin, TX, 78712-1095, USA
| | - Michael Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17 A-1090, Vienna, Austria
| | - Artur Jarmolowski
- Department of Gene Expression, Adam Mickiewicz University, Poznań, Poland
| | - Tino Koester
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Sascha Laubinger
- Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Qingshun Quinn Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lianfeng Gu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Present address: Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiao-Ning Zhang
- Biology Department, School of Arts and Sciences, St. Bonaventure University, 3261 West State Road, St. Bonaventure, NY, 14778, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Center of Medical Biochemistry, Dr.-Bohr-Gasse 9/3, A-1030, Vienna, Austria
| | - Maria Kalyna
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| |
Collapse
|
11
|
Hao DC, Chen H, Xiao PG, Jiang T. A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales. Curr Genomics 2022; 23:207-216. [PMID: 36777007 PMCID: PMC9878827 DOI: 10.2174/1389202923666220527112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The multiple isoforms are often generated from a single gene via Alternative Splicing (AS) in plants, and the functional diversity of the plant genome is significantly increased. Despite well-studied gene functions, the specific functions of isoforms are little known, therefore, the accurate prediction of isoform functions is exceedingly wanted. Methods: Here we perform the first global analysis of AS of Dichocarpum, a medicinal genus of Ranunculales, by utilizing full-length transcriptome datasets of five Chinese endemic Dichocarpum taxa. Multiple software were used to identify AS events, the gene function was annotated based on seven databases, and the protein-coding sequence of each AS isoform was translated into an amino acid sequence. The self-developed software DIFFUSE was used to predict the functions of AS isoforms. Results: Among 8,485 genes with AS events, the genes with two isoforms were the most (6,038), followed by those with three isoforms and four isoforms. Retained intron (RI, 551) was predominant among 1,037 AS events, and alternative 3' splice sites and alternative 5' splice sites were second. The software DIFFUSE was effective in predicting functions of Dichocarpum isoforms, which have not been unearthed. When compared with the sequence alignment-based database annotations, DIFFUSE performed better in differentiating isoform functions. The DIFFUSE predictions on the terms GO:0003677 (DNA binding) and GO: 0010333 (terpene synthase activity) agreed with the biological features of transcript isoforms. Conclusion: Numerous AS events were for the first time identified from full-length transcriptome datasets of five Dichocarpum taxa, and functions of AS isoforms were successfully predicted by the self-developed software DIFFUSE. The global analysis of Dichocarpum AS events and predicting isoform functions can help understand the metabolic regulations of medicinal taxa and their pharmaceutical explorations.
Collapse
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China;,Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;,Address correspondence to these authors at the School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China; Tel: 0086-411-84572552; E-mail: ; and Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Tel/Fax: 001-951-827-2991; E-mail:
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA;,Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA;,These authors contributed equally to this work.
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA;,Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China,Address correspondence to these authors at the School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China; Tel: 0086-411-84572552; E-mail: ; and Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Tel/Fax: 001-951-827-2991; E-mail:
| |
Collapse
|
12
|
Alternative Splicing and Its Roles in Plant Metabolism. Int J Mol Sci 2022; 23:ijms23137355. [PMID: 35806361 PMCID: PMC9266299 DOI: 10.3390/ijms23137355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/02/2023] Open
Abstract
Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.
Collapse
|
13
|
Zhao S, Cheng H, Xu P, Wang Y. Regulation of biosynthesis of the main flavor-contributing metabolites in tea plant ( Camellia sinensis): A review. Crit Rev Food Sci Nutr 2022; 63:10520-10535. [PMID: 35608014 DOI: 10.1080/10408398.2022.2078787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the process of adapting to the environment, tea plants (Camellia sinensis) endow tea with unique flavor and health functions, which should be attributed to secondary metabolites, including catechins, L-theanine, caffeine and terpene volatiles. Since the content of these flavor-contributing metabolites are mainly determined by the growth of tea plant, it is very important to understand their alteration and regulation mechanisms. In the present work, we first summarize the distribution, change characteristics of the main flavor-contributing metabolites in different cultivars, organs and under environmental stresses of tea plant. Subsequently, we discuss the regulating mechanisms involved in the biosynthesis of these metabolites based on the existing evidence. Finally, we propose the remarks and perspectives on the future study relating flavor-contributing metabolites. This review would contribute to the acceleration of research on the characteristic secondary metabolites and the breeding programs in tea plants.
Collapse
Affiliation(s)
- Shiqi Zhao
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Haiyan Cheng
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Ping Xu
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Yuefei Wang
- Tea Research Institute, Zhejiang University, Hangzhou, China
| |
Collapse
|
14
|
Hong WJ, Lee SK, Kim SH, Kim YJ, Moon S, Kim EJ, Silva J, Jung KH. Comparative transcriptome analysis of pollen and anther wall reveals novel insights into the regulatory mechanisms underlying anther wall development and its dehiscence in rice. PLANT CELL REPORTS 2022; 41:1229-1242. [PMID: 35249124 DOI: 10.1007/s00299-022-02852-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/15/2022] [Indexed: 05/25/2023]
Abstract
To further understand the regulatory mechanism for anther dehiscence in rice, we carried out transcriptome analysis for the following two tissues: the anther wall and pollen at the anthesis stage. With the anatomical meta-expression data, in addition to these tissues, the differentially expressed genes (DEGs) between the two tissues were further refined to identify 1,717 pollen-preferred genes and 534 anther wall-preferred genes. A GUS transgenic line and RT-qPCR analysis for anther wall-preferred genes supported the fidelity of our gene candidates for further analysis. The refined DEGs were functionally classified through Gene Ontology (GO) enrichment and MapMan analyses. Through the analysis of cis-acting elements and alternative splicing variants, we also suggest the feature of regulatory sequences in promoter regions for anther wall-preferred expression and provide information of the unique splicing variants in anther wall. Subsequently, it was found that hormone signaling and the resulting transcriptional regulation pathways may play an important role in anther dehiscence and anther wall development. Our results could provide useful insights into future research to broaden the molecular mechanism of anther dehiscence or anther wall development in rice.
Collapse
Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Su Kyoung Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Seok-Hui Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Eui-Jung Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Jeniffer Silva
- Department of Research and Development, The Bridge Biofoundry, Ciudad del Saber, Clayton, 0843-03081, Panama
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea.
| |
Collapse
|
15
|
Lin S, Chen Z, Chen T, Deng W, Wan X, Zhang Z. Theanine metabolism and transport in tea plants ( Camellia sinensis L.): advances and perspectives. Crit Rev Biotechnol 2022; 43:327-341. [PMID: 35430936 DOI: 10.1080/07388551.2022.2036692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Theanine, a tea plant-specific non-proteinogenic amino acid, is the most abundant free amino acid in tea leaves. It is also one of the most important quality components of tea because it endows the "umami" taste, relaxation-promoting, and many other health benefits of tea infusion. Its content in tea leaves is directly correlated with the quality and price of green tea. Theanine biosynthesis primarily occurs in roots and is transported to new shoots in tea plants. Recently, great advances have been made in theanine metabolism and transport in tea plants. Along with the deciphering of the genomic sequences of tea plants, new genes in theanine metabolic pathway were discovered and functionally characterized. Theanine transporters were identified and were characterized on the affinity for: theanine, substrate specificity, spatiotemporal expression, and the role in theanine root-to-shoot transport. The mechanisms underlying the regulation of theanine accumulation by: cultivars, seasons, nutrients, and environmental factors are also being rapidly uncovered. Transcription factors were identified to be critical regulators of theanine biosynthesis. In this review, we summarize the progresses in theanine: biosynthesis, catabolism, and transport processes. We also discuss the future studies on theanine in tea plants, and application of the knowledge to crops to synthesize theanine to improve the health-promoting quality of non-tea crops.
Collapse
Affiliation(s)
- Shijia Lin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Ziping Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Tingting Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| |
Collapse
|
16
|
Full-Length Transcriptome Characterization and Comparative Analysis of Chosenia arbutifolia. FORESTS 2022. [DOI: 10.3390/f13040543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As a unique tree species in the Salicaceae family, Chosenia arbutifolia is used primarily for construction materials and landscape planting in China. Compared with other Salicaceae species members, the genomic resources of C. arbutifolia are extremely scarce. Thus, in the present study, the full-length transcriptome of C. arbutifolia was sequenced by single-molecular real-time sequencing (SMRT) technology based on the PacBio platform. Then, it was compared against those of other Salicaceae species. We generated 17,397,064 subreads and 95,940 polished reads with an average length of 1812 bp, which were acquired through calibration, clustering, and polishing. In total, 50,073 genes were reconstructed, of which 48,174 open reading frames, 4281 long non-coding RNAs, and 3121 transcription factors were discovered. Functional annotation revealed that 47,717 genes had a hit in at least one of five reference databases. Moreover, a set of 12,332 putative SSR markers were screened among the reconstructed genes. Single-copy and special orthogroups, and divergent and conserved genes, were identified and analyzed to find divergence among C. arbutifolia and the five Salicaceae species. To reveal genes involved in a specific function and pathway, enrichment analyses for GO and KEGG were also performed. In conclusion, the present study empirically confirmed that SMRT sequencing realistically depicted the C. arbutifolia transcriptome and provided a comprehensive reference for functional genomic research on Salicaceae species.
Collapse
|
17
|
Sun M, Zhao Y, Shao X, Ge J, Tang X, Zhu P, Wang J, Zhao T. EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily ( Lilium lancifolium Thunb). Appl Bionics Biomech 2022; 2022:7641048. [PMID: 35126662 PMCID: PMC8816598 DOI: 10.1155/2022/7641048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete transcriptomic profile. We obtained a total of 815,624 CCS (Circular Consensus Sequence) reads with an average length of 1295 bp. The tiger lily transcriptome has been sequenced for the first time using third-generation long-read technology. Furthermore, unigenes (38,707), lncRNAs (6852), and TF members (768) were determined based on the transcriptome data, followed by evaluating SSRs (3319). It has also been revealed that 105 out of 128 primer pairs effectively amplified PCR products. Around 15,608 transcripts were allocated to 25 distinct KOG Clusters, and 10,706 unigenes were grouped into 52 functional categories in the annotated transcripts. Until now, no tiger lily lncRNAs have been discovered. Results of this study may serve as an extensive set of reference transcripts and help us learn more about the transcriptomes of tiger lilies and pave the path for further research.
Collapse
Affiliation(s)
- Mingwei Sun
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | | | - Xiaobin Shao
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Jintao Ge
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Xueyan Tang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Pengbo Zhu
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Jiangying Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Tongli Zhao
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| |
Collapse
|
18
|
Ding YQ, Fan K, Wang Y, Fang WP, Zhu XJ, Chen L, Sun LT, Qiu C, Ding ZT. Drought and Heat Stress-Mediated Modulation of Alternative Splicing in the Genes Involved in Biosynthesis of Metabolites Related to Tea Quality. Mol Biol 2022. [DOI: 10.1134/s0026893322020042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
Chen Q, Lin X, Tang W, Deng Q, Wang Y, Lin Y, He W, Zhang Y, Li M, Luo Y, Zhang Y, Wang X, Tang H. Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:872054. [PMID: 35909727 PMCID: PMC9326444 DOI: 10.3389/fpls.2022.872054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/20/2022] [Indexed: 05/13/2023]
Abstract
The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to the developmental cues and what relevance do these outcomes have to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored transcript isoforms raised from aTSS, aTTS, and AS. The relative contributions of these three processes to the complexity of strawberry fruit transcripts were compared. The aTSS and aTTS were more abundant than the AS. Differentially expressed transcripts unraveled the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes were observed. They were associated with protein-coding potential change and domain gain or loss as the main consequences. Those genes with switched isoforms take part in the key processes of maturation in the late stages. A case study using yeast two hybrid analysis supported the functional divergence of the two isoforms of the B-box protein 22. Our results provided a new comprehensive overview of the dynamic transcriptomic landscape during strawberry fruit development and maturation.
Collapse
Affiliation(s)
- Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ximeng Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Wenlu Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yuanxiu Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yunting Zhang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Haoru Tang
| |
Collapse
|
20
|
Zhang C, Ren H, Yao X, Wang K, Chang J. Full-length transcriptome analysis of pecan ( Carya illinoinensis) kernels. G3 GENES|GENOMES|GENETICS 2021; 11:6288450. [PMID: 34849807 PMCID: PMC8496322 DOI: 10.1093/g3journal/jkab182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022]
Abstract
Abstract
Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.
Collapse
Affiliation(s)
- Chengcai Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jun Chang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| |
Collapse
|
21
|
Mahadani P, Hazra A. Expression and splicing dynamics of WRKY family genes along physiological exigencies of tea plant (Camellia sinensis). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00784-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
22
|
Liaquat F, Munis MFH, Arif S, Haroon U, Shi J, Saqib S, Zaman W, Che S, Liu Q. PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings. Front Genet 2021; 12:635043. [PMID: 33889177 PMCID: PMC8057201 DOI: 10.3389/fgene.2021.635043] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/01/2021] [Indexed: 11/18/2022] Open
Abstract
Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba.
Collapse
Affiliation(s)
- Fiza Liaquat
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Samiah Arif
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Urooj Haroon
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saddam Saqib
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wajid Zaman
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shengquan Che
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Qunlu Liu
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
23
|
Liu H, Li S, Xiao G, Wang Q. Formation of volatiles in response to tea green leafhopper (Empoasca onukii Matsuda) herbivory in tea plants: a multi-omics study. PLANT CELL REPORTS 2021; 40:753-766. [PMID: 33616702 DOI: 10.1007/s00299-021-02674-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 05/19/2023]
Abstract
Combined transcriptome and metabolome analysis of fresh leaf infestation by tea green leafhoppers (Empoasca (Matsumurasca) onukii Matsuda) suggests roles for alternative pre-mRNA splicing and mRNAs in the regulation of aroma formation in tea plants. Oriental Beauty is a high-grade, oolong tea with a pronounced honey-like aroma and rich ripe fruit flavor that develops primarily as a result of the infestation of the fresh leaves by tea green leafhoppers (Empoasca (Matsumurasca) onukii Matsuda). Here, we used PacBio Iso-Seq and RNA-seq analyses to determine the full-length transcripts and gene expression profiles of fresh tea leaves in response to E. (M.) onukii herbivory. We investigated the relationship between RNA-seq, tea metabolites, and aroma response mechanisms in leaves infested by leafhoppers. We found 3644 differentially expressed genes, of which 2552 were up- and 1092 were down-regulated. A total of 49,913 alternative splicing events were predicted, including 324 differential AS events. Moreover, 3105 differentially expressed transcripts were also identified, of which 2295 were up- and 810 were down-regulated. The characterization of expression patterns of the key gene transcript isoforms involved in the aroma formation pathways identified 130 differentially expressed metabolites, 97 of which were up- and 33 were down-regulated. Two key aroma compounds (phenylacetaldehyde and 4-hydroxybenzaldehyde) were highly correlated with genes of the aroma formation pathways. Our results revealed that pre-mRNA AS plays a crucial role in the metabolic regulation surrounding aroma formation under leafhopper herbivory in tea plants.
Collapse
Affiliation(s)
- Huifan Liu
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Sufen Li
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Gengsheng Xiao
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Qin Wang
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
| |
Collapse
|
24
|
Zhang Y, Li P, She G, Xu Y, Peng A, Wan X, Zhao J. Molecular Basis of the Distinct Metabolic Features in Shoot Tips and Roots of Tea Plants ( Camellia sinensis): Characterization of MYB Regulator for Root Theanine Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3415-3429. [PMID: 33719427 DOI: 10.1021/acs.jafc.0c07572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The physiological and metabolic differences between shoot tips and roots of tea plants are significant, and understanding them is required for improvement of tea quality and plant growth. A high-quality full-length transcriptome sequencing on tea plant roots and shoot tips by PacBio SMRT technology was done to gain a further understanding. Approximately 160699 and 166120 full-length transcripts were recovered in roots and shoots, respectively, including 31232 and 41068 novel isoforms and 16960 and 26029 alternative splicing (AS) isoforms. These supported 21699 full-length reads and 31232 and 41068 novel transcripts from root and shoot, respectively, including 1679 long noncoding RNAs (lncRNAs) and 2772 fusion transcripts, which significantly upgrade the Camellia sinensis genome annotation. The respective 6475 and 6981 transcripts in roots and shoots differ in 3'-untranslated regions. Meanwhile, extensive analyses of novel transcripts, ASs, and lncRNAs also revealed a large number of ASs and lincRNAs closely related to the regulation of characteristic secondary metabolites including catechins, theanine, and caffeine. Finally, a root-specific CsMYB6 was characterized to regulate theanine biosynthesis by genetic and molecular analyses. CsMYB6 directly bound to and activate the promoter of theanine synthetase gene (CsTSI). The study lays a foundation for the further investigation of metabolic genomics and regulation in tea plants.
Collapse
Affiliation(s)
- Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Anqi Peng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China
| |
Collapse
|
25
|
Wang F, Chen Z, Pei H, Guo Z, Wen D, Liu R, Song B. Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology. Gene 2020; 769:145247. [PMID: 33096183 DOI: 10.1016/j.gene.2020.145247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/16/2020] [Accepted: 10/15/2020] [Indexed: 01/22/2023]
Abstract
Transcriptome profiles have been widely captured using short-read sequencing technology, but there are still limitations partially due to the read length. Here, we generated long reads using Oxford Nanopore PromethION™ technology and short reads using the Illumina sequencing platform to study the transcriptome of root, stem, and leaf of Camellia sinensis cv. Fudingdabai. We mapped the Nanopore reads to the Shuchazao of C. sinensis genome sequence, and the mapping rates ranged from 82.63% to 90.59% (average 86.44%); this is lower than that of the Illumina reads which was 87.83% to 91.14% (average 90.12%). Gene expression level was quantified using the Nanopore and Illumina data and we observed a good agreement. The same tea leaf flavor synthesis pathways were highlighted using both sequencing technologies when analyzing the differentially expressed genes between leaf and root. Alternative splicing was then analyzed, and the intron-retention was observed as the most common alternative splicing. Moreover Nanopore long reads could correct transcript isoform annotation for differential expression investigation purposes. Nanopore sequencing techniques can provide a novel reference basis for molecular analysis of tea plants.
Collapse
Affiliation(s)
- Fen Wang
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China.
| | - Zhi Chen
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Huimin Pei
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Zhiyou Guo
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Di Wen
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Rong Liu
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Baoxing Song
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China.
| |
Collapse
|
26
|
Jin L, Forte AE, Deng B, Rafsanjani A, Bertoldi K. Kirigami-Inspired Inflatables with Programmable Shapes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001863. [PMID: 32627259 DOI: 10.1002/adma.202001863] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 05/19/2023]
Abstract
Kirigami, the Japanese art of paper cutting, has recently enabled the design of stretchable mechanical metamaterials that can be easily realized by embedding arrays of periodic cuts into an elastic sheet. Here, kirigami principles are exploited to design inflatables that can mimic target shapes upon pressurization. The system comprises a kirigami sheet embedded into an unstructured elastomeric membrane. First, it is shown that the inflated shape can be controlled by tuning the geometric parameters of the kirigami pattern. Then, by applying a simple optimization algorithm, the best parameters that enable the kirigami inflatables to transform into a family of target shapes at a given pressure are identified. Furthermore, thanks to the tessellated nature of the kirigami, it is shown that we can selectively manipulate the parameters of the single units to allow the reproduction of features at different scales and ultimately enable a more accurate mimicking of the target.
Collapse
Affiliation(s)
- Lishuai Jin
- Department of Mechanics, Tianjin University, Tianjin, 300350, China
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Antonio Elia Forte
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, 20133, Italy
| | - Bolei Deng
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | | | - Katia Bertoldi
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
- Kavli Institute, Harvard University, Cambridge, MA, 02138, USA
| |
Collapse
|
27
|
Sun S, Li Y, Chu L, Kuang X, Song J, Sun C. Full-length sequencing of ginkgo transcriptomes for an in-depth understanding of flavonoid and terpenoid trilactone biosynthesis. Gene 2020; 758:144961. [PMID: 32693148 DOI: 10.1016/j.gene.2020.144961] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Ginkgo biloba L. is regarded as the most ancient living tree, and its kernel has been used as a traditional Chinese medicine for more than 2,000 years. The leaf extracts of this tree have been among the bestselling herbal remedies in Western countries since the last century. To understand the biosynthesis of the pharmacologically active ingredients in G. biloba, flavonoids and terpenoid trilactones (TTLs), we sequenced the transcriptomes of G. biloba leaves, kernels and testae with Iso-Seq and RNA-Seq technologies and obtained 152,524 clean consensus reads. When these reads were used to improve the annotation of the G. biloba genome, 4,856 novel genes, 25,583 new isoforms of previously annotated genes and 4,363 lncRNAs were discovered. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that genes involved in growth, regulation and response to stress were more likely to be regulated by alternative splicing (AS) or alternative polyadenylation (APA), which represent the two most important posttranscriptional regulation mechanisms. It was found that some of the characterized genes involved in the biosynthesis of flavonoids and TTLs were also possibly regulated by AS and APA. Using phylogenetic and gene expression pattern analyses, some candidate genes for the biosynthesis of flavonoids and TTLs were screened. After qRT-PCR validation, the final candidate genes for flavonoid biosynthesis included three UDP-glycosyltransferases and one MYB transcription factor, while the candidate genes for TTL biosynthesis included two cytochrome P450 and one WRKY transcription factor. Our study suggested that Iso-Seq may play an important role in improving genome annotation, elucidating AS and APA mechanisms and discovering candidate genes involved in the biosynthesis of some secondary metabolites.
Collapse
Affiliation(s)
- Sijie Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Lihua Chu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xuejun Kuang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Chao Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China.
| |
Collapse
|
28
|
Majeed A, Singh A, Sharma RK, Jaitak V, Bhardwaj P. Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta. Mol Genet Genomics 2020; 295:1401-1414. [DOI: 10.1007/s00438-020-01709-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 07/03/2020] [Indexed: 12/12/2022]
|
29
|
Zhang Y, Rahmani RS, Yang X, Chen J, Shi T. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC Genomics 2020; 21:429. [PMID: 32586276 PMCID: PMC7315500 DOI: 10.1186/s12864-020-06853-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 01/29/2023] Open
Abstract
Background Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Results Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
Collapse
Affiliation(s)
- Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
30
|
Yang T, Li H, Tai Y, Dong C, Cheng X, Xia E, Chen Z, Li F, Wan X, Zhang Z. Transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root (Camellia sinensis L.). Sci Rep 2020; 10:6868. [PMID: 32321966 PMCID: PMC7176667 DOI: 10.1038/s41598-020-63835-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
Free amino acids, including theanine, glutamine and glutamate, contribute greatly to the pleasant taste and multiple health benefits of tea. Amino acids in tea plants are mainly synthesized in roots and transported to new shoots, which are significantly affected by nitrogen (N) level and forms. However, the regulatory amino acid metabolism genes have not been systemically identified in tea plants. Here, we investigated the dynamic changes of free amino acid contents in response to N deficiency and forms in tea plant roots, and systemically identified the genes associated amino acid contents in individual metabolism pathways. Our results showed that glutamate-derived amino acids are the most dynamic in response to various forms of N and N deficiency. We then performed transcriptomic analyses of roots treated with N deficiency and various forms of N, and differentially expressed amino acid metabolic genes in each pathway were identified. The analyses on expression patterns and transcriptional responses of metabolic genes to N treatments provided novel insights for the molecular basis of high accumulation of theanine in tea plant root. These analyses also identified potential regulatory genes in dynamic amino acid metabolism in tea plant root. Furthermore, our findings indicated that the dynamic expression levels of CsGDH, CsAlaDC, CsAspAT, CsSDH, CsPAL, CsSHMT were highly correlated with changes of amino acid contents in their corresponding pathways. Herein, this study provides comprehensive insights into transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root.
Collapse
Affiliation(s)
- Tianyuan Yang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Huiping Li
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yuling Tai
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chunxia Dong
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xunmin Cheng
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ziping Chen
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Fang Li
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei, China.
| |
Collapse
|
31
|
Zhong F, Huang L, Qi L, Ma Y, Yan Z. Full-length transcriptome analysis of Coptis deltoidea and identification of putative genes involved in benzylisoquinoline alkaloids biosynthesis based on combined sequencing platforms. PLANT MOLECULAR BIOLOGY 2020; 102:477-499. [PMID: 31902069 DOI: 10.1007/s11103-019-00959-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/30/2019] [Indexed: 05/20/2023]
Abstract
The study carry out comprehensive transcriptome analysis of C. deltoidea and exploration of BIAs biosynthesis and accumulation based on UHPLC-MS/MS and combined sequencing platforms. Coptis deltoidea is an important medicinal plant with a long history of medicinal use, which is rich in benzylisoquinoline alkaloids (BIAs). In this study, Ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) and combined sequencing platforms were performed for exploration of BIAs biosynthesis, accumulation and comprehensive transcriptome analysis of C. deltoidea. By metabolism profiling, the accumulation of ten BIAs was analyzed using UHPLC-MS/MS and different contents were observed in different organs. From transcriptome sequencing result, we applied single-molecule real-time (SMRT) sequencing to C. deltoidea and generated a total of 75,438 full-length transcripts. We proposed the candidate biosynthetic pathway of tyrosine, precursor of BIAs, and identified 64 full length-transcripts encoding enzymes putatively involved in BIAs biosynthesis. RNA-Seq data indicated that the majority of genes exhibited relatively high expression level in roots. Transport of BIAs was also important for their accumulation. Here, 9 ABC transporters and 2 MATE transporters highly homologous to known alkaloid transporters related with BIAs transport in roots and rhizomes were identified. These findings based on the combined sequencing platforms provide valuable genetic information for C. deltoidea and the results of transcriptome combined with metabolome analysis can help us better understand BIAs biosynthesis and transport in this medicinal plant. The information will be critical for further characterization of C. deltoidea transcriptome and molecular-assisted breeding for this medicinal plant with scarce resources.
Collapse
Affiliation(s)
- Furong Zhong
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ling Huang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Luming Qi
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yuntong Ma
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Zhuyun Yan
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| |
Collapse
|
32
|
Tan C, Liu H, Ren J, Ye X, Feng H, Liu Z. Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC PLANT BIOLOGY 2019; 19:517. [PMID: 31771515 PMCID: PMC6880451 DOI: 10.1186/s12870-019-2133-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/12/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Anther development has been extensively studied at the transcriptional level, but a systematic analysis of full-length transcripts on a genome-wide scale has not yet been published. Here, the Pacific Biosciences (PacBio) Sequel platform and next-generation sequencing (NGS) technology were combined to generate full-length sequences and completed structures of transcripts in anthers of Chinese cabbage. RESULTS Using single-molecule real-time sequencing (SMRT), a total of 1,098,119 circular consensus sequences (CCSs) were generated with a mean length of 2664 bp. More than 75% of the CCSs were considered full-length non-chimeric (FLNC) reads. After error correction, 725,731 high-quality FLNC reads were estimated to carry 51,501 isoforms from 19,503 loci, consisting of 38,992 novel isoforms from known genes and 3691 novel isoforms from novel genes. Of the novel isoforms, we identified 407 long non-coding RNAs (lncRNAs) and 37,549 open reading frames (ORFs). Furthermore, a total of 453,270 alternative splicing (AS) events were identified and the majority of AS models in anther were determined to be approximate exon skipping (XSKIP) events. Of the key genes regulated during anther development, AS events were mainly identified in the genes SERK1, CALS5, NEF1, and CESA1/3. Additionally, we identified 104 fusion transcripts and 5806 genes that had alternative polyadenylation (APA). CONCLUSIONS Our work demonstrated the transcriptome diversity and complexity of anther development in Chinese cabbage. The findings provide a basis for further genome annotation and transcriptome research in Chinese cabbage.
Collapse
Affiliation(s)
- Chong Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China
| | - Hongxin Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China
| | - Jie Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China
| | - Xueling Ye
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China
| | - Zhiyong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, People's Republic of China.
| |
Collapse
|
33
|
Lin L, Cai W, Du Z, Zhang W, Xu Q, Sun W, Chen M. Establishing a System for Functional Characterization of Full-Length cDNAs of Camellia sinensis. Int J Mol Sci 2019; 20:ijms20235929. [PMID: 31775391 PMCID: PMC6929147 DOI: 10.3390/ijms20235929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis) is enriched with bioactive secondary metabolites, and is one of the most popular nonalcoholic beverages globally. Two tea reference genomes have been reported; however, the functional analysis of tea genes has lagged, mainly due to tea’s recalcitrance to genetic transformation and the absence of alternative high throughput heterologous expression systems. A full-length cDNA collection with a streamlined cloning system is needed in this economically important woody crop species. RNAs were isolated from nine different vegetative tea tissues, pooled, then used to construct a normalized full-length cDNA library. The titer of unamplified and amplified cDNA library was 6.89 × 106 and 1.8 × 1010 cfu/mL, respectively; the library recombinant rate was 87.2%. Preliminary characterization demonstrated that this collection can complement existing tea reference genomes and facilitate rare gene discovery. In addition, to streamline tea cDNA cloning and functional analysis, a binary vector (pBIG2113SF) was reengineered, seven tea cDNAs isolated from this library were successfully cloned into this vector, then transformed into Arabidopsis. One FL-cDNA, which encodes a putative P1B-type ATPase 5 (CsHMA5), was characterized further as a proof of concept. We demonstrated that overexpression of CsHMA5 in Arabidopsis resulted in copper hyposensitivity. Thus, our data demonstrated that this represents an efficient system for rare gene discovery and functional characterization of tea genes. The integration of a tea FL-cDNA collection with efficient cloning and a heterologous expression system would facilitate functional annotation and characterization of tea genes.
Collapse
Affiliation(s)
- Lin Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weiwei Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Zhenghua Du
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Wenjing Zhang
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weijiang Sun
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| | - Mingjie Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| |
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
Hoang NV, Furtado A, Perlo V, Botha FC, Henry RJ. The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome. Front Genet 2019; 10:654. [PMID: 31396260 PMCID: PMC6664245 DOI: 10.3389/fgene.2019.00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.
Collapse
Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| |
Collapse
|
36
|
Clark S, Yu F, Gu L, Min XJ. Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato. FRONTIERS IN PLANT SCIENCE 2019; 10:689. [PMID: 31191588 PMCID: PMC6546887 DOI: 10.3389/fpls.2019.00689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/08/2019] [Indexed: 05/17/2023]
Abstract
Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).
Collapse
Affiliation(s)
- Sarah Clark
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
| | - Feng Yu
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Jia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
- *Correspondence: Xiang Jia Min,
| |
Collapse
|