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Dai H, Xie W, Xia E. SK-Unet++: An improved Unet++ network with adaptive receptive fields for automatic segmentation of ultrasound thyroid nodule images. Med Phys 2024; 51:1798-1811. [PMID: 37606374 DOI: 10.1002/mp.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND The quality of segmentation of thyroid nodules in ultrasound images is a crucial factor in preventing the cancerization of thyroid nodules. However, the existing standards for the ultrasound imaging of cancerous nodules have limitations, and changes of the echo pattern of thyroid nodules pose challenges in accurately segmenting nodules, which can affect the diagnostic results of medical professionals. PURPOSE The aim of this study is to address the challenges related to segmentation accuracy due to noise, low contrast, morphological scale variations, and blurred edges of thyroid nodules in ultrasound images and improve the accuracy of ultrasound-based thyroid nodule segmentation, thereby aiding the clinical diagnosis of thyroid nodules. METHOD In this study, the dataset of thyroid ultrasound images was obtained from Hunan Provincial People's Hospital, consisting of a total of 3572 samples used for the training, validation, and testing of this model at a ratio of 8:1:1. A novel SK-Unet++ network was used to enhance the segmentation accuracy of thyroid nodules. SK-Unet++ is a novel deep learning architecture that adds the adaptive receptive fields based on the selective kernel (SK) attention mechanisms into the Unet++ network. The convolution blocks of the original UNet++ encoder part were replaced with finer SK convolution blocks in SK-Unet++. First, multiple skip connections were incorporated so that SK-Unet++ can make information from previous layers of the neural network to bypass certain layers and directly propagate to subsequent layers. The feature maps of the corresponding locations were fused on the channel, resulting in enhanced segmentation accuracy. Second, we added the adaptive receptive fields. The adaptive receptive fields were used to capture multiscale spatial features better by dynamically adjusting its receptive field. The assessment metrics contained dice similarity coefficient (Dsc), accuracy (Acc), precision (Pre), recall (Re), and Hausdorff distance, and all comparison experiments used the paired t-tests to assess whether statistically significant performance differences existed (p < 0.05). And to address the multi-comparison problem, we performed the false discovery rate (FDR) correction after the test. RESULTS The segmentation model had an Acc of 80.6%, Dsc of 84.7%, Pre of 77.5%, Re of 71.7%, and an average Hausdorff distance of 15.80 mm. Ablation experimental results demonstrated that each module in the network could contribute to the improved performance (p < 0.05) and determined the best combination of parameters. A comparison with other state-of-the-art methods showed that SK-Unet++ significantly outperformed them in terms of segmentation performance (p < 0.05), with a more accurate segmentation contour. Additionally, the adaptive weight changes of the SK module were monitored during the training process, and the resulting change curves demonstrated their convergence. CONCLUSION Our proposed method demonstrates favorable performance in the segmentation of ultrasound images of thyroid nodules. Results confirmed that SK-Unet++ is a feasible and effective method for the automatic segmentation of thyroid nodules in ultrasound images. The high accuracy achieved by our method can facilitate efficient screening of patients with thyroid nodules, ultimately reducing the workload of clinicians and radiologists.
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Affiliation(s)
- Hong Dai
- Department of Ultrasound Medicine, Hunan Provincial Peoples Hospital, Changsha, China
| | - Wufei Xie
- School of Automation, Central South University, Changsha, China
| | - E Xia
- School of Automation, Central South University, Changsha, China
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Han M, Lin S, Zhu B, Tong W, Xia E, Wang Y, Yang T, Zhang S, Wan X, Liu J, Niu Q, Zhu J, Bao S, Zhang Z. Dynamic DNA Methylation Regulates Season-Dependent Secondary Metabolism in the New Shoots of Tea Plants. J Agric Food Chem 2024; 72:3984-3997. [PMID: 38357888 DOI: 10.1021/acs.jafc.3c08568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Plant secondary metabolites are critical quality-conferring compositions of plant-derived beverages, medicines, and industrial materials. The accumulations of secondary metabolites are highly variable among seasons; however, the underlying regulatory mechanism remains unclear, especially in epigenetic regulation. Here, we used tea plants to explore an important epigenetic mark DNA methylation (5mC)-mediated regulation of plant secondary metabolism in different seasons. Multiple omics analyses were performed on spring and summer new shoots. The results showed that flavonoids and theanine metabolism dominated in the metabolic response to seasons in the new shoots. In summer new shoots, the genes encoding DNA methyltransferases and demethylases were up-regulated, and the global CG and CHG methylation reduced and CHH methylation increased. 5mC methylation in promoter and gene body regions influenced the seasonal response of gene expression; the amplitude of 5mC methylation was highly correlated with that of gene transcriptions. These differentially methylated genes included those encoding enzymes and transcription factors which play important roles in flavonoid and theanine metabolic pathways. The regulatory role of 5mC methylation was further verified by applying a DNA methylation inhibitor. These findings highlight that dynamic DNA methylation plays an important role in seasonal-dependent secondary metabolism and provide new insights for improving tea quality.
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Affiliation(s)
- Mengxue Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shijia Lin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Biying Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Yuanrong Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Tianyuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Shupei Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Jianjun Liu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
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Liu YL, Gao SY, Jin G, Zhou MY, Gao Q, Guo C, Yang YZ, Niu LZ, Xia E, Guo ZH, Ma PF, Li DZ. BambooBase: A comprehensive database of bamboo omics and systematics. Mol Plant 2024:S1674-2052(24)00073-X. [PMID: 38419327 DOI: 10.1016/j.molp.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Shu-Yang Gao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guihua Jin
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Qijuan Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China; School of Computer and Artificial Intelligence, Hefei Normal University, Hefei, Anhui 230061, China
| | - Cen Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yi-Zhou Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Liang-Zhong Niu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Gao Q, Tong W, Li F, Wang Y, Wu Q, Wan X, Xia E. TPIA2: an updated tea plant information archive for Camellia genomics. Nucleic Acids Res 2024; 52:D1661-D1667. [PMID: 37650644 PMCID: PMC10767884 DOI: 10.1093/nar/gkad701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
The genus Camellia consists of about 200 species, which include many economically important species widely used for making tea, ornamental flowers and edible oil. Here, we present an updated tea plant information archive for Camellia genomics (TPIA2; http://tpia.teaplants.cn) by integrating more novel large-scale genomic, transcriptomic, metabolic and genetic variation datasets as well as a variety of useful tools. Specifically, TPIA2 hosts all currently available and well assembled 10 Camellia genomes and their comprehensive annotations from three major sections of Camellia. A collection of 15 million SNPs and 950 950 small indels from large-scale genome resequencing of 350 diverse tea accessions were newly incorporated, followed by the implementation of a novel 'Variation' module to facilitate data retrieval and analysis of the functionally annotated variome. Moreover, 116 Camellia transcriptomes were newly assembled and added, leading to a significant extension of expression profiles of Camellia genes to 13 developmental stages and eight abiotic/biotic treatments. An updated 'Expression' function has also been implemented to provide a comprehensive gene expression atlas for Camellia. Two novel analytic tools (e.g. Gene ID Convert and Population Genetic Analysis) were specifically designed to facilitate the data exchange and population genomics in Camellia. Collectively, TPIA2 provides diverse updated valuable genomic resources and powerful functions, and will continue to be an important gateway for functional genomics and population genetic studies in Camellia.
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Affiliation(s)
- Qijuan Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- School of Computer and Artificial Intelligence, Hefei Normal University, Hefei 230061, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- School of Science, Anhui Agricultural University, Hefei 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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Samarina L, Fedorina J, Kuzmina D, Malyukova L, Manakhova K, Kovalenko T, Matskiv A, Xia E, Tong W, Zhang Z, Ryndin A, Orlov YL, Khlestkina EK. Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions. Int J Mol Sci 2023; 24:14538. [PMID: 37833988 PMCID: PMC10572165 DOI: 10.3390/ijms241914538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon-sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g-1, and the L-theanine content varied from 0.2 to 5.8 mg g-1 dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3'-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3'5'Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3'5'Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops.
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Affiliation(s)
- Lidiia Samarina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Jaroslava Fedorina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Daria Kuzmina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Karina Manakhova
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Tatyana Kovalenko
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Yuriy L. Orlov
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Elena K. Khlestkina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 196632 Saint Petersburg, Russia
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Fu Y, Yang S, Liu B, Xia E, Huang D. Multi-UAV Cooperative Trajectory Planning Based on the Modified Cheetah Optimization Algorithm. Entropy (Basel) 2023; 25:1277. [PMID: 37761576 PMCID: PMC10529251 DOI: 10.3390/e25091277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023]
Abstract
The capacity for autonomous functionality serves as the fundamental ability and driving force for the cross-generational upgrading of unmanned aerial vehicles (UAVs). With the disruptive transformation of artificial intelligence technology, autonomous trajectory planning based on intelligent algorithms has emerged as a key technique for enhancing UAVs' capacity for autonomous behavior, thus holding significant research value. To address the challenges of UAV trajectory planning in complex 3D environments, this paper proposes a multi-UAV cooperative trajectory-planning method based on a Modified Cheetah Optimization (MCO) algorithm. Firstly, a spatiotemporal cooperative trajectory planning model is established, incorporating UAV-cooperative constraints and performance constraints. Evaluation criteria, including fuel consumption, altitude, and threat distribution field cost functions, are introduced. Then, based on its parent Cheetah Optimization (CO) algorithm, the MCO algorithm incorporates a logistic chaotic mapping strategy and an adaptive search agent strategy, thereby improving the home-returning mechanism. Finally, extensive simulation experiments are conducted using a considerably large test dataset containing functions with the following four characteristics: unimodal, multimodal, separable, and inseparable. Meanwhile, a strategy for dimensionality reduction searching is employed to solve the problem of autonomous trajectory planning in real-world scenarios. The results of a conducted simulation demonstrate that the MCO algorithm outperforms several other related algorithms, showcasing smaller trajectory costs, a faster convergence speed, and stabler performance. The proposed algorithm exhibits a certain degree of correctness, effectiveness, and advancement in solving the problem of multi-UAV cooperative trajectory planning.
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Affiliation(s)
- Yuwen Fu
- School of Automation, Central South University, Changsha 410017, China; (Y.F.); (E.X.)
| | - Shuai Yang
- School of Software Engineering, South China University of Technology, Guangzhou 510641, China;
| | - Bo Liu
- College of Advanced Interdisciplinary Studies, National University of Defense Technology, Changsha 410073, China;
| | - E Xia
- School of Automation, Central South University, Changsha 410017, China; (Y.F.); (E.X.)
| | - Duan Huang
- School of Computer Science and Technology, Central South University, Changsha 410017, China
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Wang Y, Samarina L, Mallano AI, Tong W, Xia E. Recent progress and perspectives on physiological and molecular mechanisms underlying cold tolerance of tea plants. Front Plant Sci 2023; 14:1145609. [PMID: 36866358 PMCID: PMC9971632 DOI: 10.3389/fpls.2023.1145609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Tea is one of the most consumed and widely planted beverage plant worldwide, which contains many important economic, healthy, and cultural values. Low temperature inflicts serious damage to tea yields and quality. To cope with cold stress, tea plants have evolved a cascade of physiological and molecular mechanisms to rescue the metabolic disorders in plant cells caused by the cold stress; this includes physiological, biochemical changes and molecular regulation of genes and associated pathways. Understanding the physiological and molecular mechanisms underlying how tea plants perceive and respond to cold stress is of great significance to breed new varieties with improved quality and stress resistance. In this review, we summarized the putative cold signal sensors and molecular regulation of the CBF cascade pathway in cold acclimation. We also broadly reviewed the functions and potential regulation networks of 128 cold-responsive gene families of tea plants reported in the literature, including those particularly regulated by light, phytohormone, and glycometabolism. We discussed exogenous treatments, including ABA, MeJA, melatonin, GABA, spermidine and airborne nerolidol that have been reported as effective ways to improve cold resistance in tea plants. We also present perspectives and possible challenges for functional genomic studies on cold tolerance of tea plants in the future.
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Affiliation(s)
- Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Lidia Samarina
- Federal Research Centre the Subtropical Scientific Centre, The Russian Academy of Sciences, Sochi, Russia
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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Zhang Z, Song C, Zhao J, Xia E, Wen W, Zeng L, Benedito VA. Editorial: Secondary metabolites and metabolism in tea plants. Front Plant Sci 2023; 14:1143022. [PMID: 36866382 PMCID: PMC9972074 DOI: 10.3389/fpls.2023.1143022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 01/04/2024]
Affiliation(s)
- Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Jian Zhao
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lanting Zeng
- South China Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Vagner A. Benedito
- School of Agriculture and Food, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV, United States
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Wang Y, Huang J, Xie N, Zhang D, Tong W, Xia E. The complete chloroplast genome sequence of Camellia atrothea (Ericales: Theaceae). Mitochondrial DNA B Resour 2023; 8:536-540. [PMID: 37124997 PMCID: PMC10142311 DOI: 10.1080/23802359.2023.2204972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Camellia atrothea H.T. Chang, H.S. Wang & B.H. Chen 1983 is a native Camellia species in China, which has significant economic and breeding values. Here, we assembled and analyzed the complete chloroplast genome sequence of C. atrothea based on the whole genome sequencing data from Illumina NovaSeq6000 platform. Results show that the complete chloroplast genome of C. atrothea is 157,099 bp in length, and comprises a large single-copy (LSC, 86,643 bp) region, a small single-copy (SSC, 18,276 bp) region, and a pair of inverted repeats (IRs, 26,090 bp) region. Annotation of the C. atrothea chloroplast genome predicts a total of 133 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content accounts for 37.30% of the genome, which is clearly consistent with that of other previously published Camellia species from section Thea. Phylogenetic analyses of the whole chloroplast genome sequences of 14 Camellia species using Actinidia chinensis as outgroup reveals that C. atrothea has a close relationship with C. leptophylla.
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Affiliation(s)
- Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Na Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Dandan Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- CONTACT Enhua Xia State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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10
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Ma Z, Hu Y, Li X, Liu R, Xia E, Xu P, Yang Y. Stereoselective synthesis of α-glucosides with glucosyl (Z)-Ynenoates as donors. Carbohydr Res 2023; 523:108710. [PMID: 36370627 DOI: 10.1016/j.carres.2022.108710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
A SPhosAuNTf2-promoted DMF-modulated glycosylation approach with glycosyl (Z)-ynenoates as donors was developed for highly α-selective synthesis of various linkage types of α-glucans. The substituent groups were also found to play a significant role in the α-selective glucosylation reactions. The glycosylation approach was effectively applied to the stereospecific synthesis of the α-1,6-linked triglucoside.
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Affiliation(s)
- Zhi Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yi Hu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiaona Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Rongkun Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - E Xia
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - You Yang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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11
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Liu L, Roessler K, Bilke S, Ding Y, Erlandson D, Fu Y, Hariharan B, Katz S, Lee J, Schulman C, Song F, Vijayaraghavan R, Wenz P, Xia E, Yan H, Zhu Y, Zhao C, Dockter J, Pawlowski T, Day J. 925P Analytical performance of a next-generation sequencing (NGS) assay kit for assessing homologous recombination deficiency (HRD) from solid tumor samples. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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12
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. Plant J 2022; 111:406-421. [PMID: 35510493 DOI: 10.1011/tpj.15799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 05/27/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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13
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. Plant J 2022; 111:406-421. [PMID: 35510493 DOI: 10.1111/tpj.15799] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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14
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Li P, Fu J, Xu Y, Shen Y, Zhang Y, Ye Z, Tong W, Zeng X, Yang J, Tang D, Li P, Zuo H, Wu Q, Xia E, Wang S, Zhao J. CsMYB1 integrates the regulation of trichome development and catechins biosynthesis in tea plant domestication. New Phytol 2022; 234:902-917. [PMID: 35167117 PMCID: PMC9311817 DOI: 10.1111/nph.18026] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/02/2022] [Indexed: 05/09/2023]
Abstract
Tea trichomes synthesize numerous specialized metabolites to protect plants from environmental stresses and contribute to tea flavours, but little is known about the regulation of trichome development. Here, we showed that CsMYB1 is involved in the regulation of trichome formation and galloylated cis-catechins biosynthesis in tea plants. The variations in CsMYB1 expression levels are closely correlated with trichome indexes and galloylated cis-catechins contents in tea plant populations. Genome resequencing showed that CsMYB1 may be selected in modern tea cultivars, since a 192-bp insertion in CsMYB1 promoter was found exclusively in modern tea cultivars but not in the glabrous wild tea Camellia taliensis. Several enhancers in the 192-bp insertion increased CsMYB1 transcription in modern tea cultivars that coincided with their higher galloylated cis-catechins contents and trichome indexes. Biochemical analyses and transgenic data showed that CsMYB1 interacted with CsGL3 and CsWD40 and formed a MYB-bHLH-WD40 (MBW) transcriptional complex to activate the trichome regulator genes CsGL2 and CsCPC, and the galloylated cis-catechins biosynthesis genes anthocyanidin reductase and serine carboxypeptidase-like 1A. CsMYB1 integratively regulated trichome formation and galloylated cis-catechins biosynthesis. Results suggest that CsMYB1, trichome and galloylated cis-catechins are coincidently selected during tea domestication by harsh environments for improved adaption and by breeders for better tea flavours.
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Affiliation(s)
- Penghui Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Jiamin Fu
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Yihua Shen
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Zhili Ye
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Xiangsheng Zeng
- College of AgronomyAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Jihong Yang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Dingkun Tang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Ping Li
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Hao Zuo
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics and Crop Gene EditingSchool of Life SciencesLinyi UniversityShuangling RoadLinyi276000China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural University130 West Changjiang RoadHefei230036China
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15
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Li P, Xia E, Fu J, Xu Y, Zhao X, Tong W, Tang Q, Tadege M, Fernie AR, Zhao J. Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis). Plant J 2022; 110:1144-1165. [PMID: 35277905 DOI: 10.1111/tpj.15729] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 05/20/2023]
Abstract
Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.
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Affiliation(s)
- Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jiamin Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yujie Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xuecheng Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, Oklahoma, 73401, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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16
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Tang W, Dai R, Yan W, Zhang W, Bin Y, Xia E, Xia J. Identifying multi-functional bioactive peptide functions using multi-label deep learning. Brief Bioinform 2021; 23:6396787. [PMID: 34651655 DOI: 10.1093/bib/bbab414] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/05/2021] [Accepted: 09/12/2021] [Indexed: 12/27/2022] Open
Abstract
The bioactive peptide has wide functions, such as lowering blood glucose levels and reducing inflammation. Meanwhile, computational methods such as machine learning are becoming more and more important for peptide functions prediction. Most of the previous studies concentrate on the single-functional bioactive peptides prediction. However, the number of multi-functional peptides is on the increase; therefore, novel computational methods are needed. In this study, we develop a method MLBP (Multi-Label deep learning approach for determining the multi-functionalities of Bioactive Peptides), which can predict multiple functions including anti-cancer, anti-diabetic, anti-hypertensive, anti-inflammatory and anti-microbial simultaneously. MLBP model takes the peptide sequence vector as input to replace the biological and physiochemical features used in other peptides predictors. Using the embedding layer, the dense continuous feature vector is learnt from the sequence vector. Then, we extract convolution features from the feature vector through the convolutional neural network layer and combine with the bidirectional gated recurrent unit layer to improve the prediction performance. The 5-fold cross-validation experiments are conducted on the training dataset, and the results show that Accuracy and Absolute true are 0.695 and 0.685, respectively. On the test dataset, Accuracy and Absolute true of MLBP are 0.709 and 0.697, with 5.0 and 4.7% higher than those of the suboptimum method, respectively. The results indicate MLBP has superior prediction performance on the multi-functional peptides identification. MLBP is available at https://github.com/xialab-ahu/MLBP and http://bioinfo.ahu.edu.cn/MLBP/.
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Affiliation(s)
- Wending Tang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China
| | - Ruyu Dai
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China
| | - Wenhui Yan
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Wei Zhang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China
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17
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Zhang W, Xia E, Dai R, Tang W, Bin Y, Xia J. PredAPP: Predicting Anti-Parasitic Peptides with Undersampling and Ensemble Approaches. Interdiscip Sci 2021; 14:258-268. [PMID: 34608613 DOI: 10.1007/s12539-021-00484-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022]
Abstract
Anti-parasitic peptides (APPs) have been regarded as promising therapeutic candidate drugs against parasitic diseases. Due to the fact that the experimental techniques for identifying APPs are expensive and time-consuming, there is an urgent need to develop a computational approach to predict APPs on a large scale. In this study, we provided a computational method, termed PredAPP (Prediction of Anti-Parasitic Peptides) that could effectively identify APPs using an ensemble of well-performed machine learning (ML) classifiers. Firstly, to solve the class imbalance problem, a balanced training dataset was generated by the undersampling method. We found that the balanced dataset based on cluster centroid achieved the best performance. Then, nine groups of features and six ML algorithms were combined to generate 54 classifiers and the output of these classifiers formed 54 feature representations, and in each feature group, we selected the feature representation with best performance for classification. Finally, the selected feature representations were integrated using logistic regression algorithm to construct the prediction model PredAPP. On the independent dataset, PredAPP achieved accuracy and AUC of 0.880 and 0.922, respectively, compared to 0.739 and 0.873 of AMPfun, a state-of-the-art method to predict APPs. The web server of PredAPP is freely accessible at http://predapp.xialab.info and https://github.com/xialab-ahu/PredAPP .
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Ruyu Dai
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Wending Tang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, 230601, Anhui, China.
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China. .,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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18
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Tong W, Li R, Huang J, Zhao H, Ge R, Wu Q, Mallano AI, Wang Y, Li F, Deng W, Li Y, Xia E. Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants. Plant J 2021; 106:1312-1327. [PMID: 33730390 DOI: 10.1111/tpj.15237] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The tea plant (Camellia sinensis) is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base-resolution DNA methylation map of tea plants under chilling stress. We found that, compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG and CHH (where H = A, T, or C), which is further proven to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, whereas non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. The DNA methylation and expression divergence of duplicated genes in the tea plant increases with evolutionary age and selective pressure. Moreover, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly downregulated, whereas demethylase genes are upregulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into duplicated gene evolution and chilling tolerance in tea plants.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali I Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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19
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Samarina LS, Bobrovskikh AV, Doroshkov AV, Malyukova LS, Matskiv AO, Rakhmangulov RS, Koninskaya NG, Malyarovskaya VI, Tong W, Xia E, Manakhova KA, Ryndin AV, Orlov YL. Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [ Camellia sinensis (L.) Kuntze]. Front Genet 2020; 11:611283. [PMID: 33424935 PMCID: PMC7786056 DOI: 10.3389/fgene.2020.611283] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Cold and drought are two of the most severe threats affecting the growth and productivity of the tea plant, limiting its global spread. Both stresses cause osmotic changes in the cells of the tea plant by decreasing their water potential. To develop cultivars that are tolerant to both stresses, it is essential to understand the genetic responses of tea plant to these two stresses, particularly in terms of the genes involved. In this study, we combined literature data with interspecific transcriptomic analyses (using Arabidopsis thaliana and Solanum lycopersicum) to choose genes related to cold tolerance. We identified 45 stress-inducible candidate genes associated with cold and drought responses in tea plants based on a comprehensive homologous detection method. Of these, nine were newly characterized by us, and 36 had previously been reported. The gene network analysis revealed upregulated expression in ICE1-related cluster of bHLH factors, HSP70/BAM5 connected genes (hexokinases, galactinol synthases, SnRK complex, etc.) indicating their possible co-expression. Using qRT-PCR we revealed that 10 genes were significantly upregulated in response to both cold and drought in tea plant: HSP70, GST, SUS1, DHN1, BMY5, bHLH102, GR-RBP3, ICE1, GOLS1, and GOLS3. SnRK1.2, HXK1/2, bHLH7/43/79/93 were specifically upregulated in cold, while RHL41, CAU1, Hydrolase22 were specifically upregulated in drought. Interestingly, the expression of CIP was higher in the recovery stage of both stresses, indicating its potentially important role in plant recovery after stress. In addition, some genes, such as DHN3, bHLH79, PEI54, SnRK1.2, SnRK1.3, and Hydrolase22, were significantly positively correlated between the cold and drought responses. CBF1, GOLS1, HXK2, and HXK3, by contrast, showed significantly negative correlations between the cold and drought responses. Our results provide valuable information and robust candidate genes for future functional analyses intended to improve the stress tolerance of the tea plant and other species.
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Affiliation(s)
- Lidiia S Samarina
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Alexandr V Bobrovskikh
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia.,Institute Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V Doroshkov
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia.,Institute Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lyudmila S Malyukova
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Alexandra O Matskiv
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Ruslan S Rakhmangulov
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Natalia G Koninskaya
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Valentina I Malyarovskaya
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Karina A Manakhova
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Alexey V Ryndin
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Yuriy L Orlov
- Biotechnology Department, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia.,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
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20
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Gao Q, Jin X, Xia E, Wu X, Gu L, Yan H, Xia Y, Li S. Identification of Orphan Genes in Unbalanced Datasets Based on Ensemble Learning. Front Genet 2020; 11:820. [PMID: 33133122 PMCID: PMC7567012 DOI: 10.3389/fgene.2020.00820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/08/2020] [Indexed: 11/13/2022] Open
Abstract
Orphan genes are associated with regulatory patterns, but experimental methods for identifying orphan genes are both time-consuming and expensive. Designing an accurate and robust classification model to detect orphan and non-orphan genes in unbalanced distribution datasets poses a particularly huge challenge. Synthetic minority over-sampling algorithms (SMOTE) are selected in a preliminary step to deal with unbalanced gene datasets. To identify orphan genes in balanced and unbalanced Arabidopsis thaliana gene datasets, SMOTE algorithms were then combined with traditional and advanced ensemble classified algorithms respectively, using Support Vector Machine, Random Forest (RF), AdaBoost (adaptive boosting), GBDT (gradient boosting decision tree), and XGBoost (extreme gradient boosting). After comparing the performance of these ensemble models, SMOTE algorithms with XGBoost achieved an F1 score of 0.94 with the balanced A. thaliana gene datasets, but a lower score with the unbalanced datasets. The proposed ensemble method combines different balanced data algorithms including Borderline SMOTE (BSMOTE), Adaptive Synthetic Sampling (ADSYN), SMOTE-Tomek, and SMOTE-ENN with the XGBoost model separately. The performances of the SMOTE-ENN-XGBoost model, which combined over-sampling and under-sampling algorithms with XGBoost, achieved higher predictive accuracy than the other balanced algorithms with XGBoost models. Thus, SMOTE-ENN-XGBoost provides a theoretical basis for developing evaluation criteria for identifying orphan genes in unbalanced and biological datasets.
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Affiliation(s)
- Qijuan Gao
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
| | - Xiu Jin
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiangwei Wu
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Lichuan Gu
- School of Information and Computer Science, Anhui Agricultural University, Hefei, China
| | - Hanwei Yan
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yingchun Xia
- School of Information and Computer Science, Anhui Agricultural University, Hefei, China
| | - Shaowen Li
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
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21
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Yang T, Lu X, Wang Y, Xie Y, Ma J, Cheng X, Xia E, Wan X, Zhang Z. HAK/KUP/KT family potassium transporter genes are involved in potassium deficiency and stress responses in tea plants (Camellia sinensis L.): expression and functional analysis. BMC Genomics 2020; 21:556. [PMID: 32791963 PMCID: PMC7430841 DOI: 10.1186/s12864-020-06948-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/24/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Tea plant is one of the most important non-alcoholic beverage crops worldwide. While potassium (K+) is an essential macronutrient and greatly affects the growth and development of plants, the molecular mechanism underlying K+ uptake and transport in tea plant root, especially under limited-K+ conditions, is still poorly understood. In plants, HAK/KUP/KT family members play a crucial role in K+ acquisition and translocation, growth and development, and response to stresses. Nevertheless, the biological functions of these genes in tea plant are still in mystery, especially their roles in K+ uptake and stress responses. RESULTS In this study, a total of 21 non-redundant HAK/KUP/KT genes (designated as CsHAKs) were identified in tea plant. Phylogenetic and structural analysis classified the CsHAKs into four clusters (I, II, III, IV), containing 4, 8, 4 and 5 genes, respectively. Three major categories of cis-acting elements were found in the promoter regions of CsHAKs. Tissue-specific expression analysis indicated extremely low expression levels in various tissues of cluster I CsHAKs with the exception of a high root expression of CsHAK4 and CsHAK5, a constitutive expression of clusters II and III CsHAKs, and a moderate cluster IV CsHAKs expression. Remarkably, the transcript levels of CsHAKs in roots were significantly induced or suppressed after exposure to K+ deficiency, salt and drought stresses, and phytohormones treatments. Also notably, CsHAK7 was highly expressed in all tissues and was further induced under various stress conditions. Therefore, functional characterization of CsHAK7 was performed, and the results demostrated that CsHAK7 locates on plasma membrane and plays a key role in K+ transport in yeast. Taken together, the results provide promising candidate CsHAKs for further functional studies and contribute to the molecular breeding for new tea plants varieties with highly efficient utilization of K+. CONCLUSION This study demonstrated the first genome-wide analysis of CsHAK family genes of tea plant and provides a foundation for understanding the classification and functions of the CsHAKs in tea plants.
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Affiliation(s)
- Tianyuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xin Lu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yan Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yunxia Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jingzhen Ma
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xunmin Cheng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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22
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Xia E, Tong W, Hou Y, An Y, Chen L, Wu Q, Liu Y, Yu J, Li F, Li R, Li P, Zhao H, Ge R, Huang J, Mallano AI, Zhang Y, Liu S, Deng W, Song C, Zhang Z, Zhao J, Wei S, Zhang Z, Xia T, Wei C, Wan X. The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation. Mol Plant 2020; 13:1013-1026. [PMID: 32353625 DOI: 10.1016/j.molp.2020.04.010] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/29/2020] [Accepted: 04/24/2020] [Indexed: 05/19/2023]
Abstract
Tea plant is an important economic crop, which is used to produce the world's oldest and most widely consumed tea beverages. Here, we present a high-quality reference genome assembly of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes. LTR retrotransposons (LTR-RTs) account for 70.38% of the genome, and we present evidence that LTR-RTs play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and introns. Genes, particularly those coding for terpene biosynthesis proteins, associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant genome. Phylogenetic analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations, supporting the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through introduction. Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome, particularly those associated with tea quality and stress resistance. The genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cultivars of tea plants.
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Affiliation(s)
- Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Linbo Chen
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yunlong Liu
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Jie Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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24
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Yue J, Wang R, Ma X, Liu J, Lu X, Balaso Thakar S, An N, Liu J, Xia E, Liu Y. Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. Comput Struct Biotechnol J 2020; 18:774-783. [PMID: 32280432 PMCID: PMC7132054 DOI: 10.1016/j.csbj.2020.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 12/31/2022] Open
Abstract
Crocus sativus, containing remarkably amounts of crocin, picrocrocin and safranal, is the source of saffron with tremendous medicinal, economic and cultural importance. Here, we present a high-quality full-length transcriptome of the sterile triploid C. sativus, using the PacBio SMRT sequencing technology. This yields 31,755 high-confidence predictions of protein-coding genes, with 50.1% forming paralogous gene pairs. Analysis on distribution of Ks values suggests that the current genome of C. sativus is probably a product resulting from at least two rounds of whole-genome duplication (WGD) events occurred at ~28 and ~114 million years ago (Mya), respectively. We provide evidence demonstrating that the recent β WGD event confers a major impact on family expansion of secondary metabolite genes, possibly leading to an enhanced accumulation of three distinct compounds: crocin, picrocrocin and safranal. Phylogenetic analysis unravels that the founding member (CCD2) of CCD enzymes necessary for the biosynthesis of apocarotenoids in C. sativus might be evolved from the CCD1 family via the β WGD event. Based on the gene expression profiling, CCD2 is found to be expressed at an extremely high level in the stigma. These findings may shed lights on further genomic refinement of the characteristic biosynthesis pathways and promote germplasm utilization for the improvement of saffron quality.
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Affiliation(s)
- Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,School of Computer and Information, Hefei University of Technology, Hefei 230009, China.,State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Ran Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaojing Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jiayi Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaohui Lu
- College of Information Technology, Jiaxing Vocational Technical College, Jiaxing 314000, China
| | - Sambhaji Balaso Thakar
- State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China.,Department of Biotechnology, Shivaji University, Kolhapur 416003, India
| | - Ning An
- School of Computer and Information, Hefei University of Technology, Hefei 230009, China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yongsheng Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,State Key Laboratory of Tea Plant Biology and School of Horticulture, Anhui Agricultural University, Hefei 230036, China.,Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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25
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Hu Z, Ban Q, Hao J, Zhu X, Cheng Y, Mao J, Lin M, Xia E, Li Y. Genome-Wide Characterization of the C-repeat Binding Factor (CBF) Gene Family Involved in the Response to Abiotic Stresses in Tea Plant ( Camellia sinensis). Front Plant Sci 2020; 11:921. [PMID: 32849669 PMCID: PMC7396485 DOI: 10.3389/fpls.2020.00921] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/05/2020] [Indexed: 05/18/2023]
Abstract
C-repeat (CRT)/dehydration responsive element (DRE)-binding factor CBFs, a small family of genes encoding transcriptional activators, play important roles in plant cold tolerance. In this study, a comprehensive genome-wide analysis was carried out to identify and characterize the functional dynamics of CsCBFs in tea plant (Camellia sinensis). A total of 6 CBF genes were obtained from the tea plant genome and named CBF1-6. All of the CsCBFs had an AP2/ERF DNA-binding domain and nuclear localization signal (NLS) sequence. CsCBF-eGFP fusion and DAPI staining analysis confirmed the nuclear localization of the CsCBFs. Transactivation assays showed that the CsCBFs, except CsCBF1, had transcriptional activity. CsCBF expression was differentially induced by cold, heat, PEG, salinity, ABA, GA, MeJA, and SA stresses. In particular, the CsCBF genes were significantly induced by cold treatments. To further characterize the functions of CsCBF genes, we overexpressed the CsCBF3 gene in Arabidopsis thaliana plants. The resulting transgenic plants showed increased cold tolerance compared with the wild-type Arabidopsis plant. The enhanced cold tolerance of the transgenic plants was potentially achieved through an ABA-independent pathway. This study will help to increase our understanding of CsCBF genes and their contributions to stress tolerance in tea plants.
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Ahmad MZ, Li P, She G, Xia E, Benedito VA, Wan XC, Zhao J. Genome-Wide Analysis of Serine Carboxypeptidase-Like Acyltransferase Gene Family for Evolution and Characterization of Enzymes Involved in the Biosynthesis of Galloylated Catechins in the Tea Plant ( Camellia sinensis). Front Plant Sci 2020; 11:848. [PMID: 32670320 PMCID: PMC7330524 DOI: 10.3389/fpls.2020.00848] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/26/2020] [Indexed: 05/14/2023]
Abstract
Tea (Camellia sinensis L.) leaves synthesize and concentrate a vast array of galloylated catechins (e.g., EGCG and ECG) and non-galloylated catechins (e.g., EGC, catechin, and epicatechin), together constituting 8%-24% of the dry leaf mass. Galloylated catechins account for a major portion of soluble catechins in tea leaves (up to 75%) and make a major contribution to the astringency and bitter taste of the green tea, and their pharmacological activity for human health. However, the catechin galloylation mechanism in tea plants is largely unknown at molecular levels. Previous studies indicated that glucosyltransferases and serine carboxypeptidase-like acyltransferases (SCPL) might be involved in the process. However, details about the roles of SCPLs in the biosynthesis of galloylated catechins remain to be elucidated. Here, we performed the genome-wide identification of SCPL genes in the tea plant genome. Several SCPLs were grouped into clade IA, which encompasses previously characterized SCPL-IA enzymes with an acylation function. Twenty-eight tea genes in this clade were differentially expressed in young leaves and vegetative buds. We characterized three SCPL-IA enzymes (CsSCPL11-IA, CsSCPL13-IA, CsSCPL14-IA) with galloylation activity toward epicatechins using recombinant enzymes. Not only the expression levels of these SCPLIA genes coincide with the accumulation of galloylated catechins in tea plants, but their recombinant enzymes also displayed β-glucogallin:catechin galloyl acyltransferase activity. These findings provide the first insights into the identities of genes encoding glucogallin:catechin galloyl acyltransferases with an active role in the biosynthesis of galloylated catechins in tea plants.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Vagner A. Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Xiao Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Jian Zhao,
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Zhu J, He Y, Yan X, Liu L, Guo R, Xia X, Cheng D, Mi X, Samarina L, Liu S, Xia E, Wei C. Duplication and transcriptional divergence of three Kunitz protease inhibitor genes that modulate insect and pathogen defenses in tea plant ( Camellia sinensis). Hortic Res 2019; 6:126. [PMID: 31754433 PMCID: PMC6856355 DOI: 10.1038/s41438-019-0208-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 05/30/2023]
Abstract
Kunitz protease inhibitors (KPIs) are ubiquitous in plants and act as crucial compounds in defense responses against insect attack and pathogen infection. However, the influence of gene duplication on the postdivergence of the CsKPI genes involved in biotic stresses in tea plant is not well known. Here, we identified three CsKPI genes from tea plant (Camellia sinensis) and characterized their expression and evolutionary patterns among plant species. We found that CsKPI1, CsKPI2, and CsKPI3 diverged from their common ancestor 72.94 million years ago (MYA), and the tandem duplication of CsKPI2 and CsKPI3 occurred 26.78 MYA. An in vitro protein assay showed that the three CsKPI proteins were functional and inhibited the production of p-nitroanilide (PNA) from an artificial substrate. The three CsKPI-GFP fusion proteins localized to the cytoplasm. We showed that salicylic acid (SA) and transcripts of CsKPI2 and CsKPI3 significantly accumulated after infection with Glomerella cingulata. The application of exogenous SA stimulated the high expression of both CsKPI2 and CsKPI3 by activating cis-elements within their promoters. Under Ectropis oblique attack, CsKPI1 expression and jasmonic acid (JA) levels were more abundant in both insect-damaged leaf tissues and undamaged neighboring leaves. The application of jasmonic acid methyl ester elicited high expression levels of CsKPI1, suggesting that CsKPI1 accumulation requires JA production in tea plant. The overall findings suggest that the transcriptional divergence of KPI genes after duplication led to the specialized role of CsKPI1 in the physiological response to insect stress; the functional conservation between CsKPI2 and CsKPI3 confers resistance to pathogen infection in tea plant.
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Affiliation(s)
- Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Yaxian He
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xiaomei Yan
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Lu Liu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Daojie Cheng
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Lidiia Samarina
- Russian Research Institute of Floriculture and Subtropical Crops, 354002 Yana Fabritsiusa st. 2/28, Sochi, Russian Federation
| | - Shenrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
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Shi X, Saravelos SH, Zhou Q, Huang X, Xia E, Li TC. Prevention of postoperative adhesion reformation by intermittent intrauterine balloon therapy: a randomised controlled trial. BJOG 2019; 126:1259-1266. [PMID: 31207009 DOI: 10.1111/1471-0528.15843] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 01/04/2023]
Affiliation(s)
- X Shi
- Department of Hysteroscopic Centre Fuxing Hospital the Eighth Clinical Medical College Capital Medical University Beijing China
| | - SH Saravelos
- IVF Unit Hammersmith Hospital Imperial College London UK
- Assisted Conception Unit Department of Obstetrics and Gynaecology Prince of Wales Hospital Chinese University of Hong Kong Hong Kong China
| | - Q Zhou
- Department of Hysteroscopic Centre Fuxing Hospital the Eighth Clinical Medical College Capital Medical University Beijing China
| | - X Huang
- Department of Hysteroscopic Centre Fuxing Hospital the Eighth Clinical Medical College Capital Medical University Beijing China
| | - E Xia
- Department of Hysteroscopic Centre Fuxing Hospital the Eighth Clinical Medical College Capital Medical University Beijing China
| | - TC Li
- Department of Hysteroscopic Centre Fuxing Hospital the Eighth Clinical Medical College Capital Medical University Beijing China
- Assisted Conception Unit Department of Obstetrics and Gynaecology Prince of Wales Hospital Chinese University of Hong Kong Hong Kong China
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Xia E, Li F, Tong W, Yang H, Wang S, Zhao J, Liu C, Gao L, Tai Y, She G, Sun J, Cao H, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Wu Q, Ge R, Zhao H, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Zhao S, Bennetzen JL, Wei C, Wan X. The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. Sci Data 2019; 6:122. [PMID: 31308375 PMCID: PMC6629666 DOI: 10.1038/s41597-019-0127-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/25/2019] [Indexed: 11/25/2022] Open
Abstract
Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.
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Affiliation(s)
- Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chun Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Liping Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yuling Tai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Sun
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Haisheng Cao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiang Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenzhao Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Shihua Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Haijing Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Junlan Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Chengying Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | | | - Bei Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Dai Shan
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Congbing Fang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Yue
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Daxiang Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Changjun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | | | - Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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Huang H, Yao Q, Xia E, Gao L. Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant ( Camellia sinensis L.) Associated with Tea Flavor. J Agric Food Chem 2018; 66:9828-9838. [PMID: 30198713 DOI: 10.1021/acs.jafc.8b01995] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tea-specialized metabolites contribute to rich flavors and healthy function of tea. Their accumulation patterns and underlying regulatory mechanism are significantly different under different nitrogen (N) conditions during adaptation stage. Here, we find that flavonoids associated with tea flavor are dominated by different metabolic and transcriptional responses among the four N conditions (N-deficiency, nitrate, ammonia, and nitric oxide). Nitrogen-deficiency tea plants accumulate diverse flavonoids, corresponding with higher expression of hub genes including F3H, FNS, UFGT, bHLH35, and bHLH36. Compared with N-deficiency, N-supply tea plants significantly increase proline, glutamine, and theanine, which are also associated with tea flavor, especially under NH4+-supply. As NH4+-tolerant species, tea plant exploits the adaptive strategy by substantial accumulation of amino acids including theanine to adapt excess NH4+, which attributes to, at least in part, efficient N transport and assimilation, and active protein degradation. A distinct divergence of N reallocation in young shoots of tea plant under different N sources contributes to diverse tea flavor.
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Affiliation(s)
- Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204 , China
| | - Qiuyang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204 , China
| | - Enhua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204 , China
| | - Lizhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204 , China
- Institution of Genomics and Bioinformatics , South China Agricultural University , Guangzhou 510642 , China
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Tai Y, Liu C, Yu S, Yang H, Sun J, Guo C, Huang B, Liu Z, Yuan Y, Xia E, Wei C, Wan X. Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis). BMC Genomics 2018; 19:616. [PMID: 30111282 PMCID: PMC6094456 DOI: 10.1186/s12864-018-4999-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 08/08/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The leaves of tea plants (Camellia sinensis) are used to produce tea, which is one of the most popular beverages consumed worldwide. The nutritional value and health benefits of tea are mainly related to three abundant characteristic metabolites; catechins, theanine and caffeine. Weighted gene co-expression network analysis (WGCNA) is a powerful system for investigating correlations between genes, identifying modules among highly correlated genes, and relating modules to phenotypic traits based on gene expression profiling. Currently, relatively little is known about the regulatory mechanisms and correlations between these three secondary metabolic pathways at the omics level in tea. RESULTS In this study, levels of the three secondary metabolites in ten different tissues of tea plants were determined, 87,319 high-quality unigenes were assembled, and 55,607 differentially expressed genes (DEGs) were identified by pairwise comparison. The resultant co-expression network included 35 co-expression modules, of which 20 modules were significantly associated with the biosynthesis of catechins, theanine and caffeine. Furthermore, we identified several hub genes related to these three metabolic pathways, and analysed their regulatory relationships using RNA-Seq data. The results showed that these hub genes are regulated by genes involved in all three metabolic pathways, and they regulate the biosynthesis of all three metabolites. It is notable that light was identified as an important regulator for the biosynthesis of catechins. CONCLUSION Our integrated omics-level WGCNA analysis provides novel insights into the potential regulatory mechanisms of catechins, theanine and caffeine metabolism, and the identified hub genes provide an important reference for further research on the molecular biology of tea plants.
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Affiliation(s)
- Yuling Tai
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuwei Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jiameng Sun
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Chunxiao Guo
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Bei Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zhaoye Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Yi Yuan
- School of Life Science, Anhui Agricultural University, Hefei, 230036 China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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Yokoi S, Xia E, Kanematsu S, Suenaga Y, Moriya Y, Yoshino I, Iizasa T. P2.02-063 Oncogenic microRNAs Associated with Poor Prognosis Are Up-Regulated on the Amplicon in Squamous Cell Lung Carcinoma. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Marimuthu K, Ng O, Khong W, Xia E, Xu W, Teo Y, Tan E, Ong RT, Lye D, Chow A, Krishnan P, Ang B. Halting NDM-producing enterobacteriaceae spread with the reactive infection control strategy: a real-world experience analyzed using a novel spatiotemporal epidemiologic risk measure (Epi-score) and whole-genome sequencing (WGS). Antimicrob Resist Infect Control 2015. [PMCID: PMC4474789 DOI: 10.1186/2047-2994-4-s1-o41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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34
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Affiliation(s)
- E Xia
- Hysteroscopic Center, Fuxing Hospital, Capital Medical University, Beijing, China
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35
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Song D, Xia E, Xiao Y, Li TC, Huang X, Liu Y. Management of false passage created during hysteroscopic adhesiolysis for Asherman’s syndrome. J OBSTET GYNAECOL 2015. [DOI: 10.3109/01443615.2015.1030601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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36
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Xiao Y, Peng X, Ma N, Li TC, Xia E. The expression of cyclooxygenase-2 and vascular endothelial growth factor in the endometrium during the peri-implantation period in women with and without polyps. HUM FERTIL 2014; 17:67-71. [PMID: 24471989 DOI: 10.3109/14647273.2013.868933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE This prospective study was designed to determine whether the expression of cyclooxygenase-2 (COX-2) and vascular endothelial growth factor (VEGF) in the endometrial tissue obtained from the peri-implantation period of women with endometrial polyp (EP) differs from that of control subjects without a polyp. METHODS Endometrial samples were collected from 30 patients with EP and 30 control subjects without EP, in the mid-secretory phase. The expression of COX-2 and VEGF in the endometrium was examined with the use of immunohistochemistry. RESULTS COX-2 and VEGF were predominantly expressed in endometrial glands. The expression of COX-2 and VEGF in the endometrium obtained from women with EP was lower than that of control subjects. CONCLUSION The reduced expression of COX-2 and VEGF in the endometrium of women with EP may account for the association between EP and infertility.
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Affiliation(s)
- Y Xiao
- Hysterosopic Center, Fuxing Hospital, Capital Medical University , Beijing , P. R. China
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Xia E, Song D, Liu Y. Clinical Analysis of Intrauterine Adhesions after Uterine Artery Embolisation. J Minim Invasive Gynecol 2012. [DOI: 10.1016/j.jmig.2012.08.680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Xia E, Guo Y, Xiao Y. Analysis on the Pelvic Lesions and Fertility Outcome of 294 Cases Infertile Women Treated by Laparoscopy. J Minim Invasive Gynecol 2012. [DOI: 10.1016/j.jmig.2012.08.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Xia E, Peng X. T Uterus Treated by Transcervical Uterine Incision: 2 Cases Successful Pregnancy Reports. J Minim Invasive Gynecol 2011. [DOI: 10.1016/j.jmig.2011.08.599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Xia E. Cystic Adenomyosis – Four Cases Report and Literature Review. J Minim Invasive Gynecol 2010. [DOI: 10.1016/j.jmig.2010.08.408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Xia E, Liu Y, Huang X, Zheng J, Yu D, Ma N, Li Y, Qu J. Hysteroscopy Combined with Laparoscopic Metroplasty for the Treatment of Complete Bicornuate Uterus – Two Cases Report. J Minim Invasive Gynecol 2010. [DOI: 10.1016/j.jmig.2010.08.579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Xia E. Laparoscopic Cervical Cerclage Using 5-mm Mer-Silene Tape. J Minim Invasive Gynecol 2009. [DOI: 10.1016/j.jmig.2009.08.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Peng X, Li T, Xia E, Xia C, Liu Y, Yu D. A comparison of oestrogen receptor and progesterone receptor expression in endometrial polyps and endometrium of premenopausal women. J OBSTET GYNAECOL 2009; 29:340-6. [DOI: 10.1080/01443610902878775] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Xia E, Wang B. Study on Benign Lesions of Uteri and Cervix Treating by Laparoscopic Supracervical Hysterectomy Combined with Transcervical Resection Surgery. J Minim Invasive Gynecol 2008. [DOI: 10.1016/j.jmig.2008.09.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Malcolm BA, Liu R, Lahser F, Agrawal S, Belanger B, Butkiewicz N, Chase R, Gheyas F, Hart A, Hesk D, Ingravallo P, Jiang C, Kong R, Lu J, Pichardo J, Prongay A, Skelton A, Tong X, Venkatraman S, Xia E, Girijavallabhan V, Njoroge FG. SCH 503034, a mechanism-based inhibitor of hepatitis C virus NS3 protease, suppresses polyprotein maturation and enhances the antiviral activity of alpha interferon in replicon cells. Antimicrob Agents Chemother 2006; 50:1013-20. [PMID: 16495264 PMCID: PMC1426438 DOI: 10.1128/aac.50.3.1013-1020.2006] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cleavage of the hepatitis C virus (HCV) polyprotein by the viral NS3 protease releases functional viral proteins essential for viral replication. Recent studies by Foy and coworkers strongly suggest that NS3-mediated cleavage of host factors may abrogate cellular response to alpha interferon (IFN-alpha) (E. Foy, K. Li, R. Sumpter, Jr., Y.-M. Loo, C. L. Johnson, C. Wang, P. M. Fish, M. Yoneyama, T. Fujita, S. M. Lemon, and M. Gale, Jr., Proc. Natl. Acad. Sci. USA 102:2986-2991, 2005, and E. Foy, K. Li, C. Wang, R. Sumpter, Jr., M. Ikeda, S. M. Lemon, and M. Gale, Jr., Science 300:1145-1148, 2003). Blockage of NS3 protease activity therefore is expected to inhibit HCV replication by both direct suppression of viral protein production as well as by restoring host responsiveness to IFN. Using structure-assisted design, a ketoamide inhibitor, SCH 503034, was generated which demonstrated potent (overall inhibition constant, 14 nM) time-dependent inhibition of the NS3 protease in cell-free enzyme assays as well as robust in vitro activity in the HCV replicon system, as monitored by immunofluorescence and real-time PCR analysis. Continuous exposure of replicon-bearing cell lines to six times the 90% effective concentration of SCH 503034 for 15 days resulted in a greater than 4-log reduction in replicon RNA. The combination of SCH 503034 with IFN was more effective in suppressing replicon synthesis than either compound alone, supporting the suggestion of Foy and coworkers that combinations of IFN with protease inhibitors would lead to enhanced therapeutic efficacy.
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Affiliation(s)
- B A Malcolm
- Virology, Schering-Plough Research Institute, 2015 Galloping Hill Rd., Kenilworth, New Jersey 07033, USA
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Xia E, Xia E, Chen F. [Severe complications of hysteroscopic surgeries: an analysis of 35 cases]. Zhonghua Fu Chan Ke Za Zhi 2001; 36:596-9. [PMID: 16134521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVE To investigate the methods of earlier diagnosis, treatment and precautions on the severe complications of hysteroscopic procedures. METHODS There were 12 921 cases of diagnostic hysteroscopy and 2 221 cases of operative hysteroscopy were performed. For diagnostic hysteroscopy B ultrasonography were scaned meanwhile and fluid media were used to distend the uterus. For operation hysteroscopy B ultrasonography or laparoscopy was used for monitoring. RESULTS Thirty five cases of severe complications encountered. There were 9 cases of severe intraoperative bleeding. Foley catheter inserting, bleeding spots coagulating, uterine cavity tampon or hysterectomy were used to stop intraoperative and postoperative bleeding successfully. Eleven cases of uterine perforation were treated by conservativetherapy, laparoscopy or hysterectomy. An air embolism happened on hysteroscopic examination was survived with aggressive rescue. There were 4 cases of postoperative infection that had history of pelvic inflammatory disease and cured by antibiotics. Diuretic agent and saline infusion were used to treat 5 cases of transurethral resection of prostate (TURP) syndrome effectively. For 4 cases of post-ablationsterilization syndrome (PASS) dilating the cervix canal and expelling the hematometra, transcervical resection of adhesions or hysterectomy were managed effectively. One case of endometrial adenocarcinoma stage I a was diagnosed 8 years after transcervical resection of endometrium (TCRE) & transcervical resection of polyp (TCRP), and radical hysterectomy plus selective pelvic lymphadenectomy was performed. CONCLUSIONS Foley catheter insertion is a simple and efficient method to stop uterine bleeding. Uterine adhesion is a high risk factor of uterine perforation. Monitoring by B ultrasonography or laparoscopy could not prevent uterine perforation. Prevention was essential for air embolism. Control the pressure of irrigating flow and operating time can reduce the incidence of TURP syndrome. To intensify follow-up is the best method to detect PASS and uterine adenocarcinoma.
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Affiliation(s)
- E Xia
- Hysteroscopic Center, Fuxing Hospital Affiliate of Capital University of Medical Sciences, Beijing 100038, China
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Ingravallo P, Lahser F, Xia E, Sodowich B, Lai VC, Hong Z, Zhong W. Characterization of monoclonal antibodies that specifically recognize the palm subdomain of hepatitis C virus nonstructural protein 5B polymerase. Virus Res 2001; 75:179-87. [PMID: 11325472 DOI: 10.1016/s0168-1702(01)00239-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase (RdRp) which plays an essential role in viral RNA replication. Antibodies that specifically recognize NS5B will have utilities in monitoring NS5B production and subcellular localization, as well as in structure-function studies. In this report, three mouse monoclonal antibodies (mAbs), 16A9C9, 16D9A4 and 20A12C7, against a recombinant NS5B protein (genotype 1a, H-77 strain) were produced. These mAbs specifically recognize HCV NS5B, but not RdRps of polivirus (PV), bovine viral diarrhea virus (BVDV) or GB virus B (GBV-B). The mAbs can readily detect NS5B in cellular lysates of human osteosarcoma Saos2 cells constitutively expressing the nonstructural region of HCV (NS3-NS4A-NS4B-NS5A-NS5B). NS5B proteins of different HCV genotypes/subtypes (1a, 1b, 2a, 2c, 5a) showed varied affinity for these mAbs. Interestingly, the epitopes for the mAbs were mapped to the palm subdomain (amino acid 188-370) of the HCV RdRp as determined by immunoblotting analysis of a panel of HCV/GBV-B chimeric NS5B proteins. The binding site was mapped between amino acid 231 and 267 of NS5B for 16A9C9, and between 282 and 372 for 16D9A4 and 20A12C7. Furthermore, these mAbs showed no inhibitory effect on the NS5B polymerase activity in vitro.
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Affiliation(s)
- P Ingravallo
- Department of Antiviral Therapy, Schering-Plough Research Institute, Kenilworth, NJ 07033, USA
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Feng L, Song J, Wong F, Xia E. Incidence of deep venous thrombosis after gynaecological laparoscopy. Chin Med J (Engl) 2001; 114:632-5. [PMID: 11780442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
OBJECTIVE To evaluate the incidence of deep venous thrombosis (DVT) after gynaecological laparoscopy. METHODS The incidence of DVT was studied in 72 consecutive patients who underwent gynaecological laparoscopy in the Liverpool Health Service between May and September 1997. B-mode ultrasound supplemented by Doppler was used to examine venous patency and intraluminal echoes to diagnose DVT. Sixty-one patients who had pneumoperitoneum less than 60 minutes were classified a minor procedure and 11 who had pneumoperitoneum more than 60 minutes were classified as major procedure. Two Doppler ultrasound scans were planned for every patient. The first one was done within 24 hours and the second was performed on day 7 post-surgery. All 72 patients had the first scan and 40 out of 61 in the minor procedure group and 9 out of 11 in the major procedure had the second scan. Twenty-three patients who did not come for the second scan were followed up by phone. RESULTS No DVT was found in our study. CONCLUSION This study confirms an impression that gynaecological laparoscopic procedure has a very low incidence of DVT. If it occurs, the diagnosis and treatment must be made as soon as possible so that the fatal complications such as pulmonary embolus can be avoided.
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Affiliation(s)
- L Feng
- Department of Gynaecology, Beijing Tiantan Hospital, Capital University of Medical Sciences, Beijing 100050, China.
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Zhang J, Xia E, Zhang J. [Effect of mifepristone on the expression of tumor necrosis factor-alpha and transforming growth factor-beta in decidua of early pregnancy]. Zhonghua Fu Chan Ke Za Zhi 2001; 36:27-9. [PMID: 11778540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To investigate the effect of mifepristone on the expression of tumor necrosis factor-alpha(TNF-alpha) and transforming growth factor-beta(TGF-beta) in decidua of early pregnancy. METHODS Thirty artificial abortion women as control and thirty drug abortion women were enrolled for study. The expressions of TNF-alpha and TGF-beta in decidua were measured with immunohistochemical method. RESULTS There was no significant difference of TNF-alpha positive expression rates between drug abortion group (73.33%) and artificial abortion group (70.00%, P > 0.05). TGF-beta expression rate of drug abortion group was similar to that of artificial abortion group. The highly-positive (++ and +++) TNF-alpha expression rate in drug abortion group was significantly higher than that in artificial abortion group (P < 0.05). TGF-beta expression degree in decidua of drug abortion group was significantly lower than that of artificial abortion group (P < 0.05). The ratio of TNF-alpha/TGF-beta in drug abortion group is higher than that in artificial abortion group. CONCLUSION TGF-beta has great effect on regulating the embryo development of early pregnancy. The change of TNF-alpha may be the reason of abortion. Mifepristone may interfere with embryo growth by inhibiting the activity of TGF-beta or by stimulating the secretion of TNF-alpha.
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Affiliation(s)
- J Zhang
- Department of Obstetrics and Gynecology, Beijing 402 Hospital, Beijing 100039, China
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Duan H, Xia E, Liang Y. [Study on the electrothermal tissue effects during transcervical resection of endometrium]. Zhonghua Fu Chan Ke Za Zhi 1999; 34:479-81. [PMID: 11360599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
OBJECTIVE To investigate the tissue electrothermal effects and to seek the appropriate setting of operative wattage during transcervical resection of endometrium (TCRE). METHODS The power setting were 60 W, 80 W, 100 W for cutting and 30 W, 60 W, 80 W, 100 W for coagulation when performing endometrial resection in vitro or in vivo with operating time 3-5 seconds or 6-8 seconds respectively. After operation the uterine specimens were stained by hemaloxylin-eosin, and respiratory enzyme dehydronicotinamide adenine dinucleotide phosphate diaphorase methods for evaluating the tissue damage. RESULTS (1) The depth of endometrial damage under cutting was considerably less severe than those under coagulation with the same power setting. (2) When the power of cutting and coagulation were 80 W, 100 W and 30 W, 60 W respectively and operating time prolonged more than 5 seconds, the thermal damage covered endometrium and 2-3 mm of myometrium in depth. (3) At such wattage and operating time the deepest destruction was only 16.27% of uterine wall. CONCLUSION (1) There is significant difference in the depth of thermal damage between cutting and coagulation during hysteros copic surgery. (2) The appropriate power setting should be 80-100 W for cutting and 30-60 W for coagulation.
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Affiliation(s)
- H Duan
- Beijing Fuxing Hospital, Beijing 100038
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