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Zhang B, Ma Z, Guo H, Chen S, Liu J. Single-cell RNA-sequencing provides new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass leaf blades. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108857. [PMID: 38905728 DOI: 10.1016/j.plaphy.2024.108857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
As an important warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) flourishes in warm areas around the world due to the existence of the C4 photosynthetic pathway. However, how C4 photosynthesis operates in bermudagrass leaves is still poorly understood. In this study, we performed single-cell RNA-sequencing on 5296 cells from bermudagrass leaf blades. Eight cell clusters corresponding to mesophyll, bundle sheath, epidermis and vascular bundle cells were successfully identified using known cell marker genes. Expression profiling indicated that genes encoding NADP-dependent malic enzymes (NADP-MEs) were highly expressed in bundle sheath cells, whereas NAD-ME genes were weakly expressed in all cell types, suggesting C4 photosynthesis of bermudagrass leaf blades might be NADP-ME type rather than NAD-ME type. The results also indicated that starch synthesis-related genes showed preferential expression in bundle sheath cells, whereas starch degradation-related genes were highly expressed in mesophyll cells, which agrees with the observed accumulation of starch-filled chloroplasts in bundle sheath cells. Gene co-expression analysis further revealed that different families of transcription factors were co-expressed with multiple C4 photosynthesis-related genes, suggesting a complex transcription regulatory network of C4 photosynthesis might exist in bermudagrass leaf blades. These findings collectively provided new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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2
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Zhao B, Gao Y, Ma Q, Wang X, Zhu JK, Li W, Wang B, Yuan F. Global dynamics and cytokinin participation of salt gland development trajectory in recretohalophyte Limonium bicolor. PLANT PHYSIOLOGY 2024; 195:2094-2110. [PMID: 38588029 DOI: 10.1093/plphys/kiae199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/23/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
Salt gland is an epidermal Na+ secretory structure that enhances salt resistance in the recretohalophyte sea lavender (Limonium bicolor). To elucidate the salt gland development trajectory and related molecular mechanisms, we performed single-cell RNA sequencing of L. bicolor protoplasts from young leaves at salt gland initiation and differentiation stages. Dimensionality reduction analyses defined 19 transcriptionally distinct cell clusters, which were assigned into 4 broad populations-promeristem, epidermis, mesophyll, and vascular tissue-verified by in situ hybridization. Cytokinin was further proposed to participate in salt gland development by the expression patterns of related genes and cytological evidence. By comparison analyses of Single-cell RNA sequencing with exogenous application of 6-benzylaminopurine, we delineated 5 salt gland development-associated subclusters and defined salt gland-specific differentiation trajectories from Subclusters 8, 4, and 6 to Subcluster 3 and 1. Additionally, we validated the participation of TRIPTYCHON and the interacting protein Lb7G34824 in salt gland development, which regulated the expression of cytokinin metabolism and signaling-related genes such as GLABROUS INFLORESCENCE STEMS 2 to maintain cytokinin homeostasis during salt gland development. Our results generated a gene expression map of young leaves at single-cell resolution for the comprehensive investigation of salt gland determinants and cytokinin participation that helps elucidate cell fate determination during epidermis formation and evolution in recretohalophytes.
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Affiliation(s)
- Boqing Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yaru Gao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Qiuyu Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Weiqiang Li
- Jilin Da'an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
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Lv Z, Jiang S, Kong S, Zhang X, Yue J, Zhao W, Li L, Lin S. Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:1679. [PMID: 38931111 PMCID: PMC11207393 DOI: 10.3390/plants13121679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
"Omics" typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics characterizes and quantifies all genes of an organism collectively, studying their interrelationships and their impacts on the organism. However, conventional transcriptomic sequencing techniques target population cells, and their results only reflect the average expression levels of genes in population cells, as they are unable to reveal the gene expression heterogeneity and spatial heterogeneity among individual cells, thus masking the expression specificity between different cells. Single-cell transcriptomic sequencing and spatial transcriptomic sequencing techniques analyze the transcriptome of individual cells in plant or animal tissues, enabling the understanding of each cell's metabolites and expressed genes. Consequently, statistical analysis of the corresponding tissues can be performed, with the purpose of achieving cell classification, evolutionary growth, and physiological and pathological analyses. This article provides an overview of the research progress in plant single-cell and spatial transcriptomics, as well as their applications and challenges in plants. Furthermore, prospects for the development of single-cell and spatial transcriptomics are proposed.
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Affiliation(s)
- Zhuo Lv
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Shuaijun Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Shuxin Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Xu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Jiahui Yue
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Wanqi Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Feng L, Yan W, Tang X, Wu H, Pan Y, Lu D, Ling-Hu Q, Liu Y, Liu Y, Song X, Ali M, Fang L, Guo H, Li B. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis. Commun Biol 2024; 7:474. [PMID: 38637717 PMCID: PMC11026412 DOI: 10.1038/s42003-024-06142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.
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Affiliation(s)
- Li Feng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Wei Yan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xianli Tang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Huihui Wu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yajie Pan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Dongdong Lu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Qianyan Ling-Hu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yuelin Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Liang Fang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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Sun X, Liu Z, Liu R, Bucher J, Zhao J, Visser RGF, Bonnema G. Transcriptomic analyses to summarize gene expression patterns that occur during leaf initiation of Chinese cabbage. HORTICULTURE RESEARCH 2024; 11:uhae059. [PMID: 38689699 PMCID: PMC11059812 DOI: 10.1093/hr/uhae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
In Chinese cabbage, rosette leaves expose their adaxial side to the light converting light energy into chemical energy, acting as a source for the growth of the leafy head. In the leafy head, the outer heading leaves expose their abaxial side to the light while the inner leaves are shielded from the light and have become a sink organ of the growing Chinese cabbage plant. Interestingly, variation in several ad/abaxial polarity genes is associated with the typical leafy head morphotype. The initiation of leaf primordia and the establishment of leaf ad/abaxial polarity are essential steps in the initiation of marginal meristem activity leading to leaf formation. Understanding the molecular genetic mechanisms of leaf primordia formation, polar differentiation, and leaf expansion is thus relevant to understand leafy head formation. As Brassica's are mesa-hexaploids, many genes have multiple paralogues, complicating analysis of the genetic regulation of leaf development. In this study, we used laser dissection of Chinese cabbage leaf primordia and the shoot apical meristem (SAM) to compare gene expression profiles between both adaxial and abaxial sides and the SAM aiming to capture transcriptome changes underlying leaf primordia development. We highlight genes with roles in hormone pathways and transcription factors. We also assessed gene expression gradients along expanded leaf blades from the same plants to analyze regulatory links between SAM, leaf primordia and the expanding rosette leaf. The catalogue of differentially expressed genes provides insights in gene expression patterns involved in leaf development and form a starting point to unravel leafy head formation.
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Affiliation(s)
- XiaoXue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Zihan Liu
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Rui Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Johan Bucher
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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He Z, Luo Y, Zhou X, Zhu T, Lan Y, Chen D. scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases. Nucleic Acids Res 2024; 52:D1629-D1638. [PMID: 37638765 PMCID: PMC10767885 DOI: 10.1093/nar/gkad706] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/20/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023] Open
Abstract
Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at the single-cell level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct a plant single-cell database, scPlantDB, which is publicly available at https://biobigdata.nju.edu.cn/scplantdb. We integrated single-cell transcriptomic profiles from 67 high-quality datasets across 17 plant species, comprising approximately 2.5 million cells. The data underwent rigorous collection, manual curation, strict quality control and standardized processing from public databases. scPlantDB offers interactive visualization of gene expression at the single-cell level, facilitating the exploration of both single-dataset and multiple-dataset analyses. It enables systematic comparison and functional annotation of markers across diverse cell types and species while providing tools to identify and compare cell types based on these markers. In summary, scPlantDB serves as a comprehensive database for investigating cell types and markers within plant cell atlases. It is a valuable resource for the plant research community.
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Affiliation(s)
- Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuting Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yangming Lan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Feng Y, Zhao Y, Ma Y, Liu D, Shi H. Single-cell transcriptome analyses reveal cellular and molecular responses to low nitrogen in burley tobacco leaves. PHYSIOLOGIA PLANTARUM 2023; 175:e14118. [PMID: 38148214 DOI: 10.1111/ppl.14118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Abstract
Tobacco (Nicotiana tabacum) is cultivated and consumed worldwide. It requires great amounts of nitrogen (N) to achieve the best yield and quality. With a view to sustainable and environmentally friendly agriculture, developing new genotypes with high productivity under low N conditions is an important approach. It is unclear how genes in tobacco are expressed at the cellular level and the precise mechanisms by which cells respond to environmental stress, especially in the case of low N. Here, we characterized the transcriptomes in tobacco leaves grown in normal and low-N conditions by performing scRNA-seq. We identified 10 cell types with 17 transcriptionally distinct cell clusters with the assistance of marker genes and constructed the first single-cell atlas of tobacco leaves. Distinct gene expression patterns of cell clusters were observed under low-N conditions, and the mesophyll cells were the most important responsive cell type and displayed heterogene responses among its three subtypes. Pseudo-time trajectory analysis revealed low-N stress decelerates the differentiation towards mesophyll cells. In combination with scRNA-seq, WGCNA, and bulk RNA-seq results, we found that genes involved in porphyrin metabolism, nitrogen metabolism, carbon fixation, photosynthesis, and photosynthesis-antenna pathway play an essential role in response to low N. Moreover, we identified COL16, GATA24, MYB73, and GLK1 as key TFs in the regulation of N-responsive genes. Collectively, our findings are the first observation of the cellular and molecular responses of tobacco leaves under low N stress and lay the cornerstone for future tobacco scRNA-seq investigations.
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Affiliation(s)
- Yuqing Feng
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
| | - Yuanyuan Zhao
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
| | - Yanjun Ma
- Technology Center, Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd, Beijing, China
| | - Deshui Liu
- Technology Center, Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd, Beijing, China
| | - Hongzhi Shi
- College of Tobacco, Henan Agricultural University, Zhengzhou, Henan, P.R.China
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Zhang J, Ahmad M, Gao H. Application of single-cell multi-omics approaches in horticulture research. MOLECULAR HORTICULTURE 2023; 3:18. [PMID: 37789394 PMCID: PMC10521458 DOI: 10.1186/s43897-023-00067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.
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Affiliation(s)
- Jun Zhang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mayra Ahmad
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Liao RY, Wang JW. Analysis of meristems and plant regeneration at single-cell resolution. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102378. [PMID: 37172363 DOI: 10.1016/j.pbi.2023.102378] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 05/14/2023]
Abstract
Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden cell states, and continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers to distinguish between distinct plant cell populations, delineate cell cycle continuums, and infer continuous differentiation trajectories of diverse cell types in shoots, roots, and floral and vascular meristems with unprecedented resolution. We then highlight the emerging power of scRNA-seq to dissect cell heterogeneity in regenerating tissues and uncover the cellular basis of cell reprogramming and stem cell commitment during plant regeneration. We conclude by discussing related outstanding questions in the field.
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Affiliation(s)
- Ren-Yu Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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