1
|
Mei X, Zhu K, Yan D, Jia H, Luo W, Ye J, Deng X. Developing a simple and rapid method for cell-specific transcriptome analysis through laser microdissection: insights from citrus rind with broader implications. PLANT METHODS 2024; 20:113. [PMID: 39068421 PMCID: PMC11282741 DOI: 10.1186/s13007-024-01242-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: 12/07/2023] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND With the rapid development of single-cell sequencing technology, histological studies are no longer limited to conventional homogenized tissues. Laser microdissection enables the accurate isolation of specific tissues or cells, and when combined with next-generation sequencing, it can reveal important biological processes at the cellular level. However, traditional laser microdissection techniques have often been complicated and time-consuming, and the quality of the RNA extracted from the collected samples has been inconsistent, limiting follow-up studies. Therefore, an improved, simple, and efficient laser microdissection method is urgently needed. RESULTS We omitted the sample fixation and cryoprotectant addition steps. Instead, fresh samples were embedded in Optimal Cutting Temperature medium within 1.5 ml centrifuge tube caps, rapidly frozen with liquid nitrogen, and immediately subjected to cryosectioning. A series of section thicknesses of citrus rind were tested for RNA extraction, which showed that 18 μm thickness yielded the highest quality RNA. By shortening the dehydration time to one minute per ethanol gradient and omitting the tissue clearing step, the resulting efficient dehydration and preserved morphology ensured high-quality RNA extraction. We also propose a set of laser microdissection parameters by adjusting the laser power to optimal values, reducing the aperture size, and lowering the pulse frequency. Both the epidermal and subepidermal cells from the citrus rind were collected, and RNA extraction was completed within nine hours. Using this efficient method, the transcriptome sequencing of the isolated tissues generated high-quality data with average Q30 values and mapping rates exceeding 91%. Moreover, the transcriptome analysis revealed significant differences between the cell layers, further confirming the effectiveness of our isolation approach. CONCLUSIONS We developed a simple and rapid laser microdissection method and demonstrated its effectiveness through a study based on citrus rind, from which we generated high-quality transcriptomic data. This fast and efficient method of cell isolation, combined with transcriptome sequencing not only contributes to precise histological studies at the cellular level in citrus but also provides a promising approach for cell-specific transcriptome analysis in a broader range of other plant tissues.
Collapse
Affiliation(s)
- Xuehan Mei
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kaijie Zhu
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Danni Yan
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Huihui Jia
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wangyao Luo
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Junli Ye
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiuxin Deng
- National Key Lab for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| |
Collapse
|
2
|
Yue H, Chen G, Zhang Z, Guo Z, Zhang Z, Zhang S, Turlings TCJ, Zhou X, Peng J, Gao Y, Zhang D, Shi X, Liu Y. Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf. PLANT, CELL & ENVIRONMENT 2024; 47:2660-2674. [PMID: 38619176 DOI: 10.1111/pce.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/16/2024]
Abstract
Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.
Collapse
Affiliation(s)
- Hao Yue
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Gong Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhuo Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhaojiang Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanhong Zhang
- Institute of Vegetable, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Songbai Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ted C J Turlings
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Jing Peng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Gao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Xiaobin Shi
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| |
Collapse
|
3
|
Yao J, Chu Q, Guo X, Shao W, Shang N, Luo K, Li X, Chen H, Cheng Q, Mo F, Zheng D, Xu F, Guo F, Zhu QH, Deng S, Chu C, Xu X, Liu H, Fan L. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. Dev Cell 2024:S1534-5807(24)00334-4. [PMID: 38848718 DOI: 10.1016/j.devcel.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.
Collapse
Affiliation(s)
- Jie Yao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qinjie Chu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xing Guo
- BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China
| | - Wenwen Shao
- BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China
| | - Nianmin Shang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Kang Luo
- College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China
| | - Xiaohan Li
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Hongyu Chen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qing Cheng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Fangyu Mo
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Dihuai Zheng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Fu Guo
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Shuiguang Deng
- College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xun Xu
- BGI Research, Shenzhen 518103, China
| | - Huan Liu
- BGI Research, Shenzhen 518103, China.
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China.
| |
Collapse
|
4
|
Szabała BM, Święcicka M, Łyżnik LA. Microinjection of the CRISPR/Cas9 editing system through the germ pore of a wheat microspore induces mutations in the target Ms2 gene. Mol Biol Rep 2024; 51:706. [PMID: 38824203 DOI: 10.1007/s11033-024-09644-w] [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: 04/03/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Microinjection is a direct procedure for delivering various compounds via micropipette into individual cells. Combined with the CRISPR/Cas9 editing technology, it has been used to produce genetically engineered animal cells. However, genetic micromanipulation of intact plant cells has been a relatively unexplored area of research, partly due to the cytological characteristics of these cells. This study aimed to gain insight into the genetic micromanipulation of wheat microspores using microinjection procedures combined with the CRISPR/Cas9 editing system targeting the Ms2 gene. METHODS AND RESULTS Microspores were first reprogrammed by starvation and heat shock treatment to make them structurally suitable for microinjection. The large central vacuole was fragmented and the nucleus with cytoplasm was positioned in the center of the cell. This step and an additional maltose gradient provided an adequate source of intact single cells in the three wheat genotypes. The microcapillary was inserted into the cell through the germ pore to deliver a working solution with a fluorescent marker. This procedure was much more efficient and less harmful to the microspore than inserting the microcapillary through the cell wall. The CRISPR/Cas9 binary vectors injected into reprogrammed microspores induced mutations in the target Ms2 gene with deletions ranging from 1 to 16 bp. CONCLUSIONS This is the first report of successful genome editing in an intact microspore/wheat cell using the microinjection technique and the CRISPR/Cas9 editing system. The study presented offers a range of molecular and cellular biology tools that can aid in genetic micromanipulation and single-cell analysis.
Collapse
Affiliation(s)
- Bartosz M Szabała
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland.
| | - Magdalena Święcicka
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
| | - Leszek A Łyżnik
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
| |
Collapse
|
5
|
Liu Q, Ma W, Chen R, Li S, Wang Q, Wei C, Hong Y, Sun H, Cheng Q, Zhao J, Kang J. Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308384. [PMID: 38634607 PMCID: PMC11199978 DOI: 10.1002/advs.202308384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/27/2024] [Indexed: 04/19/2024]
Abstract
Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA-seq and scATAC-seq datasets, accurate data integration remains a challenge, particularly when investigating cell-type-specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress. In contrast to commonly used computational integration at cell-type level, 12,968 peak-to-gene linkage is captured at the bona fide single-cell level and construct TRNs at an unprecedented resolution. Furthermore, the unprecedented datasets allow to more accurately reconstruct the coordinated changes of gene expression and chromatin states during cellular state transition. During root tip development, chromatin accessibility of initial cells precedes gene expression, suggesting that changes in chromatin accessibility may prime cells for subsequent differentiation steps. Pseudo-time trajectory analysis reveal that osmotic stress can shift the functional differentiation of trichoblast. Candidate stress-related gene-linked cis-regulatory elements (gl-cCREs) as well as potential target genes are also identified, and uncovered large cellular heterogeneity under osmotic stress.
Collapse
Affiliation(s)
- Qing Liu
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Wei Ma
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Ruiying Chen
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | | | - Qifan Wang
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Cai Wei
- BGI ResearchBeijing102601China
| | - Yiguo Hong
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Hai‐Xi Sun
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Qi Cheng
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiMinistry of Education of China‐Hebei Province Joint Innovation Center for Efficient Green Vegetable IndustryInternational Joint R & D Center of Hebei Province in Modern Agricultural BiotechnologyCollege of Life SciencesCollege of HorticultureHebei Agricultural UniversityBaoding071000China
| | - Jingmin Kang
- BGI ResearchBeijing102601China
- BGI ResearchShenzhen518083China
| |
Collapse
|
6
|
Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024; 17:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
Collapse
Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| |
Collapse
|
7
|
Guo H, Zhang L, Guo H, Cui X, Fan Y, Li T, Qi X, Yan T, Chen A, Shi F, Zeng F. Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration. PLANT PHYSIOLOGY 2024; 195:1414-1431. [PMID: 38401160 DOI: 10.1093/plphys/kiae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.
Collapse
Affiliation(s)
- Huihui Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiwang Cui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiushan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Tongdi Yan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Aiyun Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fengjuan Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| |
Collapse
|
8
|
Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. THE PLANT CELL 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
Collapse
Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| |
Collapse
|
9
|
Ramírez Gonzales LY, Cannarozzi G, Jäggi L, Assefa K, Chanyalew S, Dell'Acqua M, Tadele Z. The role of omics in improving the orphan crop tef. Trends Genet 2024; 40:449-461. [PMID: 38599921 DOI: 10.1016/j.tig.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.
Collapse
Affiliation(s)
| | - Gina Cannarozzi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Lea Jäggi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Kebebew Assefa
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | - Solomon Chanyalew
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | | | - Zerihun Tadele
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland.
| |
Collapse
|
10
|
Luna-García V, Bernal Gallardo JJ, Rethoret-Pasty M, Pasha A, Provart NJ, de Folter S. A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. PLANT PHYSIOLOGY 2024; 195:410-429. [PMID: 38088205 DOI: 10.1093/plphys/kiad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 05/02/2024]
Abstract
Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.
Collapse
Affiliation(s)
- Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Judith Jazmin Bernal Gallardo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Martin Rethoret-Pasty
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
- Polytech Nice Sophia, Université Côte d'Azur, 930 Rte des Colles, 06410 Biot, France
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| |
Collapse
|
11
|
Bawa G, Liu Z, Yu X, Tran LSP, Sun X. Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape. TRENDS IN PLANT SCIENCE 2024; 29:249-265. [PMID: 37914553 DOI: 10.1016/j.tplants.2023.10.002] [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: 11/10/2022] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Single cell RNA-sequencing (scRNA-seq) advancements have helped detect transcriptional heterogeneities in biological samples. However, scRNA-seq cannot currently provide high-resolution spatial transcriptome information or identify subcellular organs in biological samples. These limitations have led to the development of spatially enhanced-resolution omics-sequencing (Stereo-seq), which combines spatial information with single cell transcriptomics to address the challenges of scRNA-seq alone. In this review, we discuss the advantages of Stereo-seq technology. We anticipate that the application of such an integrated approach in plant research will advance our understanding of biological process in the plant transcriptomics era. We conclude with an outlook of how such integration will enhance crop improvement.
Collapse
Affiliation(s)
- George Bawa
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Zhixin Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Xiaole Yu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
| | - Xuwu Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China.
| |
Collapse
|
12
|
Raza A, Tabassum J, Fakhar AZ, Sharif R, Chen H, Zhang C, Ju L, Fotopoulos V, Siddique KHM, Singh RK, Zhuang W, Varshney RK. Smart reprograming of plants against salinity stress using modern biotechnological tools. Crit Rev Biotechnol 2023; 43:1035-1062. [PMID: 35968922 DOI: 10.1080/07388551.2022.2093695] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/08/2022] [Indexed: 01/19/2023]
Abstract
Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.
Collapse
Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Ali Zeeshan Fakhar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Luo Ju
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Rakesh K Singh
- Crop Diversification and Genetics, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch's Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Wang W, Garg V, Varshney RK, Liu H. Single cell RNA-seq in phytohormone signaling: a promising future. TRENDS IN PLANT SCIENCE 2023; 28:1208-1210. [PMID: 37550122 DOI: 10.1016/j.tplants.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023]
Abstract
Phytohormone signaling regulates plant growth and development. Single cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to decipher hormone-mediated spatiotemporal gene regulatory networks. In a recent study, Nolan et al. used time-series scRNA-seq to identify the cortex as a key site for brassinosteroid (BR)-mediated gene expression and revealed a signaling network during cell phase transition.
Collapse
Affiliation(s)
- Wenyi Wang
- College of Agriculture, South China Agriculture University, Guangzhou, Guangdong 510642, China
| | - Vanika Garg
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China.
| |
Collapse
|
15
|
Liu Z, Yang J, Long Y, Zhang C, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J, Wang E. Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. NATURE PLANTS 2023; 9:1734-1748. [PMID: 37749242 DOI: 10.1038/s41477-023-01524-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Establishing legume-rhizobial symbiosis requires precise coordination of complex responses in a time- and cell type-specific manner. Encountering Rhizobium, rapid changes of gene expression levels in host plants occur in the first few hours, which prepare the plants to turn off defence and form a symbiotic relationship with the microbes. Here, we applied single-nucleus RNA sequencing to characterize the roots of Medicago truncatula at 30 min, 6 h and 24 h after nod factor treatment. We found drastic global gene expression reprogramming at 30 min in the epidermis and cortex and most of these changes were restored at 6 h. Moreover, plant defence response genes are activated at 30 min and subsequently suppressed at 6 h in non-meristem cells. Only in the cortical cells but not in other cell types, we found the flavonoid synthase genes required to recruit rhizobia are highly expressed 30 min after inoculation with nod factors. A gene module enriched for symbiotic nitrogen fixation genes showed that MtFER (MtFERONIA) and LYK3 (LysM domain receptor-like kinase 3) share similar responses to symbiotic signals. We further found that MtFER can be phosphorylated by LYK3 and it participates in rhizobial symbiosis. Our results expand our understanding of dynamic spatiotemporal symbiotic responses at the single-cell level.
Collapse
Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Jun Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Chi Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dapeng Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaowei Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dong
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li Zhao
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Chengwu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| |
Collapse
|
16
|
Delannoy E, Batardiere B, Pateyron S, Soubigou-Taconnat L, Chiquet J, Colcombet J, Lang J. Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq. PLANT COMMUNICATIONS 2023; 4:100676. [PMID: 37644724 PMCID: PMC10504604 DOI: 10.1016/j.xplc.2023.100676] [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: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are orchestrated within organs and depend on specific cell types is poorly known. Here, using single-cell RNA sequencing (scRNA-seq) technology on three independent biological replicates, we identified several cell populations representing the core transcriptional responses of wild-type Arabidopsis leaves inoculated with the bacterial pathogen Pseudomonas syringae DC3000. Among these populations, we retrieved major cell types of the leaves (mesophyll, guard, epidermal, companion, and vascular S cells) with which we could associate characteristic transcriptional reprogramming and regulators, thereby specifying different cell-type responses to the pathogen. Further analyses of transcriptional dynamics, on the basis of inference of cell trajectories, indicated that the different cell types, in addition to their characteristic defense responses, can also share similar modules of gene reprogramming, uncovering a ubiquitous antagonism between immune and susceptible processes. Moreover, it appears that the defense responses of vascular S cells, epidermal cells, and mesophyll cells can evolve along two separate paths, one converging toward an identical cell fate, characterized mostly by lignification and detoxification functions. As this divergence does not correspond to the differentiation between immune and susceptible cells, we speculate that this might reflect the discrimination between cell-autonomous and non-cell-autonomous responses. Altogether our data provide an upgraded framework to describe, explore, and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.
Collapse
Affiliation(s)
- Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Bastien Batardiere
- UMR MIA Paris-Saclay, Université Paris-Saclay, AgroParisTech, INRAE, 91120 Palaiseau, France
| | - Stéphanie Pateyron
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Julien Chiquet
- UMR MIA Paris-Saclay, Université Paris-Saclay, AgroParisTech, INRAE, 91120 Palaiseau, France
| | - Jean Colcombet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Julien Lang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France.
| |
Collapse
|
17
|
Wong A, Chi W, Yu J, Bi C, Tian X, Yang Y, Gehring C. Plant adenylate cyclases have come full circle. NATURE PLANTS 2023; 9:1389-1397. [PMID: 37709954 DOI: 10.1038/s41477-023-01486-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/07/2023] [Indexed: 09/16/2023]
Abstract
In bacteria, fungi and animals, 3'-5'-cyclic adenosine monophosphate (cAMP) and adenylate cyclases (ACs), enzymes that catalyse the formation of 3',5'-cAMP from ATP, are recognized as key signalling components. In contrast, the presence of cAMP and its biological roles in higher plants have long been a matter of controversy due to the generally lower amounts in plant tissues compared with that in animal and bacterial cells, and a lack of clarity on the molecular nature of the generating and degrading enzymes, as well as downstream effectors. While treatment with 3',5'-cAMP elicited many plant responses, ACs were, however, somewhat elusive. This changed when systematic searches with amino acid motifs deduced from the conserved catalytic centres of annotated ACs from animals and bacteria identified candidate proteins in higher plants that were subsequently shown to have AC activities in vitro and in vivo. The identification of active ACs moonlighting within complex multifunctional proteins is consistent with their roles as molecular tuners and regulators of cellular and physiological functions. Furthermore, the increasing number of ACs identified as part of proteins with different domain architectures suggests that there are many more hidden ACs in plant proteomes and they may affect a multitude of mechanisms and processes at the molecular and systems levels.
Collapse
Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China.
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.
| | - Wei Chi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Jia Yu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Chuyun Bi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Yixin Yang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
| |
Collapse
|
18
|
Martinez-Garcia M, Olmos PM. Handling Ill-Conditioned Omics Data With Deep Probabilistic Models. IEEE J Biomed Health Inform 2023; 27:4601-4610. [PMID: 37224378 DOI: 10.1109/jbhi.2023.3279493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The advent of high-throughput technologies has produced an increase in the dimensionality of omics datasets, which limits the application of machine learning methods due to the great unbalance between the number of observations and features. In this scenario, dimensionality reduction is essential to extract the relevant information within these datasets and project it in a low-dimensional space, and probabilistic latent space models are becoming popular given their capability to capture the underlying structure of the data as well as the uncertainty in the information. This article aims to provide a general classification and dimensionality reduction method based on deep latent space models that tackles two of the main problems that arise in omics datasets: the presence of missing data and the limited number of observations against the number of features. We propose a semi-supervised Bayesian latent space model that infers a low-dimensional embedding driven by the target label: the Deep Bayesian Logistic Regression (DBLR) model. During inference, the model also learns a global vector of weights that allows it to make predictions given the low-dimensional embedding of the observations. Since this kind of dataset is prone to overfitting, we introduce an additional probabilistic regularization method based on the semi-supervised nature of the model. We compared the performance of the DBLR against several state-of-the-art methods for dimensionality reduction, both in synthetic and real datasets with different data types. The proposed model provides more informative low-dimensional representations, outperforms the baseline methods in classification, and can naturally handle missing entries.
Collapse
|
19
|
Dai YW, Wang WM, Zhou X. Development of a CD8 + T cell-based molecular classification for predicting prognosis and heterogeneity in triple-negative breast cancer by integrated analysis of single-cell and bulk RNA-sequencing. Heliyon 2023; 9:e19798. [PMID: 37810147 PMCID: PMC10559128 DOI: 10.1016/j.heliyon.2023.e19798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Background Triple-negative breast cancer (TNBC), although the most intractable subtype, is characterized by abundant immunogenicity, which enhances responsiveness to immunotherapeutic measures. Methods First, we identified CD8+ T cell core genes (TRCG) based on single-cell sequence and traditional transcriptome sequencing and then used this data to develop a first-of-its-kind classification system based on CD8+ T cells in patients with TNBC. Next, TRCG-related patterns were systematically analyzed, and their correlation with genomic features, immune activity (microenvironment associated with immune infiltration), and clinicopathological characteristics were assessed in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), the Cancer Genome Atlas (TCGA), GSE103091, GSE96058 databases. Additionally, a CD8+ T cell-related prognostic signature (TRPS) was developed to quantify a patient-specific TRCG pattern. What's more, the genes-related TRPS was validated by polymerase chain reaction (PCR) experiment. Results This study, for the first time, distinguished two subsets in patients with TNBC based on the TRCG. The immune microenvironment and prognostic stratification between these have distinct heterogeneity. Furthermore, this study constructed a novel scoring system named TRPS, which we show to be a robust prognostic marker for TNBC that is related to the intensity of immune infiltration and immunotherapy. Moreover, the levels of genes related the TRPS were validated by quantitative Real-Time PCR. Conclusions Consequently, this study unraveled an association between the TRCG and the tumor microenvironment in TNBC. TRPS model represents an effective tool for survival prediction and treatment guidance in TNBC that can also help identify individual variations in TME and stratify patients who are sensitive to anticancer immunotherapy.
Collapse
Affiliation(s)
- Yin-wei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
| | - Wei-ming Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiang Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
| |
Collapse
|
20
|
Rogers HJ. How far can omics go in unveiling the mechanisms of floral senescence? Biochem Soc Trans 2023; 51:1485-1493. [PMID: 37387359 PMCID: PMC10586764 DOI: 10.1042/bst20221097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Floral senescence is of fundamental interest in understanding plant developmental regulation, it is of ecological and agricultural interest in relation to seed production, and is of key importance to the production of cut flowers. The biochemical changes occurring are well-studied and involve macromolecular breakdown and remobilisation of nutrients to developing seeds or other young organs in the plant. However, the initiation and regulation of the process and inter-organ communication remain to be fully elucidated. Although ethylene emission, which becomes autocatalytic, is a key regulator in some species, in other species it appears not to be as important. Other plant growth regulators such as cytokinins, however, seem to be important in floral senescence across both ethylene sensitive and insensitive species. Other plant growth regulators are also likely involved. Omics approaches have provided a wealth of data especially in ornamental species where genome data is lacking. Two families of transcription factors: NAC and WRKY emerge as major regulators, and omics information has been critical in understanding their functions. Future progress would greatly benefit from a single model species for understanding floral senescence; however, this is challenging due to the diversity of regulatory mechanisms. Combining omics data sets can be powerful in understanding different layers of regulation, but in vitro biochemical and or genetic analysis through transgenics or mutants is still needed to fully verify mechanisms and interactions between regulators.
Collapse
|
21
|
Wang L, Wan MC, Liao RY, Xu J, Xu ZG, Xue HC, Mai YX, Wang JW. The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution. Dev Cell 2023; 58:1429-1444.e6. [PMID: 37321217 DOI: 10.1016/j.devcel.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/13/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Bryophytes represent a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, a comprehensive understanding of the cell types and transcriptional states that underpin the temporal development of bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define the cellular taxonomy of Marchantia polymorpha across asexual reproduction phases. We identify two maturation and aging trajectories of the main plant body of M. polymorpha at single-cell resolution: the gradual maturation of tissues and organs along the tip-to-base axis of the midvein and the progressive decline of meristem activities in the tip along the chronological axis. Specifically, we observe that the latter aging axis is temporally correlated with the formation of clonal propagules, suggesting an ancient strategy to optimize allocation of resources to producing offspring. Our work thus provides insights into the cellular heterogeneity that underpins the temporal development and aging of bryophytes.
Collapse
Affiliation(s)
- Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Mu-Chun Wan
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), 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
| | - Ren-Yu Liao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), 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
| | - Jie Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), 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
| | - Hao-Chen Xue
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), 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
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; Core Facility Center of CEMPS, SIPPE, CAS, Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), 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.
| |
Collapse
|
22
|
Zhu J, Moreno-Pérez A, Coaker G. Understanding plant pathogen interactions using spatial and single-cell technologies. Commun Biol 2023; 6:814. [PMID: 37542114 PMCID: PMC10403533 DOI: 10.1038/s42003-023-05156-8] [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: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted in the identification of multiple immune receptors in model and crop species as well as signaling overlap in surface-localized and intracellular immune receptors. However, scientists still have a limited understanding of how plants respond to diverse pathogens with spatial and cellular resolution. Recent advancements in single-cell, single-nucleus and spatial technologies can now be applied to plant-pathogen interactions. Here, we outline the current state of these technologies and highlight outstanding biological questions that can be addressed in the future.
Collapse
Affiliation(s)
- Jie Zhu
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alba Moreno-Pérez
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
| |
Collapse
|
23
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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.
| |
Collapse
|
24
|
Cheng Z, Mu C, Li X, Cheng W, Cai M, Wu C, Jiang J, Fang H, Bai Y, Zheng H, Geng R, Xu J, Xie Y, Dou Y, Li J, Mu S, Gao J. Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo ( Phyllostachys edulis). HORTICULTURE RESEARCH 2023; 10:uhad122. [PMID: 37554343 PMCID: PMC10405134 DOI: 10.1093/hr/uhad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/01/2023] [Indexed: 08/10/2023]
Abstract
Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1642 species worldwide. However, little is known about the transcriptional atlas that underpins root cell-type differentiation. Here, we set up a modified protocol for protoplast preparation and report single-cell transcriptomes of 14 279 filtered single cells derived from the basal root tips of moso bamboo. We identified four cell types and defined new cell-type-specific marker genes for the basal root. We reconstructed the developmental trajectories of the root cap, epidermis, and ground tissues and elucidated critical factors regulating cell fate determination. According to in situ hybridization and pseudotime trajectory analysis, the root cap and epidermis originated from a common initial cell lineage, revealing the particularity of bamboo basal root development. We further identified key regulatory factors for the differentiation of these cells and indicated divergent root developmental pathways between moso bamboo and rice. Additionally, PheWOX13a and PheWOX13b ectopically expressed in Arabidopsis inhibited primary root and lateral root growth and regulated the growth and development of the root cap, which was different from WOX13 orthologs in Arabidopsis. Taken together, our results offer an important resource for investigating the mechanism of root cell differentiation and root system architecture in perennial woody species of Bambusoideae.
Collapse
Affiliation(s)
- Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xiangyu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Miaomiao Cai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hui Fang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Ruiman Geng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Juan Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Shaohua Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| |
Collapse
|
25
|
Verbon EH, Liberman LM, Zhou J, Yin J, Pieterse CMJ, Benfey PN, Stringlis IA, de Jonge R. Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions. MOLECULAR PLANT 2023; 16:1160-1177. [PMID: 37282370 PMCID: PMC10527033 DOI: 10.1016/j.molp.2023.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 03/30/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Growth- and health-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is such a bacterium that efficiently colonizes roots, modifies the architecture of the root system to increase its size, and induces systemic resistance to make plants more resistant to pests and pathogens. Our previous work suggested that WCS417-induced phenotypes are controlled by root cell-type-specific mechanisms. However, it remains unclear how WCS417 affects these mechanisms. In this study, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. We found that the cortex and endodermis have the most differentially expressed genes, even though they are not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, and mutant analysis suggests that this downregulation facilitates WCS417-driven root architectural changes. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis of WCS417-colonized roots. Using an endodermal barrier mutant, we showed the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Comparison of the transcriptome profiles in the two epidermal cell types that are in direct contact with WCS417-trichoblasts that form root hairs and atrichoblasts that do not-implies a difference in potential for defense gene activation. While both cell types respond to WCS417, trichoblasts displayed both higher basal and WCS417-dependent activation of defense-related genes compared with atrichoblasts. This suggests that root hairs may activate root immunity, a hypothesis that is supported by differential immune responses in root hair mutants. Taken together, these results highlight the strength of cell-type-specific transcriptional profiling to uncover "masked" biological mechanisms underlying beneficial plant-microbe associations.
Collapse
Affiliation(s)
- Eline H Verbon
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Louisa M Liberman
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jiayu Zhou
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Jie Yin
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Philip N Benfey
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands; Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos str., 11855 Athens, Greece.
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands.
| |
Collapse
|
26
|
Liang X, Ma Z, Ke Y, Wang J, Wang L, Qin B, Tang C, Liu M, Xian X, Yang Y, Wang M, Zhang Y. Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection. PLANT, CELL & ENVIRONMENT 2023; 46:2222-2237. [PMID: 36929646 DOI: 10.1111/pce.14585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 06/08/2023]
Abstract
As a perennial woody plant, the rubber tree (Hevea brasiliensis) must adapt to various environmental challenges through gene expression in multiple cell types. It is still unclear how genes in this species are expressed at the cellular level and the precise mechanisms by which cells respond transcriptionally to environmental stimuli, especially in the case of pathogen infection. Here, we characterized the transcriptomes in Hevea leaves during early powdery mildew infection using single-cell RNA sequencing. We identified 10 cell types and constructed the first single-cell atlas of Hevea leaves. Distinct gene expression patterns of the cell clusters were observed under powdery mildew infection, which was especially significant in the epidermal cells. Most of the genes involved in host-pathogen interactions in epidermal cells exhibited a pattern of dramatically increased expression with increasing pseudotime. Interestingly, we found that the HbCNL2 gene, encoding a nucleotide-binding leucine-rich repeat protein, positively modulated the defence of rubber leaves against powdery mildew. Overexpression of the HbCNL2 gene triggered a typical cell death phenotype in tobacco leaves and a higher level of reactive oxygen species in the protoplasts of Hevea leaves. The HbCNL2 protein was located in the cytomembrane and nucleus, and its leucine-rich repeat domain interacted with the histidine kinase-like ATPase domain of the molecular chaperone HbHSP90 in the nucleus. Collectively, our results provide the first observation of the cellular and molecular responses of Hevea leaves to biotrophic pathogen infection and can guide the identification of disease-resistance genes in this important tree species.
Collapse
Affiliation(s)
- Xiaoyu Liang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Zhan Ma
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yuhang Ke
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Jiali Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Lifeng Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bi Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chaorong Tang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Mingyang Liu
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Xuemei Xian
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Ye Yang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Meng Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yu Zhang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| |
Collapse
|
27
|
Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 2023; 617:785-791. [PMID: 37165193 PMCID: PMC10657638 DOI: 10.1038/s41586-023-06053-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.
Collapse
Affiliation(s)
- Bruno Guillotin
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ramin Rahni
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Mohammed Ateequr Mohammed
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Sunil Kenchanmane Raju
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Carlos Ortiz Ramírez
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- UGA-LANGEBIO Cinvestav, Guanajuato, México
| | | | - Simon C Groen
- Department of Nematology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
28
|
Roth MG, Westrick NM, Baldwin TT. Fungal biotechnology: From yesterday to tomorrow. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1135263. [PMID: 37746125 PMCID: PMC10512358 DOI: 10.3389/ffunb.2023.1135263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 09/26/2023]
Abstract
Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.
Collapse
Affiliation(s)
- Mitchell G. Roth
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Nathaniel M. Westrick
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas T. Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
29
|
Depuydt T, De Rybel B, Vandepoele K. Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE 2023; 28:283-296. [PMID: 36307271 DOI: 10.1016/j.tplants.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
Collapse
Affiliation(s)
- Thomas Depuydt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium; Ghent University, Bioinformatics Institute Ghent, Ghent, Belgium.
| |
Collapse
|
30
|
Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
Collapse
Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| |
Collapse
|
31
|
Feng D, Liang Z, Wang Y, Yao J, Yuan Z, Hu G, Qu R, Xie S, Li D, Yang L, Zhao X, Ma Y, Lohmann JU, Gu X. Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips. BMC Biol 2022; 20:274. [PMID: 36482454 PMCID: PMC9733338 DOI: 10.1186/s12915-022-01473-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored. RESULTS To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus. CONCLUSIONS We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution.
Collapse
Affiliation(s)
- Dan Feng
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhe Liang
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yifan Wang
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jiaying Yao
- grid.459340.fAnnoroad Gene Technology, Beijing, 100176 China
| | - Zan Yuan
- grid.459340.fAnnoroad Gene Technology, Beijing, 100176 China
| | - Guihua Hu
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ruihong Qu
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shang Xie
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dongwei Li
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Liwen Yang
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinai Zhao
- grid.7700.00000 0001 2190 4373Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Yanfei Ma
- grid.7700.00000 0001 2190 4373Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jan U. Lohmann
- grid.7700.00000 0001 2190 4373Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Xiaofeng Gu
- grid.418873.1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
32
|
Yang Y, Chaffin TA, Ahkami AH, Blumwald E, Stewart CN. Plant synthetic biology innovations for biofuels and bioproducts. Trends Biotechnol 2022; 40:1454-1468. [PMID: 36241578 DOI: 10.1016/j.tibtech.2022.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/26/2022] [Accepted: 09/15/2022] [Indexed: 01/21/2023]
Abstract
Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. This review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.
Collapse
Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Timothy Alexander Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charles Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| |
Collapse
|
33
|
Wang FX, Shang GD, Wang JW. Towards a hierarchical gene regulatory network underlying somatic embryogenesis. TRENDS IN PLANT SCIENCE 2022; 27:1209-1217. [PMID: 35810071 DOI: 10.1016/j.tplants.2022.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
Collapse
Affiliation(s)
- Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China.
| |
Collapse
|
34
|
De-la-Cruz IM, Kariñho-Betancourt E, Núñez-Farfán J, Oyama K. Gene family evolution and natural selection signatures in Datura spp. (Solanaceae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.916762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Elucidating the diversification process of congeneric species makes it necessary to identify the factors promoting species variation and diversification. Comparative gene family analysis allows us to elucidate the evolutionary history of species by identifying common genetic/genomic mechanisms underlying species responses to biotic and abiotic environments at the genomic level. In this study, we analyzed the high-quality transcriptomes of four Datura species, D. inoxia, D. pruinosa, D. stramonium, and D. wrightii. We performed a thorough comparative gene family analysis to infer the role of selection in molecular variation, changes in protein physicochemical properties, and gain/loss of genes during their diversification processes. The results revealed common and species-specific signals of positive selection, physicochemical divergence and/or expansion of metabolic genes (e.g., transferases and oxidoreductases) associated with terpene and tropane metabolism and some resistance genes (R genes). The gene family analysis presented here is a valuable tool for understanding the genome evolution of economically and ecologically significant taxa such as the Solanaceae family.
Collapse
|
35
|
Kawa D, Brady SM. Root cell types as an interface for biotic interactions. TRENDS IN PLANT SCIENCE 2022; 27:1173-1186. [PMID: 35792025 DOI: 10.1016/j.tplants.2022.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 05/27/2023]
Abstract
Root responses to environmental stresses show a high level of cell type and developmental stage specificity. Interactions with beneficial and pathogenic organisms - including microbes and parasites - elicit a set of transcriptional responses unique to each root cell type, often dependent on their differentiation state. Localized changes to the cell wall and to the integrity of root cell types can serve as a physical barrier for a range of pests. Conversely, certain microorganisms weaken existing barriers within root cell types. Interactions with microorganisms vary between roots of different developmental origins and cellular architectures. Here we provide an overview of the molecular, architectural, and structural properties of root cell types crucial to both maintaining beneficial interactions and protecting from pathogens.
Collapse
Affiliation(s)
- Dorota Kawa
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
| |
Collapse
|
36
|
Conde D, Triozzi PM, Pereira WJ, Schmidt HW, Balmant KM, Knaack SA, Redondo-López A, Roy S, Dervinis C, Kirst M. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus. Development 2022; 149:dev200632. [PMID: 36178121 PMCID: PMC9720752 DOI: 10.1242/dev.200632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/20/2022] [Indexed: 07/25/2023]
Abstract
Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials - a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.
Collapse
Affiliation(s)
- Daniel Conde
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid 28223, Spain
| | - Paolo M. Triozzi
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Wendell J. Pereira
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Henry W. Schmidt
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kelly M. Balmant
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Sara A. Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Arturo Redondo-López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid 28223, Spain
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
- Department of Computer Sciences, University of Wisconsin, Madison, WI 53792, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53792, USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
37
|
Zhou P, Chen H, Dang J, Shi Z, Shao Y, Liu C, Fan L, Wu Q. Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. FRONTIERS IN PLANT SCIENCE 2022; 13:988594. [PMID: 36340347 PMCID: PMC9627484 DOI: 10.3389/fpls.2022.988594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
The peltate glandular trichomes (PGTs) on Nepeta tenuifolia leaves can secrete and store bioactive essential oils. ScRNA-seq is a powerful tool for uncovering heterogeneous cells and exploring the development and differentiation of specific cells. Due to leaves rich in PGTs, the young leaves were used to isolated protoplasts and successfully captured 33,254 protoplasts for sequencing purposes. After cell type annotation, all the cells were partitioned into six broad populations with 19 clusters. Cells from PGTs were identified based on the expression patterns of trichome-specific genes, monoterpene biosynthetic genes, and metabolic analysis of PGT secretions. The developmental trajectories of PGTs were delineated by pseudotime analysis. Integrative analysis of scRNA-seq data from N. tenuifolia leaves and Arabidopsis thaliana shoot revealed that PGTs were specific to N. tenuifolia. Thus, our results provide a promising basis for exploring cell development and differentiation in plants, especially glandular trichome initiation and development.
Collapse
Affiliation(s)
- Peina Zhou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Hongyu Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Jingjie Dang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Zunrui Shi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Yongfang Shao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Chanchan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| |
Collapse
|
38
|
Liu Z, Yu X, Qin A, Zhao Z, Liu Y, Sun S, Liu H, Guo C, Wu R, Yang J, Hu M, Bawa G, Sun X. Research strategies for single-cell transcriptome analysis in plant leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:27-37. [PMID: 35904970 DOI: 10.1111/tpj.15927] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The recent and continuous improvement in single-cell RNA sequencing (scRNA-seq) technology has led to its emergence as an efficient experimental approach in plant research. However, compared with single-cell research in animals and humans, the application of scRNA-seq in plant research is limited by several challenges, including cell separation, cell type annotation, cellular function analysis, and cell-cell communication networks. In addition, the unavailability of corresponding reliable and stable analysis methods and standards has resulted in the relative decentralization of plant single-cell research. Considering these shortcomings, this review summarizes the research progress in plant leaf using scRNA-seq. In addition, it describes the corresponding feasible analytical methods and associated difficulties and problems encountered in the current research. In the end, we provide a speculative overview of the development of plant single-cell transcriptome research in the future.
Collapse
Affiliation(s)
- Zhixin Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Zihao Zhao
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yumeng Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Susu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Hao Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jincheng Yang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Mengke Hu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| |
Collapse
|
39
|
Jeckel AM, Beran F, Züst T, Younkin G, Petschenka G, Pokharel P, Dreisbach D, Ganal-Vonarburg SC, Robert CAM. Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches. Front Physiol 2022; 13:1001032. [PMID: 36237530 PMCID: PMC9552321 DOI: 10.3389/fphys.2022.1001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Herbivorous insects encounter diverse plant specialized metabolites (PSMs) in their diet, that have deterrent, anti-nutritional, or toxic properties. Understanding how they cope with PSMs is crucial to understand their biology, population dynamics, and evolution. This review summarizes current and emerging cutting-edge methods that can be used to characterize the metabolic fate of PSMs, from ingestion to excretion or sequestration. It further emphasizes a workflow that enables not only to study PSM metabolism at different scales, but also to tackle and validate the genetic and biochemical mechanisms involved in PSM resistance by herbivores. This review thus aims at facilitating research on PSM-mediated plant-herbivore interactions.
Collapse
Affiliation(s)
- Adriana Moriguchi Jeckel
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Franziska Beran
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias Züst
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Gordon Younkin
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Georg Petschenka
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Prayan Pokharel
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Domenic Dreisbach
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Stephanie Christine Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Christelle Aurélie Maud Robert
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
- *Correspondence: Christelle Aurélie Maud Robert,
| |
Collapse
|
40
|
Wu J, Liang J, Lin R, Cai X, Zhang L, Guo X, Wang T, Chen H, Wang X. Investigation of Brassica and its relative genomes in the post-genomics era. HORTICULTURE RESEARCH 2022; 9:uhac182. [PMID: 36338847 PMCID: PMC9627752 DOI: 10.1093/hr/uhac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.
Collapse
Affiliation(s)
| | | | | | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xinlei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | | |
Collapse
|
41
|
Ganesh A, Shukla V, Mohapatra A, George AP, Bhukya DPN, Das KK, Kola VSR, Suresh A, Ramireddy E. Root Cap to Soil Interface: A Driving Force Toward Plant Adaptation and Development. PLANT & CELL PHYSIOLOGY 2022; 63:1038-1051. [PMID: 35662353 DOI: 10.1093/pcp/pcac078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has a specialized organ called the 'root cap'. The root cap assists the roots in penetrating the ground, absorbing water and minerals, avoiding heavy metals and regulating the rhizosphere microbiota. Furthermore, root-cap-derived auxin governs the lateral root patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aid in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphological and physiological characteristics for the root-soil interaction and their response toward various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type-enriched genes. We compiled root cap cell-type-enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor (TF) binding site enrichment. Further, the putative gene regulatory networks derived from root-cap-enriched genes and their TF regulators highlight the species-specific biological functions of root cap genes across the four plant species.
Collapse
Affiliation(s)
- Alagarasan Ganesh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vishnu Shukla
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Ankita Mohapatra
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Abin Panackal George
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Durga Prasad Naik Bhukya
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Krishna Kodappully Das
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Vijaya Sudhakara Rao Kola
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Aparna Suresh
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| | - Eswarayya Ramireddy
- Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, Andhra Pradesh 517507, India
| |
Collapse
|
42
|
Source-To-Sink Transport of Sugar and Its Role in Male Reproductive Development. Genes (Basel) 2022; 13:genes13081323. [PMID: 35893060 PMCID: PMC9329892 DOI: 10.3390/genes13081323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Sucrose is produced in leaf mesophyll cells via photosynthesis and exported to non-photosynthetic sink tissues through the phloem. The molecular basis of source-to-sink long-distance transport in cereal crop plants is of importance due to its direct influence on grain yield-pollen grains, essential for male fertility, are filled with sugary starch, and rely on long-distance sugar transport from source leaves. Here, we overview sugar partitioning via phloem transport in rice, especially where relevant for male reproductive development. Phloem loading and unloading in source leaves and sink tissues uses a combination of the symplastic, apoplastic, and/or polymer trapping pathways. The symplastic and polymer trapping pathways are passive processes, correlated with source activity and sugar gradients. In contrast, apoplastic phloem loading/unloading involves active processes and several proteins, including SUcrose Transporters (SUTs), Sugars Will Eventually be Exported Transporters (SWEETs), Invertases (INVs), and MonoSaccharide Transporters (MSTs). Numerous transcription factors combine to create a complex network, such as DNA binding with One Finger 11 (DOF11), Carbon Starved Anther (CSA), and CSA2, which regulates sugar metabolism in normal male reproductive development and in response to changes in environmental signals, such as photoperiod.
Collapse
|
43
|
Schenck CA, Busta L. Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism. PLANT MOLECULAR BIOLOGY 2022; 109:355-367. [PMID: 34816350 DOI: 10.1007/s11103-021-01220-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.
Collapse
Affiliation(s)
- Craig A Schenck
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA
| |
Collapse
|
44
|
Hartmann FSF, Udugama IA, Seibold GM, Sugiyama H, Gernaey KV. Digital models in biotechnology: Towards multi-scale integration and implementation. Biotechnol Adv 2022; 60:108015. [PMID: 35781047 DOI: 10.1016/j.biotechadv.2022.108015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022]
Abstract
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.
Collapse
Affiliation(s)
- Fabian S F Hartmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Isuru A Udugama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
| | - Gerd M Seibold
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
45
|
Backhaus AE, Lister A, Tomkins M, Adamski NM, Simmonds J, Macaulay I, Morris RJ, Haerty W, Uauy C. High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat. PLANT PHYSIOLOGY 2022; 189:1536-1552. [PMID: 35377414 PMCID: PMC9237664 DOI: 10.1093/plphys/kiac156] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/13/2022] [Indexed: 05/03/2023]
Abstract
Spikelets are the fundamental building blocks of Poaceae inflorescences, and their development and branching patterns determine the various inflorescence architectures and grain yield of grasses. In wheat (Triticum aestivum), the central spikelets produce the most and largest grains, while spikelet size gradually decreases acropetally and basipetally, giving rise to the characteristic lanceolate shape of wheat spikes. The acropetal gradient corresponds with the developmental age of spikelets; however, the basal spikelets are developed first, and the cause of their small size and rudimentary development is unclear. Here, we adapted G&T-seq, a low-input transcriptomics approach, to characterize gene expression profiles within spatial sections of individual spikes before and after the establishment of the lanceolate shape. We observed larger differences in gene expression profiles between the apical, central, and basal sections of a single spike than between any section belonging to consecutive developmental time points. We found that SHORT VEGETATIVE PHASE MADS-box transcription factors, including VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT-A2), are expressed highest in the basal section of the wheat spike and display the opposite expression gradient to flowering E-class SEPALLATA1 genes. Based on multi-year field trials and transgenic lines, we show that higher expression of VRT-A2 in the basal sections of the spike is associated with increased numbers of rudimentary basal spikelets. Our results, supported by computational modeling, suggest that the delayed transition of basal spikelets from vegetative to floral developmental programs results in the lanceolate shape of wheat spikes. This study highlights the value of spatially resolved transcriptomics to gain insights into developmental genetics pathways of grass inflorescences.
Collapse
Affiliation(s)
- Anna E Backhaus
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ashleigh Lister
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Melissa Tomkins
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | |
Collapse
|
46
|
Kleist TJ, Wudick MM. Shaping up: Recent advances in the study of plant calcium channels. Curr Opin Cell Biol 2022; 76:102080. [DOI: 10.1016/j.ceb.2022.102080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/02/2022] [Accepted: 03/13/2022] [Indexed: 12/20/2022]
|
47
|
Zhou R, Jiang F, Niu L, Song X, Yu L, Yang Y, Wu Z. Increase Crop Resilience to Heat Stress Using Omic Strategies. FRONTIERS IN PLANT SCIENCE 2022; 13:891861. [PMID: 35656008 PMCID: PMC9152541 DOI: 10.3389/fpls.2022.891861] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Varieties of various crops with high resilience are urgently needed to feed the increased population in climate change conditions. Human activities and climate change have led to frequent and strong weather fluctuation, which cause various abiotic stresses to crops. The understanding of crops' responses to abiotic stresses in different aspects including genes, RNAs, proteins, metabolites, and phenotypes can facilitate crop breeding. Using multi-omics methods, mainly genomics, transcriptomics, proteomics, metabolomics, and phenomics, to study crops' responses to abiotic stresses will generate a better, deeper, and more comprehensive understanding. More importantly, multi-omics can provide multiple layers of information on biological data to understand plant biology, which will open windows for new opportunities to improve crop resilience and tolerance. However, the opportunities and challenges coexist. Interpretation of the multidimensional data from multi-omics and translation of the data into biological meaningful context remained a challenge. More reasonable experimental designs starting from sowing seed, cultivating the plant, and collecting and extracting samples were necessary for a multi-omics study as the first step. The normalization, transformation, and scaling of single-omics data should consider the integration of multi-omics. This review reports the current study of crops at abiotic stresses in particular heat stress using omics, which will help to accelerate crop improvement to better tolerate and adapt to climate change.
Collapse
Affiliation(s)
- Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Department of Food Science, Aarhus University, Aarhus, Denmark
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lifei Niu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Lu Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuwen Yang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
48
|
Lam E, Michael TP. Wolffia, a minimalist plant and synthetic biology chassis. TRENDS IN PLANT SCIENCE 2022; 27:430-439. [PMID: 34920947 DOI: 10.1016/j.tplants.2021.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.
Collapse
Affiliation(s)
- Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
49
|
Xia K, Sun HX, Li J, Li J, Zhao Y, Chen L, Qin C, Chen R, Chen Z, Liu G, Yin R, Mu B, Wang X, Xu M, Li X, Yuan P, Qiao Y, Hao S, Wang J, Xie Q, Xu J, Liu S, Li Y, Chen A, Liu L, Yin Y, Yang H, Wang J, Gu Y, Xu X. The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Dev Cell 2022; 57:1299-1310.e4. [PMID: 35512702 DOI: 10.1016/j.devcel.2022.04.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/15/2022]
Abstract
Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biological functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single-cell location and transcriptome information for plant biology study.
Collapse
Affiliation(s)
- Keke Xia
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiming Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yu Zhao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | | | - Chao Qin
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ruiying Chen
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | | | - Guangyu Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ruilian Yin
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bangbang Mu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | | | - Mengyuan Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Xinyue Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Peisi Yuan
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yixin Qiao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Shijie Hao
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Wang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Qing Xie
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Jiangshan Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Yuxiang Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China.
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
| |
Collapse
|
50
|
Bawa G, Liu Z, Yu X, Qin A, Sun X. Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits. Int J Mol Sci 2022; 23:ijms23094497. [PMID: 35562888 PMCID: PMC9100049 DOI: 10.3390/ijms23094497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/09/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, advances in single-cell RNA sequencing (scRNA-seq) technologies have continued to change our views on biological systems by increasing the spatiotemporal resolution of our analysis to single-cell resolution. Application of scRNA-seq to plants enables the comprehensive characterization of both common and rare cell types and cell states, uncovering new cell types and revealing how cell types relate to each other spatially and developmentally. This review provides an overview of scRNA-seq methodologies, highlights the application of scRNA-seq in plant science, justifies why scRNA-seq is a master player of sequencing, and explains the role of single-cell transcriptomics technologies in environmental stress adaptation, alongside the challenges and prospects of single-cell transcriptomics. Collectively, we put forward a central role of single-cell sequencing in plant research.
Collapse
Affiliation(s)
- George Bawa
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (G.B.); (Z.L.); (X.Y.); (A.Q.)
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Zhixin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (G.B.); (Z.L.); (X.Y.); (A.Q.)
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Xiaole Yu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (G.B.); (Z.L.); (X.Y.); (A.Q.)
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Aizhi Qin
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (G.B.); (Z.L.); (X.Y.); (A.Q.)
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (G.B.); (Z.L.); (X.Y.); (A.Q.)
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Correspondence:
| |
Collapse
|