Application of Single-cell RNA Sequencing in the Study of Plant Tissues Development
MIAO Long1, WANG Wen-Hui1, HE Gen-Hua1, LI Jia-Jia1, GAO Hui-Hui1, WANG Xiao-Bo1*, QIU Li-Juan2*
1 College of Agriculture, Anhui Agricultural University, Hefei 230036, China; 2 Institute of Crop Science, Chinese Academy of Agricultural Sciences / The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) /Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Beijing 100081, China
Abstract：Single-cell RNA sequencing (scRNA-seq) is an advanced technique for characterizing the expression profiles of heterogeneous cells in the same tissue, and plays a crucial role in the study of cell development trajectory. Compared with animal cells, the application of scRNA-seq in plants is still in its infancy, and has been gradually applied in Arabidopsis, rice (Oryza sativa) and maize (Zea mays). This review summarized the common techniques of scRNA-seq and their applications in the research of tissue development mechanism, cells dynamic development trajectory, direction of cells differentiation and interaction. Additionally, this article analyzed the problems, challenges and development prospects of the application of scRNA-seq in plants, hoping to provide a theoretical basis for explore the mechanism of plant tissue development.
[1] 陈柳宏, 赵春雷, 王希, 等 . 2022. 单细胞转录组测序技术及其在植物研究中的应用[J]. 中国农学通报, 38(03): 87-93. (Chen L H, Zhan C L, Wang X, et al.2022. Single- cell transcriptome sequencing techniques and their appli‐ cations in plant research[J]. Chinese Agricultural Scienc‐ es Bulletin, 38(03): 87-93. [2] 李益, 孙超 . 2021. 植物单细胞转录组测序研究进展[J]. 生物技术通 , 37(1): 60-66. (Li Y, Sun C.2021. Research progress in single-cell RNA-seq of plant[J]. Biotechnol‐ ogy Bulletin, 37(1): 60-66. [3] 杨佳凤, 陈鹏璐, 龚熹, 等 . 2021. 单细胞转录组测序技术在细胞分类中的应用[J]. 中国细胞生物学学报 , 43(2): 476-483. (Yang J F, Chen P L, Gong X, et al.2021. Ap‐ plication of single-cell transcriptome sequencing tech‐ niques in cell classification[J]. Chinese Journal of Cell Biology, 43(2): 476-483. [4] Bezrutczyk M, Zöllner N R, Kruse C P S, et al.2021. Evi‐ dence for phloem loading via the abaxial bundle sheath cells in maize leaves[J]. Plant Cell, 33(3): 531-547. [5] Brennecke P, Anders S, Kim JK, et al.2013. Accounting for technical noise in single-cell RNA-seq experiments[J]. Nature Methods, 10(11): 1093-1095. [6] Chen H, Yin X, Guo L, et al.2021a. PlantscRNAdb: A data‐ base for plant single-cell RNA analysis[J]. Molecular Plant, 14(6): 855-857. [7] Chen Y, Tong S, Jiang Y, et al.2021b. Transcriptional land‐ scape of highly lignified poplar stems at single-cell reso‐ lution[J]. Genome Biology, 22(1): 319. [8] Conde D, Triozzi P M, Pereira W J, et al.2022. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus[J]. Development, 149(21): dev200632. [9] Denyer T, Ma X, Klesen S, et al.2019. Spatiotemporal devel‐ opmental trajectories in the Arabidopsis root revealed us‐ ing high-throughput Single-cell RNA Sequencing[J]. De‐ velopmental Cell, 48(6): 840-852.e5. [10] Eckardt N A.2021. Sweeter than sweet: a single-cell leaf vas‐culature transcriptome atlas[J]. Plant Cell, 33(3): 445-446. [11] Efroni I, Birnbaum K D.2016. The potential of single-cell pro‐filing in plants[J]. Genome Biology, 5(17): 65. [12] Efroni I, Ip P L, Nawy T, et al.2015. Quantification of cell identity from single-cell gene expression profiles[J]. Ge‐nome Biology, 16(1): 9. [13] Efroni I, Mello A, Nawy T, et al.2016. Root regeneration trig‐ gers an embryo-like sequence guided by hormonal inter‐ actions[J]. Cell, 165(7): 1721-1733. [14] Gala H P, Lanctot A, Jean-Baptiste K, et al.2021. A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana[J]. Plant Cell, 33(7): 2197-2220. [15] Geirsdottir L, David E, Keren-Shaul H, et al.2019. Cross-spe‐ cies single-cell analysis reveals divergence of the pri‐ mate microglia program[J]. Cell, 179(7): 1609-1622. e16. [16] Guo X, Liang J, Lin R, et al.2022. Single-cell transcriptome reveals differentiation between adaxial and abaxial me‐sophyll cells in Brassica rapa[J]. Plant Biotechnology journal, 20(12): 2233-2235. [17] Haber A L, Biton M, Rogel N, et al.2017. A single-cell survey of the small intestinal epithelium[J]. Nature, 551(7680): 333-339. [18] Habib N, Avraham-Davidi I, Basu A, et al.2017. Massively parallel single-nucleus RNA-seq with Dronc-seq[J]. Na‐ ture Methods, 14(10): 955-958. [19] Hain D, Gallego-Flores T, Klinkmann M, et al.2022. Molecu‐ lar diversity and evolution of neuron types in the amni‐ ote brain[J]. Science, 377(6610): eabp8202. [20] Hashimshony T, Wagner F, Sher N, et al.2012. CEL-Seq: Sin‐ gle-cell RNA-seq by multiplexed linear amplification[J]. Cell Reportsorts, 2(3): 666-673. [21] Hou Z, Liu Y, Zhang M, et al.2021. High-throughput single- cell transcriptomics reveals the female germline differen‐tiation trajectory in Arabidopsis thaliana[J]. Communica‐tions Biology, 4(1): 1149. [22] Jean-Baptiste K, McFaline-Figueroa J L, Alexandre C M, et al.2019. Dynamics of gene expression in single root cells of Arabidopsis thaliana[J]. Plant Cell, 31(5): 993-1011. [23] Kim J Y, Symeonidi E, Pang T Y, et al.2021. Distinct identi‐ ties of leaf phloem cells revealed by single cell transcrip‐ tomics[J]. Plant Cell, 33(3): 511-530. [24] Klein A M, Mazutis L, Akartuna I, et al.2015. Droplet barcod‐ ing for single-cell transcriptomics applied to embryonic stem cells[J]. Cell, 161(5): 1187-1201. [25] Li H, Dai X, Huang X, et al.2021. Single-cell RNA sequenc‐ ing reveals a high-resolution cell atlas of xylem in Popu- lus[J]. Journal of Integrative Plant Biology, 63(11): 1906-1921. [26] Li H, Wang X, Wang Y, et al.2022. Cross-species single-cell transcriptomic analysis reveals divergence of cell com‐ position and functions in mammalian ileum epithelium[J]. Cell Regeneration, 11(1): 19. [27] Liu H, Hu D, Du P, et al.2021a. Single-cell RNA-seq de‐ scribes the transcriptome landscape and identifies criti‐ cal transcription factors in the leaf blade of the allotetra‐ploid peanut (Arachis hypogaea L.)[J]. Plant Biotechnol‐ogy journal, 19(11): 2261-2276. [28] Liu Q, Liang Z, Feng D, et al.2021b. Transcriptional land‐ scape of rice roots at the single-cell resolution[J]. Molec‐ ular Plant, 14(3): 384-394. [29] Liu T, Wu H, Wu S, et al.2017. Single-cell sequencing tech‐ nologies for cardiac stem cell studies[J]. Stem Cells and Development, 26(21): 1540-1551. [30] Liu Y, Li C, Han Y, et al.2022. Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the peg[J]. Plant Biotechnology Journal, 20(9): 1648-1650. [31] Liu Z, Zhou Y, Guo J, et al.2020. Global dynamic molecular profiling of stomatal lineage cell development by Single- cell RNA sequencing[J]. Molecular Plant, 13(8): 1178-1193. [32] Mo Y, Jiao Y.2022. Advances and applications of single-cell omics technologies in plant research[J]. Plant Journal, 110(6): 1551-1563. [33] Nelms B, Walbot V.2019. Defining the developmental pro‐ gram leading to meiosis in maize[J]. Science, 364(6435): 52-56. [34] Omary M, Gil-Yarom N, Yahav C, et al.2022. A conserved su‐ perlocus regulates above- and belowground root initia‐ tion[J]. Science, 375(6584): eabf4368. [35] Park J, Shrestha R, Qiu C X, et al.2018. Single-cell transcrip‐ tomics of the mouse kidney reveals potential cellular tar‐ gets of kidney disease[J]. Science, 360(6390): 758-763. [36] Qin Y, Sun M, Li W, et al.2022. Single-cell RNA-seq reveals fate determination control of an individual fibre cell ini‐tiation in cotton (Gossypium hirsutum)[J]. Plant Biotech‐nology Journal, 20(12): 2372-2388. [37] Ramskold D, Luo S, Wang Y C, et al.2012. Full-length mRNA-seq from single-cell levels of rna and individual circulating tumor cells[J]. Nature Biotechnology, 30(8): 777-782. [38] Ransick A, Lindström N O, Liu J, et al.2019. Single-cell pro‐ filing reveals sex, lineage, and regional diversity in the mouse kidney[J]. Developmental Cell, 51(3): 399-413. e7. [39] Roszak P, Heo J O, Blob B, et al.2021. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization[J]. Science, 374(6575): eaba5531. [40] Ryu K H, Huang L, Kang H M, et al.2019. Single-cell RNA sequencing resolves molecular relationships among indi‐ vidual plant cells[J]. Plant Physiology, 179(4): 1444-1456. [41] Satija R, Farrell J A, Gennert D, et al.2015. Spatial recon‐ struction of single-cell gene expression data[J]. Nature Biotechnology, 33(5): 495-502. [42] Satterlee J W, Strable J, Scanlon M J.2020. Plant stem-cell or‐ ganization and differentiation at single-cell resolution[J]. Proceedings of the National Academy of Sciences of the USA, 117(52): 33689-33699. [43] Schmidt A, Wuest S E, Vijverberg K, et al.2011. Transcrip‐ tome analysis of the arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development[J]. PLoS Biology, 9(9): e1001155. [44] Shahan R, Hsu C W, Nolan T M, et al.2022. A single-cell ara‐ bidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants[J]. Developmental Cell, 57(4): 543-560.e9. [45] Shaw R, Tian X,Xu J.2021. Single-cell transcriptome analysis in plants: Advances and challenges[J]. Molecu‐ lar Plant, 14(1): 115-126. [46] Shulse C N, Cole B J, Ciobanu D, et al.2019. High-through‐ put single-cell transcriptome profiling of plant cell types[J]. Cell Reports, 27(7): 2241-2247.e4. [47] Soumillon M, Cacchiarelli D, Semrau S, et al.2014. Charac‐ terization of directed differentiation by high-throughput single-cell RNA-Seq[J]. bioRxiv, DOI:10.1101/003236. [48] Tao S, Liu P, Shi Y, et al.2022. Single-cell transcriptome and network analyses unveil key transcription factors regu‐ lating mesophyll cell development in maize[J]. Genes, 13(2): 374. [49] Trapnell C, Cacchiarelli D, Grimsby J, et al.2014. The dynam‐ ics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells[J]. Nature Bio‐ technology, 32(4): 381-386. [50] Treutlein B, Brownfield D G, Wu A R, et al.2014. Recon‐ structing lineage hierarchies of the distal lung epitheli‐ um using single-cell RNA-seq[J]. Nature, 509(7500): 371-375. [51] Turco G M, Rodriguez-Medina J, Siebert S, et al.2019. Mo‐ lecular mechanisms driving switch behavior in xylem cell differentiation[J]. Cell Reports, 28(2): 342-351.e4. [52] Wang J, Wang Y, Lü T, et al.2022a. An efficient and universal protoplast isolation protocol suitable for transient gene expression analysis and single-cell RNA sequencing[J]. International Journal of Molecular Sciences, 23(7): 3419. [53] Wang Q, Wu Y, Peng A, et al.2022b. Single-cell transcrip‐ tome atlas reveals developmental trajectories and a nov‐ el metabolic pathway of catechin esters in tea leaves[J]. Plant Biotechnology Journal, 20(11): 2089-2106. [54] Wang Y, Huan Q, Li K, et al.2021. Single-cell transcriptome atlas of the leaf and root of rice seedlings[J]. Journal of Genetics and Genomics, 48(10): 881-898. [55] Wang Z, Gerstein M,Snyder M.2009. RNA-seq: A revo‐ lutionary tool for transcriptomics[J]. Nature Reviews Genetics, 10(1): 57-63. [56] Xu X, Crow M, Rice B R, et al.2021. Single-cell RNA se‐ quencing of developing maize ears facilitates functional analysis and trait candidate gene discovery[J]. Develop‐ mental Cell, 56(4): 557-568.e6. [57] Yu G, Wang LG, Han Y, et al.2012. clusterProfiler: An R package for comparing biological themes among gene clusters[J]. OMICS-A Journal of Integrative Biology, 16(5): 284-287. [58] Zhang T Q, Chen Y,Wang J W.2021a. A single-cell analy‐sis of the Arabidopsis vegetative shoot apex[J]. Develop‐mental Cell, 56(7): 1056-1074.e8. [59] Zhang T Q, Chen Y, Liu Y, et al.2021b. Single-cell transcrip‐ tome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root[J]. Nature Communications, 12(1): 2053. [60] Zhang T Q, Xu Z G, Shang G D, et al.2019. A Single-cell RNA sequencing profiles the developmental landscape of Arabidopsis root[J]. Molecular Plant, 12(5): 648-660. [61] Zhao H, Guo M, Yan M, et al.2020. Comparative expression profiling reveals genes involved in megasporogenesis[J]. Plant Physiology, 182(4): 2006-2024. [62] Zhao L, He J, Cai H, et al.2014. Comparative expression pro‐filing reveals gene functions in female meiosis and ga‐metophyte development in Arabidopsis[J]. Plant Journal, 80(4): 615-628. [63] Zheng G X, Terry J M, Belgrader P, et al.2017. Massively par‐ allel digital transcriptional profiling of single cells[J]. Nature Communications, 8: 14049. [64] Zong J, Wang L, Zhu L, et al.2022. A rice single cell transcrip‐ tomic atlas defines the developmental trajectories of rice floret and inflorescence meristems[J]. New Phytologist, 234(2): 494-512.
