| 1,335 | 0 | 202 |
| 下载次数 | 被引频次 | 阅读次数 |
综述了植物单细胞测序技术的研究概况和应用进展，总结了单细胞测序的主要技术和测序方法，介绍了其在构建植物单细胞图谱中的应用现状，重点分析了单细胞测序技术在植物学相关研究中的应用现状，包括揭示细胞身份和变化轨迹、发掘及鉴定关键调控基因、分析基因调控网络、解析植物生殖系谱发育过程，阐释了植物适应环境的机制和活性物质的合成途径，探讨了植物单细胞测序技术存在的问题，并对其发展趋势进行了展望，以期为单细胞测序技术应用于植物科学研究提供参考。
Abstract：This paper provides a comprehensive overview of the research and application of single cell sequencing technology in plant. It summarizes the main technologies and sequencing methods, and introduces its applications in constructing plant single cell map. It emphatically expounds the application of single cell sequencing technology in plant research, including the identification of cell types and their change trajectory, discovery and characterization of key regulatory genes, analysis of gene regulatory network, elucidation of the development process of plant reproductive line and exploration of the mechanism of plant adaptation to environment and the synthesis of active substances in cell. The paper also discusses the existing problems in plant single cell sequencing technology and provides a prospective outlook on its future development direction. This aim is to provide valuable insights for the application of single cell sequencing technology in plant science research.
[1] LI X, LI L, YAN J B. Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize[J]. Nature Communications, 2015, 6:6648.
[2] ZIEGENHAIN C, VIETH B, PAREKH S, et al. Comparative analysis of single-cell RNA sequencing methods[J]. Molecular Cell, 2017, 65(4):631-643.
[3] RAMSK?LD D, LUO S J, WANG Y C, et al. Fulllength mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells[J]. Nature Biotechnology, 2012, 30(8):777-782.
[4] PICELLI S, BJ?RKLUND?K, FARIDANI O R, et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells[J]. Nature Methods, 2013, 10(11):1096-1098.
[5] HASHIMSHONY T, WAGNER F, SHER N, et al.CEL-seq:single-cell RNA-seq by multiplexed linear amplification[J]. Cell Reports, 2012, 2(3):666-673.
[6] HASHIMSHONY T, SENDEROVICH N, AVITAL G,et al. CEL-Seq2:sensitive highly-multiplexed singlecell RNA-Seq[J]. Genome Biology, 2016, 17:77.
[7] JAITIN D A, KENIGSBERG E, KEREN-SHAUL H, et al. Massively parallel single-cell RNA-seq for markerfree decomposition of tissues into cell types[J]. Science, 2014, 343(6172):776-779.
[8] GIERAHN T M, WADSWORTH M H 2nd, HUGHES T K,et al. Seq-Well:portable, low-cost RNA sequencing of single cells at high throughput[J]. Nature Methods, 2017, 14(4):395-398.
[9] HAN X P, WANG R Y, ZHOU Y C, et al. Mapping the mouse cell atlas by microwell-seq[J]. Cell, 2018,173(5):1307.
[10]李扬，谢美娟，陈小强，等.植物单细胞分离与转录组学分析研究进展[J].分子植物育种，2021, 19(7):2236-2242.LI Y, XIE M J, CHEN X Q, et al. Research progress on single-cell isolation and transcriptomic analysis in plant[J]. Molecular Plant Breeding, 2021, 19(7):2236-2242.
[11] HABIB N, AVRAHAM-DAVIDI I, BASU A, et al.Massively parallel single-nucleus RNA-seq with DroNcseq[J]. Nature Methods, 2017, 14(10):955-958.
[12] FARMER A, THIBIVILLIERS S, RYU K H, et al.Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level[J]. Molecular Plant, 2021, 14(3):372-383.
[13] KAUR H, JHA P, OCHATT S J, et al. Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research:recent advances and future opportunities[J]. Critical Reviews in Biotechnology,2024, 44(2):202-217.
[14] TELENIUS H, CARTER N P, BEBB C E, et al.Degenerate oligonucleotide-primed PCR:general amplification of target DNA by a single degenerate primer[J].Genomics, 1992, 13(3):718-725.
[15] ZHANG L, CUI X, SCHMITT K, et al. Whole genome amplification from a single cell:implications for genetic analysis[J]. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89(13):5847-5851.
[16] LIZARDI P M, HUANG X, ZHU Z, et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification[J]. Nature Genetics, 1998,19(3):225-232.
[17] ZONG C H, LU S J, CHAPMAN A R, et al. Genomewide detection of single-nucleotide and copy-number variations of a single human cell[J]. Science, 2012,338(6114):1622-1626.
[18] CHEN C Y, XING D, TAN L Z, et al. Single-cell whole-genome analyses by linear amplification via transposon insertion(LIANTI)[J]. Science, 2017, 356(6334):189-194.
[19] TAN L Z, XING D, CHANG C H, et al. Threedimensional genome structures of single diploid human cells[J]. Science, 2018, 361(6405):924-928.
[20] YIN Y, JIANG Y, LAM K W G, et al. Highthroughput single-cell sequencing with linear amplification[J]. Molecular Cell, 2019, 76(4):676-690.
[21] LI X, MENG D X, CHEN S J, et al. Single nucleus sequencing reveals spermatid chromosome fragmentation as a possible cause of maize haploid induction[J].Nature Communications, 2017, 8(1):991.
[22] SHI D Q, WU J, TANG H B, et al. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants[J]. Genome Research, 2019, 29(11):1889-1899.
[23] YUAN Y X, LEE H, HU H F, et al. Single-cell genomic analysis in plants[J]. Genes, 2018, 9(1):50.
[24] ROSZAK P, HEO J O, BLOB B, et al. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization[J]. Science, 2021, 374(6575):5531.
[25] NELMS B, WALBOT V. Defining the developmental program leading to meiosis in maize[J]. Science,2019, 364(6435):52-56.
[26] MACOSKO E Z, BASU A, SATIJA R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets[J]. Cell, 2015, 161(5):1202-1214.
[27] BRIGGS J A, WEINREB C, WAGNER D E, et al. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution[J]. Science, 2018, 360(6392):5780.
[28] VALIHRACH L, ANDROVIC P, KUBISTA M. Platforms for single-cell collection and analysis[J]. International Journal of Molecular Sciences, 2018, 19(3):807.
[29] XIA K K, SUN H X, LI J, et al. The single-cell stereoseq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves[J]. Developmental Cell, 2022, 57(10):1299-1310.
[30] KOU S Y, GU Q Y, DUAN L, et al. Genome-wide bisulphite sequencing uncovered the contribution of DNA methylation to rice short-term drought memory formation[J]. Journal of Plant Growth Regulation, 2022,41(7):2903-2917.
[31] ZHOU S L, JIANG W, ZHAO Y, et al. Single-cell three-dimensional genome structures of rice gametes and unicellular zygotes[J]. Nature Plants, 2019, 5(8):795-800.
[32]祝涛. UMI-ATAC-seq数据分析及植物单细胞ATACseq技术的探索[D].武汉：华中农业大学，2021.ZHU T. UMI-ATAC-seq data analysis and exploration of plant single cell ATAC-seq technology[D]. Wuhan:Huazhong Agricultural University, 2021.
[33] ZHANG S, AFANASSIEV A, GREENSTREET L, et al. Optimal transport analysis reveals trajectories in steady-state systems[J]. PLoS Computational Biology,2021, 17(12):e1009466.
[34] XI Y P, PARK S R, KIM D H, et al. Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana[J]. The Plant Journal, 2020, 103(4):1490-1502.
[35] OUYANG W Z, LUAN S P, XIANG X, et al. Profiling plant histone modification at single-cell resolution using snCUT&Tag[J]. Plant Biotechnology Journal, 2022, 20(3):420-422.
[36] RHEE S Y, BIRNBAUM K D, EHRHARDT D W.Towards building a plant cell atlas[J]. Trends in Plant Science, 2019, 24(4):303-310.
[37] HE Z H, LUO Y T, ZHOU X K, et al. scPlantDB:a comprehensive database for exploring cell types and markers of plant cell atlases[J]. Nucleic Acids Research, 2024, 52(D1):D1629-D1638.
[38] ZHANG T Q, XU Z G, SHANG G D, et al. A singlecell RNA sequencing profiles the developmental landscape of Arabidopsis root[J]. Molecular Plant, 2019, 12(5):648-660.
[39] ZHANG T Q, CHEN Y, WANG J W. A single-cell analysis of the Arabidopsis vegetative shoot apex[J].Developmental Cell, 2021, 56(7):1056-1074.
[40] LONG Y P, LIU Z J, JIA J B, et al. FlsnRNA-seq:protoplasting-free full-length single-nucleus RNA profiling in plants[J]. Genome Biology, 2021, 22(1):66.
[41] ZHAI N, XU L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration[J]. Nature Plants, 2021, 7(11):1453-1460.
[42] SUNAGA-FRANZE D Y, MUINO J M, BRAEUNING C,et al. Single-nucleus RNA sequencing of plant tissues using a nanowell-based system[J]. The Plant Journal, 2021, 108(3):859-869.
[43] LI H, DAI X R, HUANG X, et al. Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus[J]. Journal of Integrative Plant Biology,2021, 63(11):1906-1921.
[44] CONDE D, TRIOZZI P M, PEREIRA W J, et al.Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus[J]. Development, 2022, 149(21):200632.
[45] KANG M, CHOI Y, KIM H, et al. Single-cell RNAsequencing of Nicotiana attenuata Corolla cells reveals the biosynthetic pathway of a floral scent[J]. New Phytologist, 2022, 234(2):527-544.
[46] ZHANG S T, ZHU C, ZHANG X Y, et al. Single-cell RNA sequencing analysis of the embryogenic callus clarifies the spatiotemporal developmental trajectories of the early somatic embryo in Dimocarpus longan[J]. The Plant Journal, 2023, 115(5):1277-1297.
[47] ZHOU P N, CHEN H Y, DANG J J, et al. Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes[J]. Frontiers in Plant Science, 2022, 13:988594.
[48] SONG J J, FAN B J, SHAO X D, et al. Single-cell transcriptome sequencing atlas of cassava tuberous root[J]. Frontiers in Plant Science, 2023, 13:1053669.
[49] SUN S J, SHEN X F, LI Y, et al. Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism[J]. Nature Plants, 2023, 9(1):179-190.
[50] SUN Y, HAN Y F, SHENG K, et al. Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii[J]. Molecular Plant, 2023,16(4):694-708.
[51] LIU H, HU D X, DU P X, et al. Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut(Arachis hypogaea L.)[J]. Plant Biotechnology Journal, 2021, 19(11):2261-2276.
[52] D’AGOSTINO L W, YONG-VILLALOBOS L, HERRERA-ESTRELLA L, et al. Development of high-quality nuclei isolation to study plant root-microbe interaction for single-nuclei transcriptomic sequencing in soybean[J]. Plants, 2023, 12(13):2466.
[53] WANG Y, HUAN Q, LI K, et al. Single-cell transcriptome atlas of the leaf and root of rice seedlings[J]. Journal of Genetics and Genomics, 2021, 48(10):881-898.
[54] ZHANG T Q, CHEN Y, LIU Y, et al. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root[J].Nature Communications, 2021, 12(1):2053.
[55] ZONG J, WANG L, ZHU L, et al. A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems[J]. New Phytologist, 2022, 234(2):494-512.
[56] TAO S T, LIU P, SHI Y N, et al. Single-cell transcriptome and network analyses unveil key transcription factors regulating mesophyll cell development in maize[J].Genes, 2022, 13(2):374.
[57] LI X H, ZHANG X B, GAO S, et al. Single-cell RNA sequencing reveals the landscape of maize root tips and assists in identification of cell type-specific nitrateresponse genes[J]. The Crop Journal, 2022, 10(6):1589-1600.
[58] XU X S, CROW M, RICE B R, et al. Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery[J].Developmental Cell, 2021, 56(4):557-568.
[59] SATTERLEE J W, STRABLE J, SCANLON M J. Plant stem-cell organization and differentiation at single-cell resolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(52):33689-33699.
[60] CHENG Z C, MU C H, LI X Y, et al. Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo(Phyllostachys edulis)[J]. Horticulture Research, 2023, 10(8):122.
[61] CHEN H H, HU Y Y, LI P P, et al. Single-cell transcriptome sequencing revealing the difference in photosynthesis and carbohydrate metabolism between epidermal cells and non-epidermal cells of Gracilariopsis lemaneiformis(Rhodophyta)[J]. Frontiers in Plant Science,2022, 13:968158.
[62] GUO X L, LIANG J L, LIN R M, et al. Single-cell transcriptome reveals differentiation between adaxial and abaxial mesophyll cells in Brassica rapa[J]. Plant Biotechnology Journal, 2022, 20(12):2233-2235.
[63] DREISSIG S, FUCHS J, HIMMELBACH A, et al.Sequencing of single pollen nuclei reveals meiotic recombination events at megabase resolution and circumvents segregation distortion caused by postmeiotic processes[J]. Frontiers in Plant Science, 2017, 8:1620.
[64] GALA H P, LANCTOT A, JEAN-BAPTISTE K, et al.A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana[J]. The Plant Cell, 2021, 33(7):2197-2220.
[65] LIU Z X, ZHOU Y P, GUO J G, et al. Global dynamic molecular profiling of stomatal lineage cell development by single-cell RNA sequencing[J]. Molecular Plant,2020, 13(8):1178-1193.
[66] RYU K H, HUANG L, KANG H M, et al. Single-cell RNA sequencing resolves molecular relationships among individual plant cells[J]. Plant Physiology, 2019, 179(4):1444-1456.
[67] WENDRICH J R, YANG B J, VANDAMME N, et al.Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions[J]. Science,2020, 370(6518):4970.
[68] DENYER T, MA X L, KLESEN S, et al. Spatiotemporal developmental trajectories in the Arabidopsis root revealed using high-throughput single-cell RNA sequencing[J]. Developmental Cell, 2019, 48(6):840-852.
[69] SHAHAN R, HSU C W, NOLAN T M, et al. A singlecell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants[J]. Developmental Cell, 2022, 57(4):543-560.
[70] SUN G L, XIA M Z, LI J P, et al. The maize singlenucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata[J]. The Plant Cell, 2022, 34(5):1890-1911.
[71] LI R H, WANG Z F, WANG J W, et al. Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees[J]. Plant Communications, 2023, 4(5):100665.
[72] LIU Q, LIANG Z, FENG D, et al. Transcriptional landscape of rice roots at the single-cell resolution[J].Molecular Plant, 2021, 14(3):384-394.
[73] LIU Z X, WANG J J, ZHOU Y P, et al. Identification of novel regulators required for early development of vein pattern in the cotyledons by single-cell RNAsequencing[J]. The Plant Journal, 2022, 110(1):7-22.
[74] XIE Y J, JIANG S F, LI L L, et al. Single-cell RNA sequencing efficiently predicts transcription factor targets in plants[J]. Frontiers in Plant Science, 2020,11:603302.
[75] SHULSE C N, COLE B J, CIOBANU D, et al. Highthroughput single-cell transcriptome profiling of plant cell types[J]. Cell Reports, 2019, 27(7):2241-2247.
[76] JEAN-BAPTISTE K, MCFALINE-FIGUEROA J L,ALEXANDRE C M, et al. Dynamics of gene expression in single root cells of Arabidopsis thaliana[J]. The Plant Cell, 2019, 31(5):993-1011.
[77] LIU W, ZHANG Y Y, FANG X, et al. Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses[J]. Plant Communications,2022, 3(4):100306.
[78] ZHANG H S, YANG H L, HU D S, et al. Single-cell RNA sequencing of meiocytes and microspores reveals the involvement of the Rf4 gene in redox homeostasis of CMS-C maize[J]. The Crop Journal, 2021, 9(6):1237-1247.
[79] LIU A, BERGMANN D C. How to build a crop plant:defining the cis-regulatory landscape of maize[J]. Cell,2021, 184(11):2804-2806.
基本信息:
DOI：10.16445/j.cnki.1000-2340.20241031.004
中图分类号:Q943.2
引用信息:
[1]王梦迪,陈晓龙,杨超臣等.植物单细胞测序与应用研究进展[J].河南农业大学学报,2025,59(04):569-579.DOI:10.16445/j.cnki.1000-2340.20241031.004.
基金信息:
国家自然科学基金项目(32171835);国家自然科学基金青年科学基金项目(32000267); 河南省博士后科研项目(202103078)