单细胞转录组测序技术及其在植物中的应用

doi:10.16420/j.issn.0513-353x.2022-0645

摘要/Abstract

摘要：

近年来发展起来的基于高通量测序技术的高分辨率单细胞转录组测序技术,能够在单细胞水平解析植物组织的异质性,鉴定组织中的不同细胞类型,构建不同细胞类型的连续分化轨迹及其转录调控网络,并能够寻找组织中的稀有细胞类型,深入解析组织发育的分子机制。为探究单细胞转录组测序技术在植物中的应用,本文中对单细胞转录组测序技术的发展及其在植物中的应用进行了综述。首先,介绍了单细胞转录组测序技术的发展进程;其次,分析其在鉴定植物组织不同细胞类型、筛选不同细胞类型特异表达标记基因及解析植物组织发育过程的连续分化轨迹及其转录调控网络的应用中所取得的进展;最后,总结单细胞转录组测序技术在植物应用中存在的挑战及未来的研究方向。以期为单细胞转录组测序技术在更多植物物种上得以应用提供参考。

关键词: 单细胞RNA测序, 植物组织, 细胞异质性, 标记基因, 拟时分析

Abstract:

High-resolution single-cell RNA sequencing（scRNA-seq）technology based on high- throughput sequencing technology has been developed recently to resolve the heterogeneity of plant tissues at the single-cell level,identify distinct cell types in single tissue,and construct continuous cell differentiation trajectories and the transcriptional regulatory networks,in addition,it can search for rare cell types in tissues,thus deeply analyze molecular mechanisms of tissue development. To explore the application of scRNA-seq technology in plants,this paper reviews the progress of scRNA-seq technology and its application in plants. Firstly,the development course of scRNA-seq technology was overviewed; subsequently,we analyzed the progress of scRNA-seq technology in the identification of different plant tissue cell types,screening of specific expression marker genes for different cell types,and analyzing the continuous differentiation trajectories and transcriptional regulatory networks during the development of different plant tissues;finally,we summarized the challenges and future research directions of the

scRNA-seq technology applicating in plants,and aims to provide reference for the application of scRNA-seq technology in more plant species in the future.

Key words: single-cell RNA sequencing, plant tissue, cellular heterogeneity, marker gene, pseudo-timeline analysis

中图分类号:

Q813

张舒婷, 张雪莹, 朱晨, 李卓蕴, 傅卓然, 张梓浩, 赖钟雄, 林玉玲. 单细胞转录组测序技术及其在植物中的应用[J]. 园艺学报, 2022, 49(10): 2163-2173.

ZHANG Shuting, ZHANG Xueying, ZHU Chen, LI Zhuoyun, FU Zhuoran, ZHANG Zihao, LAI Zhongxiong, LIN Yuling. Single Cell Transcriptome Sequencing Technology and Its Application in Plants[J]. Acta Horticulturae Sinica, 2022, 49(10): 2163-2173.

图/表 2

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物种 Species	组织类型 Organization type	细胞类型 Cell type	标记基因 Marker gene	测序方法/平台 Sequencing method/platform	参考文献 Reference
拟南芥 Arabidopsis thaliana	静止中心及中柱细胞 Quiescent center & Stele cell	静止中心及中柱细胞 Quiescent center,stele cell	WOX5,WOL	荧光标记 Fluorescent mark	Efroni et al.,2015
	根 Root	中柱、静止中心、小柱、表皮/侧根冠及基本组织等 Stele,quiescent center,columella,epidermis/ lateral root cap,ground tissue,etc	WOX5,TOM7,WIP4	SMART-seq2	Efroni et al.,2016
		根毛、内皮层、木质部及韧皮部等 Roothair,endodermis,xylem,phloem,etc	COBL9,SCR,MYB46,APL,SUC2	10x Genomics	Denyer et al.,2019;Jean-Baptiste et al.,2019;Ryu et al.,2019;Zhang et al.,2019
	木质部 Xylem	小柱、皮层、内皮层、原木质部及韧皮部等 Columella,cortex,endodermis,protoxylem,phloem,etc	VND7	Drop-seq	Turco et al.,2019
	气孔 Stoma	表皮、早期分生组织细胞、保卫细胞及表皮扁平细胞等Epidermis,early-stage meristemoid cell,guard cell,pavement cell,etc	MUTE,EPF2,BASL,RBCS,IQD5	10x Genomics	Liu et al.,2020
	茎尖 Shoot apex	叶肉、表皮、茎分生细胞、增殖细胞、韧皮部、木质部、保卫及伴侣细胞等 Mesophyll,epidermis,shoot meristematic cell,proliferating cell,phloem,xylem,guard cell,companion cell,etc	CRR23,CDKB2;1,ATML1,STM,PDF1, SMXL5,PXY,EPF1,PP2-A1	10x Genomics	Zhang et al.,2021
	胚乳 Endosperm	珠孔胚乳、外周胚乳及合点胚乳等 Micropylar endosperm,peripheral endosperm chalazal endosperm,etc	AT2G44240, AT5G10440	snRNA-seq	Picard et al.,2021
	愈伤组织 Callus	表皮、侧根冠、静止中心及维管细胞等 Epidermis-like cell,lateral-root-cap-like cell,quiescent center-like cell,vascular-initial-like cell,etc	PLT1,SCR,WOX5,TMO5,WOX11	BD Rhapsody system	Zhai & Xu,2021
拟南芥 Arabidopsis thaliana	叶脉 Vein	维管束鞘、叶肉、保卫细胞、韧皮薄壁组织、表皮、木质部薄壁组织及伴细胞等 Bundle sheath,mesophyll cell,guard cell,phloem parenchyma,epidermis,xylem parenchyma,companion cell,etc	CDF5,RGA	10x Genomics	Liu et al.,2022
水稻 Oryza sativa	叶片 Leaf	叶肉、薄壁细胞、表皮、泡状细胞和原基细胞等 Mesophyll,parenchymal cell,epidermis,bulliform cell,primordium cell,etc	LOX2,GLP110,CYP73A2,GST23,ENOD93A	10x Genomics	Wang et al.,2020
	根 Root	表皮、皮层、根冠、内皮层、中柱及后生木质部等 Epidermis,cortex,root cap,endodermis,stele,metaxylem,etc	LOC_Os06g38960,LOC_Os03g25280,LOC_Os04g46810,LOC_Os01g73700,LOC_Os08g03450,LOC_Os03g37490,LOC_Os01g73980	10x Genomics	Liu et al.,2021
玉米 Zea mays	茎尖 Shoot apex	分生细胞、表皮、维管及原基细胞等 Meristematic cell,endodermis,vascular,primordial cell,etc	KN1	流式单细胞 Single flow cell	Satterlee et al.,2020
	根 Root	表皮、皮层、中柱、木质部及静止中心等 Endodermis,cortex,stele,xylem,quiescent center,etc	SHR	10x Genomics	Ortiz-Ramírez et al.,2021
	穗 Ears	皮层、细胞周期G2/M期、侧器官、木质部、韧皮部、分生组织表皮、髓、分生组织及维管等 Cortex,cell cycle G2/M phase,lateral organ,xylem,phloem,meristem epidermis,pith,meristem,vasculature,etc	KN1,BD,BA1,RA3,HDZIV8,YAB14,TMO5,CYCB1;2,APL,SHR1	10x Genomics	Xu et al.,2021
杨树 Populus	木质部 Xylem	导管、纤维、射线薄壁细胞及木质部前体细胞等 Vessel cell,fiber cell,ray parenchyma cell,xylem precursor cell,etc	TUB8,LAC5,EXP6,ABR1	Drop-seq	Li et al.,2021
花生 Arachis hypogaea	叶片 Leaf	栅栏叶肉、海绵状叶肉、表皮、原基、韧皮部、维管束及实质及气孔细胞等 Xpalisade mesophyll cell,spongy mesophyll cell,epidermal cell,primordial cell,phloem cell,vascular cell,parenchymal cell,stomata cell,etc	RBCS,LTP7,LHCB,GSTF,GSTL、SUC2,KCS11,BPC1	10x Genomics	Liu et al.,2021
草莓 Fragaria vesca	叶片 Leaf	表皮、叶肉、韧皮部、分生细胞、木质部及维管束鞘细胞等 Epidermal cell,mesophyll cell,phloem cell,meristem cell,xylem cell,bundle sheath cell,etc	LTP1,LTP3,CTL2,RBCS1A,PP2-A10,CDKB2;1,EXL2	10x Genomics	Bai et al.,2022
烟草 Nicotiana glauca	花冠 Corolla	表皮、韧皮部/木质部、绿色薄壁组织、薄壁组织及花粉等 Epidermis,phloem/xylem,chlorenchyma,parenchyma,pollen,etc	AtSWEET11/12, AtSULTR2;1	10x Genomics	Kang et al.,2022
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	增殖细胞、分生细胞、维管细胞及表皮细胞等 Proliferating cell,meristematic cell,vascular cell,epidermal cell,etc	CDKB2;1,RGF3,LAC7,LTPG16	10x Genomics	张舒婷,2022

物种 Species	组织类型 Organization type	细胞类型 Cell type	标记基因 Marker gene	测序方法/平台 Sequencing method/platform	参考文献 Reference
拟南芥 Arabidopsis thaliana	静止中心及中柱细胞 Quiescent center & Stele cell	静止中心及中柱细胞 Quiescent center,stele cell	WOX5,WOL	荧光标记 Fluorescent mark	Efroni et al.,2015
	根 Root	中柱、静止中心、小柱、表皮/侧根冠及基本组织等 Stele,quiescent center,columella,epidermis/ lateral root cap,ground tissue,etc	WOX5,TOM7,WIP4	SMART-seq2	Efroni et al.,2016
		根毛、内皮层、木质部及韧皮部等 Roothair,endodermis,xylem,phloem,etc	COBL9,SCR,MYB46,APL,SUC2	10x Genomics	Denyer et al.,2019;Jean-Baptiste et al.,2019;Ryu et al.,2019;Zhang et al.,2019
	木质部 Xylem	小柱、皮层、内皮层、原木质部及韧皮部等 Columella,cortex,endodermis,protoxylem,phloem,etc	VND7	Drop-seq	Turco et al.,2019
	气孔 Stoma	表皮、早期分生组织细胞、保卫细胞及表皮扁平细胞等Epidermis,early-stage meristemoid cell,guard cell,pavement cell,etc	MUTE,EPF2,BASL,RBCS,IQD5	10x Genomics	Liu et al.,2020
	茎尖 Shoot apex	叶肉、表皮、茎分生细胞、增殖细胞、韧皮部、木质部、保卫及伴侣细胞等 Mesophyll,epidermis,shoot meristematic cell,proliferating cell,phloem,xylem,guard cell,companion cell,etc	CRR23,CDKB2;1,ATML1,STM,PDF1, SMXL5,PXY,EPF1,PP2-A1	10x Genomics	Zhang et al.,2021
	胚乳 Endosperm	珠孔胚乳、外周胚乳及合点胚乳等 Micropylar endosperm,peripheral endosperm chalazal endosperm,etc	AT2G44240, AT5G10440	snRNA-seq	Picard et al.,2021
	愈伤组织 Callus	表皮、侧根冠、静止中心及维管细胞等 Epidermis-like cell,lateral-root-cap-like cell,quiescent center-like cell,vascular-initial-like cell,etc	PLT1,SCR,WOX5,TMO5,WOX11	BD Rhapsody system	Zhai & Xu,2021
拟南芥 Arabidopsis thaliana	叶脉 Vein	维管束鞘、叶肉、保卫细胞、韧皮薄壁组织、表皮、木质部薄壁组织及伴细胞等 Bundle sheath,mesophyll cell,guard cell,phloem parenchyma,epidermis,xylem parenchyma,companion cell,etc	CDF5,RGA	10x Genomics	Liu et al.,2022
水稻 Oryza sativa	叶片 Leaf	叶肉、薄壁细胞、表皮、泡状细胞和原基细胞等 Mesophyll,parenchymal cell,epidermis,bulliform cell,primordium cell,etc	LOX2,GLP110,CYP73A2,GST23,ENOD93A	10x Genomics	Wang et al.,2020
	根 Root	表皮、皮层、根冠、内皮层、中柱及后生木质部等 Epidermis,cortex,root cap,endodermis,stele,metaxylem,etc	LOC_Os06g38960,LOC_Os03g25280,LOC_Os04g46810,LOC_Os01g73700,LOC_Os08g03450,LOC_Os03g37490,LOC_Os01g73980	10x Genomics	Liu et al.,2021
玉米 Zea mays	茎尖 Shoot apex	分生细胞、表皮、维管及原基细胞等 Meristematic cell,endodermis,vascular,primordial cell,etc	KN1	流式单细胞 Single flow cell	Satterlee et al.,2020
	根 Root	表皮、皮层、中柱、木质部及静止中心等 Endodermis,cortex,stele,xylem,quiescent center,etc	SHR	10x Genomics	Ortiz-Ramírez et al.,2021
	穗 Ears	皮层、细胞周期G2/M期、侧器官、木质部、韧皮部、分生组织表皮、髓、分生组织及维管等 Cortex,cell cycle G2/M phase,lateral organ,xylem,phloem,meristem epidermis,pith,meristem,vasculature,etc	KN1,BD,BA1,RA3,HDZIV8,YAB14,TMO5,CYCB1;2,APL,SHR1	10x Genomics	Xu et al.,2021
杨树 Populus	木质部 Xylem	导管、纤维、射线薄壁细胞及木质部前体细胞等 Vessel cell,fiber cell,ray parenchyma cell,xylem precursor cell,etc	TUB8,LAC5,EXP6,ABR1	Drop-seq	Li et al.,2021
花生 Arachis hypogaea	叶片 Leaf	栅栏叶肉、海绵状叶肉、表皮、原基、韧皮部、维管束及实质及气孔细胞等 Xpalisade mesophyll cell,spongy mesophyll cell,epidermal cell,primordial cell,phloem cell,vascular cell,parenchymal cell,stomata cell,etc	RBCS,LTP7,LHCB,GSTF,GSTL、SUC2,KCS11,BPC1	10x Genomics	Liu et al.,2021
草莓 Fragaria vesca	叶片 Leaf	表皮、叶肉、韧皮部、分生细胞、木质部及维管束鞘细胞等 Epidermal cell,mesophyll cell,phloem cell,meristem cell,xylem cell,bundle sheath cell,etc	LTP1,LTP3,CTL2,RBCS1A,PP2-A10,CDKB2;1,EXL2	10x Genomics	Bai et al.,2022
烟草 Nicotiana glauca	花冠 Corolla	表皮、韧皮部/木质部、绿色薄壁组织、薄壁组织及花粉等 Epidermis,phloem/xylem,chlorenchyma,parenchyma,pollen,etc	AtSWEET11/12, AtSULTR2;1	10x Genomics	Kang et al.,2022
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	增殖细胞、分生细胞、维管细胞及表皮细胞等 Proliferating cell,meristematic cell,vascular cell,epidermal cell,etc	CDKB2;1,RGF3,LAC7,LTPG16	10x Genomics	张舒婷,2022