Table 1 Single-cell multi-omic approaches in plant research

Transcriptomics

Drop-seq

Arabidopsis thaliana, Populus alba × Populus glandulosa, Catharanthus roseus

seedling, root, xylem, leaf

(Shulse et al. 2019; Turco et al. 2019; Li et al. 2021; Li et al. 2023)

10 × Genomics

Arabidopsis thaliana, Arachis hypogaea, Brassica rapa, Camellia sinensis, Fragaria vesca, Medicago truncatula, Nicotiana attenuate, Oryza sativa, Populus alba, Zea mays, Marchantia polymorpha, Bombax ceiba, Gossypium hirsutum, Catharanthus roseus, Phyllostachys edulis, Hevea brasiliensis, Populus trichocarpa, Liriodendron chinense

root, cotyledon, leaf, ear inflorescence, shoot, stem, root nodule, corolla limbs and throat cups, ovule, gemmae and thalli, inner ovary wall, stem-differentiating xylem

(Bai et al. 2022; Chen et al. 2021; Denyer et al. 2019; Gala et al. 2021; Graeff et al. 2021; Guo et al. 2022; Hou et al. 2021; Jean-Baptiste et al. 2019; Kang et al. 2022; Liu et al. 2021a; Liu et al. 2021b; Liu et al. 2020; Lopez-Anido et al. 2021; Ortiz-Ramírez et al. 2021; Otero et al. 2022; Ryu et al. 2019; Shahan et al. 2022; Sun et al. 2022; Wang et al. 2022; Wang et al. 2021; Wendrich et al. 2020; Xu et al. 2021; Ye et al. 2022; Zhang et al. 2021; Zhang et al. 2019; Kim et al. 2021; Cao et al. 2023; Wang et al. 2023; Zhu et al. 2023b; Liu et al. 2022; Ding et al. 2023; Qin et al. 2022; Li et al. 2023; Sun et al. 2023; Cheng et al. 2023; Liang et al. 2023; Tung et al. 2023)

Microwell based scRNA-seq

Arabidopsis thaliana, Oryza sativa

callus, inflorescence

(Zhai and Xu 2021; Zong et al. 2022)

CEL-seq2

Zea mays

anther, shoot apical meristems

(Nelms and Walbot 2019; Satterlee et al. 2020)

mcSCRB-seq

Solanum lycopersicum

shoot-borne root

(Omary et al. 2022)

SMART-seq

Arabidopsis thaliana

root meristem, lateral root primordium

(Roszak et al. 2021; Serrano-Ron et al. 2021)

snRNA-seq 

Arabidopsis thaliana, Medicago truncatula, Oryza sativa, Zea mays, Litchi chinensis, Glycine max 

root, endosperm, leaf, floral meristems, seedlings, pistil, bud, root nodules 

(Cervantes-Pérez et al. 2022; Farmer et al. 2021; Li et al. 2023a; Marand et al. 2021; Neumann et al. 2022; Picard et al. 2021; Wang et al. 2023; Yang et al. 2023; Liu et al. 2023)

1cell-DGE

Physcomitrella patens

leaf

(Kubo et al. 2019)

scStereo-seq

Arabidopsis thaliana

leaf

(Xia et al. 2022)

Quartz-Seq2

Arabidopsis thaliana

callus

(Ogura et al. 2023)

PHYTOMap

Arabidopsis thaliana

root

(Nobori et al. 2023)

MARS-seq2.0

Eucalyptus grandis, Trochodendron aralioides

stem-differentiating xylem

(Tung et al. 2023)

Epigenomics

BRIF-seq

Zea mays

microspore

(Li et al. 2019b)

scATAC-seq

Arabidopsis thaliana, Oryza sativa, Zea mays

root, seedling, axillary buds, embryonic root, staminate, pistillate inflorescence, crown root

(Dorrity et al. 2021; Farmer et al. 2021; Feng et al. 2022; Marand et al. 2021)

sci-ATAC-seq

Arabidopsis thaliana

root

(Tu et al. 2022)

snCUT&Tag

Oryza sativa

seedling

(Ouyang et al. 2022)

scHi-C

Oryza sativa

sperm, egg, zygote

(Zhou et al. 2019)

Metabolomics

Nano-LC–ESI–MS

Torenia hybrida

petal cell

(Kajiyama et al. 2006)

Nano-ESI–MS

Catharanthus roseus, Pelargonium zon, Vicia faba

single leaf, stem, petal cell, parenchyma, epidermal, idioblast, and laticifer cells

(Lorenzo Tejedor et al. 2012; Shimizu et al. 2015; Tejedor et al. 2009; Yamamoto et al. 2019, 2016)

LAESI-MS

Allium cepa, Narcissus pseudonarcissus

single epidermal cell of bulb

(Shrestha and Vertes 2009)

UV-MALDI-ToF–MS

Tulipa suaveolens

leaf and bulb

(Gholipour et al. 2012)

LDI-ToF–MS

Arabidopsis thaliana, Hypericum perforatum, Hypericum reflexum  

individual dark glands from petals, leaves, glandular trichomes 

(Hölscher et al. 2009)

CE-MS

Allium cepa

epidermal cell

(Huang et al. 2021)

UPLC-MS

Catharanthus roseus

leaf

(Li et al. 2023)