How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis

Kułak, Karolina; Wojciechowska, Natalia; Samelak-Czajka, Anna; Jackowiak, Paulina; Bagniewska-Zadworna, Agnieszka

doi:10.1186/s13007-023-01109-8

Plant Methods

Table 1 Summary of selected scRNAs-seq studies of plant vascular tissue

From: How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis

Organ	Organism	Sample type	Platform	No. of cells	No. of clusters	Annotated cell types	Ref.
Root	Arabidopsis thaliana	Protoplasts	Drop-seq	179–989 per sample	11	Trichoblast, atrichoblast/columella, cortex, endodermis, phloem, protoxylem	Turco et al. [108]
Root	Arabidopsis thaliana	Protoplasts	Chromium 10× Genomics	9640–11,313 per sample	34	Procambium, cortex differentiating, cortex initials, endodermis (initials, early, late), epidermis initials, epidermis, trichoblast, atrichoblast, vascular initials, lateral root cap, pericycle, phloem procambium, phloem companion cells, phloem initials, phloem sieve elements, xylem initials, metaxylem, protoxylem, dividing cells, columella, initials	Yang et al. [110]
Root	Arabidopsis thaliana	Protoplasts	Smart-seq2	1242	14	P1Δ, P1D, P1 (PEAR1 reporter lines), CD (CVP2 reporter line), N57 (NAC057 and CALS7 reporter line), CALS7 (CALS7 reporter line), N73 (NAC073 reporter line)	Roszak et al. [115]
Root	Arabidopsis thaliana	Protoplasts	Chromium 10× Genomics	10,204	15	Phloem sieve element, phloem pole pericycle, metaphloem sieve element, companion cells, pericycle, early phloem, outer layers	Otero et al. [116]
Leaf	Arabidopsis thaliana	Protoplasts	Chromium 10× Genomics	5230	19	Mesophyll, epidermis, hydathode, guard cells, bundle sheath, companion cells, xylem parenchyma, phloem parenchyma, procambium cells with features relating to xylem or phloem differentiation respectively	Kim et al. [117]
Cotyledons	Arabidopsis thaliana	Protoplasts	Chromium 10× Genomics	14,117	10^a	Bundle sheath, mesophyll, phloem parenchyma, hydathode, companion cells, guard cells, epidermis, xylem parenchyma, sieve element, procambium cells with features relating to xylem or phloem differentiation respectively	Liu et al. [118]
Stem	Populus alba var. pyramidalis	Protoplasts	Chromium 10× Genomics	3170–3626 per sample	20	Xylem (fiber and vessel), xylem mother cells, xylem parenchyma, cambium region, photosynthetic cells, companion cells, phloem parenchyma, phloem mother cells, sieve element, cortex/endodermis initial cells, cortex/endodermis, cork, endoderm, epiderm	Chen et al. [119]
Stem	Populus alba × Populus glandulosa	Protoplasts	Chromium 10× Genomics	9798	12	Xylem precursor cells, fiber cells, vessels, ray parenchyma	Li et al. [31]
Shoot apex	Populus tremula × Populus alba	Nuclei	Chromium 10× Genomics	8324	18	Shoot meristematic cells, mesophyll, trichomes, vascular cells, companion cells, proliferating cells, epidermis, ground meristem	Conde et al. [120]
Stem	Populus trichocarpa	Protoplasts	Not specified	12,466	12	Vessel cells, ray cells, phloem, cambium, fiber cells	Xie et al. [159]
Stem	Populus trichocarpa, Eucalyptus grandis, Trochodendron aralioides, Liliodendron chinense	Protoplasts	Chromium 10× Genomics MARS-seq2.0	4705 (P. trichocarpa)^b 5494 (E. grandis) 1993 (T. aralioides) 2977 (L. chinense)	10	Vessel element, fusiform intermediate precursor, ray organizer, fusiform early precursor, ray precursor, fusiform organizer, libriform fiber, ray parenchyma	Tung et al. [121]

^aFor t-SNE, 11 clusters for UMAP
^bOnly cells that were used for clustering are included

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ISSN: 1746-4811

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