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Cross-species single-cell analysis

Model plant

Weed

Easy

to grow

Small

genome

Short

life cycle

(6 weeks)

Bioenergy

Crops

Arabidopsis

Medical

plants

Maize, Sorghum

Poplar, Switchgrass

Mayapple, Periwinkle, Yew

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

2 of 9

OMG: Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

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Orthologous marker gene groups

UMAP_1

UMAP_2

Reference

UMAP_1

UMAP_2

Query

Single-cell

transcriptomics

200 marker gene extraction for each cell cluster

OMGs conversion by OrthoFinder

Pairwise comparison between OMGs of reference and query sample

GeneE_1

GeneA_1

GeneA_2

GeneF_2

GeneB_2

GeneB_4

GeneC_4

GeneC_3

GeneG_3

Orthogroup 1

Orthogroup 3

Orthogroup 2

GeneA_1

GeneA_2

GeneA_3

…

GeneA_200

GeneB_1

GeneB_2

…

GeneB_200

GeneC_1

GeneC_2

…

GeneC_200

GeneD_1

…

GeneD_200

GeneE_1

GeneE_2

GeneE_3

…

GeneE_200

GeneF_1

GeneF_2

…

GeneF_200

GeneG_1

GeneG_2

…

GeneG_200

GeneH_1

…

GeneH_200

(Chau et al., 2025)

Reference

Query

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

4 of 9

Prediction of cell types in a query sample

Tomato root single-cell data

(Cantó-Pastor et al., 2024)

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

5 of 9

Prediction of cell types in a query sample

Query: Tomato

Reference: Arabidopsis

Plant Species

Cluster

Quantity of Common

Orthologous Marker Genes

(OMGs)

Plant Species

Significant Result

by Fisher Exact Test

(p-value < 0.01)

Cell type

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

6 of 9

Prediction of cell types in a query sample

Most clusters in Rice share many OMGs with the Arabidopsis xylem

Tomato clusters share significant OMGs with Arabidopsis nonhair

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

7 of 9

Prediction of cell types in a query sample

Reference: Arabidopsis

14. Phloem

13. Nonhair

12. Xylem

11. Endodermis

9. Endodermis

8. MZ

7. Cortex/Nonhair

4. MZ

3. Cortex

6. MZ

1. Hair

0. Nonhair

10. MZ

5. Cortex

2. Stele

Predicted labels

Query: Tomato

17

16

20

49

37

37

31

21

24

23

26

25

23

47

35

25

71

80

43

41

68

75

46

47

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech

8 of 9

Cell type mapping across 15 diverse species

Maize

Arabidopsis

Rice

Tomato

Cotton

Populus

Soybean

Tobacco

Cassava

Periwinkle

Field mustard

Wild strawberry

Barrel clover

15

species

264

cell clusters

1

million cells

53,600

marker genes

14 conserved cell types across 15 diverse species

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Annotate Pennycress (Thlaspi arvense)

OrthoMarkerGene

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Genetics, Bioinformatics, and Computational Biology, Virginia Tech