Table 1 An overview of single-cell research studies in plant-microbe interactions ordered by publication time. scRNA-seq = single-cell RNA sequencing, snRNA-seq = single nucleus RNA sequencing, snATAC-seq = assay for transposase-accessible chromatin using single nucleus sequencing, MERFISH = multiplexed error-robust fluorescence in situ hybridization

Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

[76]

snRNA-seq and spatial transcriptomics

Construction of the first spatially-resolved single-cell resolution integrated map of a multi-kingdom symbiotic interaction. First single-cell resolution study of the AM symbiosis.

Medicago truncatula/ Rhizophagus irregularis

The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

[60]

scRNA-seq

Description of cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development.

Medicago truncatula/ Sinorhizobium meliloti

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

[80]

Spatial metatranscriptomics

Detection of spatial interaction between the plant and its colonizing microorganisms (55 μm of resolution). Study of bacterial and fungal hotspots and the plant’s response.

Arabidopsis thaliana/ Pseudomonas syringae

Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus

[74]

scRNA-seq

Generation of wild type and mutant L. japonicus seedlings cell atlas after rhizobial infection. Identification of candidate nodulation genes.

Lotus japonicus/ Mesorhizobium loti

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

[112]

scRNA-seq

Generation of Arabidopsis cell atlas during fungal infection. Description of cell-type specific gene expression, like high expression of immune receptors in vasculature cells and coordinated expression changes of abscisic acid in the guard cells. Report of a robust correlation between cell response and its proximity to the invading fungal hyphae.

Arabidopsis thaliana/ Colletotrichum higginsianum

Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago

[75]

snRNA-seq

Time-course analysis of symbiotic perception, focusing on early cell-type specific responses to nodulation.

Medicago truncatula/ Sinorhizobium meliloti

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq

[77]

scRNA-seq

Analysis of the cellular heterogeneity within an infected leaf. Description of spatial and temporal dynamics of immune and susceptible cell-clusters.

Arabidopsis thaliana/ Pseudomonas syringae

Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection

[78]

scRNA-seq, transcriptional reporter fusion

Analysis of the cellular heterogeneity within an infected leaf. Description of spatial and temporal dynamics of immune and susceptible cell-clusters.

Arabidopsis thaliana/ Pseudomonas syringae

Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots

[113]

scRNA-seq

Study of the immune regulatory networks in major cell types of maize root tips in response to fungal infection.

Maize (Zea mays)/ Fusarium verticillioides

Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

[79]

snMultiome (snRNA-seq + snATAC-seq) and spatial transcriptomics (MERFISH)

Generation of a spatiotemporal cell map of Arabidopsis leaf infected by virulent and avirulent bacteria, involving transcription factors, putative cis-regulatory elements and target genes associated with disease and immunity. Identification of new cell populations involved in immune response. Discovery of immune response heterogeneity according to pathogen distribution.

Arabidopsis thaliana/ Pseudomonas syringae

A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean

[72]

snRNA-seq, transcriptional reporter fusion

Generation of cell atlas of soybean roots and determinate nodules. Comparison of determinate and indeterminate nodules. Description of GmCRE1 role in nodule formation and nitrogen fixation.

Soybean (Glycine max)/ Sinorhizobium fredii

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

[114]

snRNA-seq and spatial transcriptomics

Generation of cell atlas of soybean roots and determinate nodules. Identification of rare-cell subtypes with important roles in nodule function and development.

Soybean (Glycine max)/ Bradyrhizobium diazoefficiens

Single-cell resolution transcriptome atlases of soybean root organs reveal new regulatory programs controlling the nodulation process

[73]

snRNA-seq

Generation of cell atlas of soybean roots and determinate nodules. Identification of different sub-populations of

B. diazoeciens-infected cells in the

nodule. Characterization of GmFWL3 protein.

Soybean (Glycine max)/ Bradyrhizobium diazoefficiens

Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection

[115]

scRNA-seq, transcriptional reporter fusion

Study of the distinct gene expression patterns of cell clusters under powdery mildew infection. Report of HbCNL2 gene as disease-resistance gene.

Rubber tree (Hevea brasiliensis)/ Oidium heveae

Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

[71]

snRNA-seq

Analysis of the transcriptomic response of Medicago root cells to rhizobial infection.

Medicago truncatula/ Ensifer meliloti

Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula

[70]

scRNA-seq, transcriptional reporter fusion

Generation of single-cell transcriptome map of indeterminate root nodules.

Medicago truncatula/ Sinorhizobium meliloti

Development of a single-cell atlas for woodland strawberry (Fragaria vesca) leaves during early Botrytis cinerea infection using single cell RNA-seq

[69]

scRNA-seq

Generation of the first single-cell atlas of the plant pathogenic invasion process.

Woodland strawberry (Fragaria vesca)/ Botrytis cinerea