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

Abstract

Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present cell atlases with gene regulatory logic involving transcription factors, putative cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic with pathogen cells. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

“…Single-nuclei-based transcriptomics is a powerful technology for elucidating the dynamics of biological processes and understanding the diversity among distinct cell types. The snRNA-seq techniques have enabled researchers to analyze complex traits at a single-cell resolution, particularly emphasizing tissue-specific single-cell atlas, tissue developmental processes, plant-microbe interactions, and abiotic stresses (Kim et al, 2021; Cervantes-Pérez et al, 2022; Tenorio Berrío et al, 2022; Li et al, 2023; Nobori et al, 2023; Sun et al, 2023; Tang et al, 2023). To comprehensively elucidate Si deposition in soybean leaves and its consequential effects on genes specific to individual cells and their associated gene networks, we employed snRNA-seq technology.…”

“…Moreover, previous studies have primarily relied on bulk transcriptomics, which fails to report for the cellular heterogeneity and does not consider the specific cell types possessing the ability of nutrient uptake and deposition (Hao et al, 2021). The single nucleus RNA-sequencing (snRNA-seq) has enabled researchers to identify cell-specific gene expression in several organisms (Kim et al, 2021; Cervantes-Pérez et al, 2022; Shahan et al, 2022; Tenorio Berrío et al, 2022; Xia et al, 2022; Nobori et al, 2023; Sun et al, 2023).…”

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

“…This motivated us to comprehensively profile cell identities throughout Arabidopsis development, spanning all major organs present over the plant’s entire life cycle (i.e., from seed to next-generation seeds). Here, we present an initial version of a seed-to-seed atlas of Arabidopsis development that may function as a foundational dataset for more focused studies, as well as be further built upon with future single-cell/nucleus transcriptome and multi-omic studies 19 . Our seed-to-seed single-nucleus transcriptome atlas revealed a vast diversity of previously uncharacterized molecular identities that integrate both cell type and cell state, including both universal and tissue-specific cell type marker genes, which will be a powerful platform for hypothesis generation of specific cell populations along the spatiotemporal axis of Arabidopsis development.…”

Evolution of plant cell-type-specificcis-regulatory elements

“…For example epidermal bulliform cells in grasses change their turgor pressure to roll the leaf to slow water loss under stressful conditions, with the TF, ZINC FINGER HOMEODOMAIN 1 (ZHD1), modulating leaf rolling by influencing rice (Oryza sativa) bulliform cell development 14,15 . Several studies have identified CREs functioning in a cell-type-specific manner within various plant species [16][17][18][19][20][21][22][23] . Despite these findings, our understanding of CREs exhibiting evolutionarily conserved or divergent cell-type-specific activities remains limited.Through single-cell assay for transposase accessible chromatin sequencing (scATAC-seq), we constructed an expansive single-cell reference atlas of accessible chromatin regions (ACRs) within rice.…”