Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants

C Chen, Y Ge, L Lu - Frontiers in Plant Science, 2023 - frontiersin.org
Single-cell and spatial transcriptomics have diverted researchers' attention from the
multicellular level to the single-cell level and spatial information. Single-cell transcriptomes …

Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology

SA Cervantes-Pérez, S Thibivillliers, S Tennant… - Plant Science, 2022 - Elsevier
Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a
single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation …

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

Z Liu, J Yang, Y Long, C Zhang, D Wang, X Zhang… - Nature Plants, 2023 - nature.com
Establishing legume–rhizobial symbiosis requires precise coordination of complex
responses in a time-and cell type-specific manner. Encountering Rhizobium, rapid changes …

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

L Zhang, C He, Y Lai, Y Wang, L Kang, A Liu, C Lan… - Genome biology, 2023 - Springer
Background Homoeologs are defined as homologous genes resulting from allopolyploidy.
Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs …

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

C Grones, T Eekhout, D Shi, M Neumann… - The Plant …, 2024 - academic.oup.com
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of
plant genes at an unprecedented resolution. Therefore, these technologies are gaining …

Transcription factor PagMYB31 positively regulates cambium activity and negatively regulates xylem development in poplar

Y Zhang, S Chen, L Xu, S Chu, X Yan, L Lin… - The Plant …, 2024 - academic.oup.com
Wood formation involves consecutive developmental steps, including cell division of
vascular cambium, xylem cell expansion, secondary cell wall (SCW) deposition, and …

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

M Neumann, X Xu, C Smaczniak, J Schumacher… - Nature …, 2022 - nature.com
Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell
transcriptomics allows characterization of gene expression heterogeneity in developing …

The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata

G Sun, M Xia, J Li, W Ma, Q Li, J Xie, S Bai… - The Plant …, 2022 - academic.oup.com
The unique morphology of grass stomata enables rapid responses to environmental
changes. Deciphering the basis for these responses is critical for improving food security …

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

K Serrano, M Bezrutczyk, D Goudeau, T Dao… - Nature Plants, 2024 - nature.com
The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and
widespread. Plants provide AM fungi with carbon in exchange for nutrients and water …

Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots

J Guo, D Luo, Y Chen, F Li, J Gong, F Yu… - New …, 2024 - Wiley Online Library
Bamboo with its remarkable growth rate and economic significance, offers an ideal system to
investigate the molecular basis of organogenesis in rapidly growing plants, particular in …