Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology DOI Creative Commons
Md Torikul Islam, Yang Liu, Md Mahmudul Hassan

et al.

BioDesign Research, Journal Year: 2024, Volume and Issue: 6, P. 0029 - 0029

Published: Jan. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Language: Английский

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics DOI Creative Commons
Bozeng Tang, Feng Li, Michelle T. Hulin

et al.

Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 31(10), P. 1732 - 1747.e5

Published: Sept. 22, 2023

Pathogen infection is a dynamic process. Here, we employ single-cell transcriptomics to investigate plant response heterogeneity. By generating an Arabidopsis thaliana leaf atlas encompassing 95,040 cells during by fungal pathogen, Colletotrichum higginsianum, unveil cell-type-specific gene expression, notably enrichment of intracellular immune receptors in vasculature cells. Trajectory inference identifies that had different interactions with the invading fungus. This analysis divulges transcriptional reprogramming abscisic acid signaling specifically occurring guard cells, which consistent stomatal closure dependent on direct contact Furthermore, plasticity genes involved glucosinolate biosynthesis at sites, emphasizing contribution epidermis-expressed MYB122 disease resistance. work underscores spatially dynamic, responses pathogen and provides valuable resource supports in-depth investigations plant-pathogen interactions.

Language: Английский

Citations

42
Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics DOI Creative Commons

Carolin Grones,

Thomas Eekhout, Dongbo Shi

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 812 - 828

Published: Jan. 17, 2024

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.

Language: Английский

Citations

25
Transcriptional landscape of highly lignified poplar stems at single-cell resolution DOI Creative Commons
Yang Chen, Shaofei Tong, Yuanzhong Jiang

et al.

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Nov. 22, 2021

Plant secondary growth depends on the activity of vascular cambium, which produces xylem and phloem. Wood derived from is most abundant form biomass globally has played key socio-economic subsistence roles throughout human history. However, despite intensive study development, full diversity cell types gene networks engaged are still poorly understood.

Language: Английский

Citations

84
Single‐cell RNA‐sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent DOI
Moonyoung Kang, Yuri Choi, Hyeonjin Kim

et al.

New Phytologist, Journal Year: 2022, Volume and Issue: 234(2), P. 527 - 544

Published: Jan. 25, 2022

High-throughput single-cell RNA sequencing (scRNA-Seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of density expression profiles, we can observe metabolic features each population. Here, employ scRNA-Seq technique to reveal entire biosynthetic pathway a flower volatile. The corolla wild tobacco Nicotiana attenuata emits bouquet scents that are composed mainly benzylacetone (BA). Protoplasts from N. limbs and throat cups were isolated at three different time points, transcript levels > 16 000 genes analyzed 3756 single cells. We performed unsupervised clustering analysis determine which clusters involved BA biosynthesis. was uncovered by analyzing co-expression datasets silencing candidate corolla. In conclusion, high-resolution spatiotemporal atlas provided reveals molecular underlying cell-type-specific metabolism plant.

Language: Английский

Citations

58
Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection DOI Creative Commons
Carl Procko, Travis Lee, Aleca M. Borsuk

et al.

The Plant Cell, Journal Year: 2022, Volume and Issue: 34(9), P. 3261 - 3279

Published: June 6, 2022

Like other complex multicellular organisms, plants are composed of different cell types with specialized shapes and functions. For example, most laminar leaves consist multiple photosynthetic types. These include the palisade mesophyll, which typically forms one or more layers on adaxial side leaf. Despite their importance for photosynthesis, we know little about how cells differ at molecular level from To this end, have used a combination cell-specific profiling using fluorescence-activated sorting single-cell RNA-sequencing methods to generate transcriptional blueprint mesophyll in Arabidopsis thaliana leaves. We find that despite unique morphology, otherwise transcriptionally similar Nevertheless, show some genes phenylpropanoid biosynthesis pathway both palisade-enriched expression light-regulated. Phenylpropanoid gene activity was required production ultraviolet (UV)-B protectant sinapoylmalate, may protect and/or leaf against damaging UV light. findings improve our understanding can function uniquely optimize performance, similarities.

Language: Английский

Citations

57
Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits DOI Open Access

George Bawa,

Zhixin Liu,

Xiaole Yu

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(9), P. 4497 - 4497

Published: April 19, 2022

In recent years, advances in single-cell RNA sequencing (scRNA-seq) technologies have continued to change our views on biological systems by increasing the spatiotemporal resolution of analysis resolution. Application scRNA-seq plants enables comprehensive characterization both common and rare cell types states, uncovering new revealing how relate each other spatially developmentally. This review provides an overview methodologies, highlights application plant science, justifies why is a master player sequencing, explains role transcriptomics environmental stress adaptation, alongside challenges prospects transcriptomics. Collectively, we put forward central research.

Language: Английский

Citations

50
Advances and applications of single‐cell omics technologies in plant research DOI Open Access
Yajin Mo, Yuling Jiao

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(6), P. 1551 - 1563

Published: April 15, 2022

SUMMARY Single‐cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high‐dimensional catalogs millions cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, proteomics data across species. These emerging yet thriving technologies have been fully embraced by field plant biology, a constantly expanding portfolio applications. Here, we introduce current technical advances used for single‐cell omics, especially genome transcriptome sequencing. Firstly, overview methods protoplast nucleus isolation amplification. Subsequently, use well‐executed benchmarking studies to highlight made through application omics techniques. Looking forward, offer glimpse additional hurdles future opportunities that will broad adoption revolutionary perspectives in biology.

Language: Английский

Citations

47
The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata DOI Open Access
Guiling Sun,

Mingzhang Xia,

Jieping Li

et al.

The Plant Cell, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 9, 2022

The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these is critical improving food security. We have developed a planta platform single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it identify cell types in mature developing from 33,098 maize epidermis-enriched tissues. Guard cells (GCs) subsidiary (SCs) displayed differential expression genes, besides those encoding transporters, involved abscisic acid, CO2, Ca2+, starch metabolism, blue light signaling pathways, implicating coordinated signal integration speedy stomatal responses, genes affecting wall plasticity, implying more sophisticated relationship between GCs SCs development dumbbell-shaped guard formation. trajectory identified young tissues, comparison bulk RNA-seq data MUTE defective mutant development, confirmed known features, shed on key participants development. Our study provides valuable, comprehensive, fundamental foundation further insights into function.

Language: Английский

Citations

46
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis DOI Creative Commons
Travis Lee, Tatsuya Nobori, Natanella Illouz‐Eliaz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 24, 2023

SUMMARY Extensive studies of the reference plant Arabidopsis have enabled a deep understanding tissues throughout development, yet census cell types and states development is lacking. Here, we present single-nucleus transcriptome atlas seed-to-seed employing over 800,000 nuclei, encompassing diverse set across ten developmental stages, with spatial transcriptomic validation dynamic seed silique. Cross-organ analyses revealed transcriptional conservation heterogeneity within individual influenced by organ-of-origin timing, including groups transcription factors, suggesting gatekeeping factor activation. This provides resource for study type specification continuum stimulus-response genetic perturbations at single-cell resolution.

Language: Английский

Citations

33
Spatial transcriptomics drives a new era in plant research DOI Creative Commons

Ruilian Yin,

Keke Xia, Xun Xu

et al.

The Plant Journal, Journal Year: 2023, Volume and Issue: 116(6), P. 1571 - 1581

Published: Aug. 31, 2023

SUMMARY The plant community lags far behind the animal and human fields concerning application of single‐cell methodologies. This is primarily due to challenges associated with tissue dissection limitations available technologies. However, recent advances in spatial transcriptomics enable study single‐cells derived from tissues a perspective. technology already successfully used identify cell types, reconstruct cell‐fate lineages, reveal cell‐to‐cell interactions. Future technological advancements will overcome sample processing, data analysis, integration multiple‐omics Thanks transcriptomics, we anticipate several research projects significantly advance our understanding critical aspects biology.

Language: Английский

Citations

31