Advancing our understanding of root development: Technologies and insights from diverse studies DOI
Núria S. Coll, Miguel Á. Moreno-Risueno, Lucia C. Strader

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Understanding root development is critical for enhancing plant growth and health, advanced technologies are essential unraveling the complexities of these processes. In this review, we highlight select technological innovations in study development, with a focus on transformative impact single-cell gene expression analysis. We provide high-level overview recent advancements, illustrating how RNA sequencing (scRNA-seq) has become pivotal tool biology. scRNA-seq revolutionized biology by enabling detailed, cell-specific analysis expression. This allowed researchers to create comprehensive atlases, predict cell map regulatory networks (GRNs) unprecedented precision. Complementary technologies, such as multimodal profiling bioinformatics, further enrich our understanding cellular dynamics interactions. Innovations imaging modeling, combined genetic tools like CRISPR, continue deepen knowledge formation function. Moreover, integration biosensors microfluidic devices ability plant-microbe interactions phytohormone signaling at high resolution. These collectively more system architecture its regulation environmental factors. As evolve, they promise drive breakthroughs science, substantial implications agriculture sustainability.

Language: Английский

Lost in space: what single-cell RNA sequencing cannot tell you DOI Creative Commons
Kelvin Adema, Michael A. Schon, Michael D. Nodine

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: 29(9), P. 1018 - 1028

Published: April 2, 2024

Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding spatiotemporal context cells. However, positional information is inherently lost during scRNA-seq, limiting its to characterize complex biological systems. In this review we highlight how current analysis pipelines cannot completely recover spatial information, which confounds interpretation. Various strategies exist identify location RNA, from classical in situ hybridization transcriptomics. Herein discuss possibility utilizing supervise analyses. An integrative approach will maximize each technology, and lead insights go beyond capability individual technology.

Language: Английский

Citations

11
Unraveling plant–microbe symbioses using single-cell and spatial transcriptomics DOI Creative Commons
Karen Serrano, Francesca Tedeschi, Stig Uggerhøj Andersen

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: 29(12), P. 1356 - 1367

Published: July 10, 2024

HighlightsBeneficial plant–microbe interactions are critical to plant productivity in both natural and agricultural ecosystems due benefits such as improved nutrition abiotic stress tolerance.The legume–rhizobia symbiosis plant–arbuscular mycorrhizal fungi involve continuous signaling coordination between two organisms.Within symbioses, the development of novel microbial structures is driven by symbiosis-specific gene expression a few specific cell populations.Genetic engineering take better advantage these relies on identification symbiosis-responsive genes that can serve targets for modification.Applying single-cell spatial RNA-seq study endosymbiosis facilitate improve our general understanding complex biology symbiotic interactions.AbstractPlant–microbe symbioses require intense interaction genetic successfully establish types host symbiont. Traditional methodologies lack cellular resolution fully capture complexities, but transcriptomics (ST) now allowing scientists probe at an unprecedented level detail. Here, we discuss advantages transcriptomic technologies provide studying endosymbioses highlight key recent studies. Finally, consider remaining limitations applying approaches research, which mainly related simultaneous transcripts within same cells.

Language: Английский

Citations

9
Symbiotic nitrogen fixation: a launchpad for investigating old and new challenges DOI Creative Commons
Maurizio Chiurazzi, Giovanna Frugis, Lorella Navazio

et al.

Journal of Experimental Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 26, 2025

Language: Английский

Citations

1
Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism DOI Creative Commons

Ershang Han,

Zhenxing Geng, Yue Qin

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(8), P. 100978 - 100978

Published: May 22, 2024

Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell analysis with publicly available scRNA-seq using SingleCellGGM algorithm. The identified 149 modules, which we considered to be expression programs (GEPs). By examining their spatiotemporal expression, GEPs specifically expressed in major root cell types along developmental trajectories. These define regulating development at different stages and enriched relevant regulators. As examples, GEP specific for the quiescent center (QC) contains 20 genes QC stem niche homeostasis, four sieve elements (SEs) from early late stages, early-stage containing 17 known SE also metabolic pathways cell-type-specific suggesting existence metabolism roots. Using GEPs, discovered verified columella-specific gene, NRL27, as regulator auxin-related gravitropism response. Our thus systematically reveals that regulate provides ample resources biology studies.

Language: Английский

Citations

7
Cellular insights into legume root infection by rhizobia DOI Creative Commons
Fernanda de Carvalho‐Niebel, Joëlle Fournier, Anke Becker

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 81, P. 102597 - 102597

Published: July 27, 2024

Legume plants establish an endosymbiosis with nitrogen-fixing rhizobia bacteria, which are taken up from the environment anew by each host generation. This requires a dedicated genetic program on side to control microbe invasion, involving coordinated reprogramming of cells create infection structures that facilitate inward movement symbiont. Infection initiates in epidermis, different legumes utilizing distinct strategies for crossing this cell layer, either between (intercellular infection) or transcellularly (infection thread infection). Recent discoveries plant using fluorescent-based imaging approaches have illuminated spatiotemporal dynamics infection, underscoring importance investigating process at dynamic single-cell level. Extending fluorescence-based live-dynamic bacterial partner opens exciting prospect learning how individual reprogram rhizospheric host-confined state during early root infection.

Language: Английский

Citations

7
About How Nitrate Controls Nodulation: Will Soybean Spill the Bean? DOI Open Access

E. Guillierme,

Kris Gevaert, Sofie Goormachtig

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

ABSTRACT Legumes have the beneficial capacity to establish symbiotic interactions with rhizobia, which provide their host plants fixed nitrogen. However, in presence of nitrogen, this process is rapidly repressed avoid unnecessary investments carbon symbiosis. Several players involved regulating nodulation response nitrate availability been identified, including peptide hormones, microRNAs and transcription factors. Nevertheless, how these molecular are linked each other what underlying mechanisms at play inhibit remain unresolved. Nitrate‐mediated control seems differ between model legumes, such as Medicago Lotus , compared legume crops soybean. A deeper understanding regulatory processes, particularly soybean, expected contribute establishing increased efficiency modern agricultural systems, hence improving sustainability by reducing need for environmentally hazardous nitrogen fertilizers. This review describes state art nitrate‐regulated while drawing parallels described legumes addressing knowledge gaps that require future study.

Language: Английский

Citations

0
The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza DOI Creative Commons
Elise Schnabel, Sagar Bashyal,

Cameron W. Corbett

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Aug. 10, 2024

Legumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance their symbiosis with rhizobia. Several proteins key this pathway have been discovered, but AON is not completely understood.

Language: Английский

Citations

3
Single-Cell Transcriptomics Applied in Plants DOI Creative Commons
Yanyan Sun, Jian Sun,

Chunjing Lin

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(18), P. 1561 - 1561

Published: Sept. 17, 2024

Single-cell RNA sequencing (scRNA-seq) is a high-tech method for characterizing the expression patterns of heterogeneous cells in same tissue and has changed our evaluation biological systems by increasing number individual analyzed. However, full potential scRNA-seq, particularly plant science, not yet been elucidated. To explore utilization scRNA-seq technology plants, we firstly conducted comprehensive review significant findings past few years. Secondly, introduced research applications to tissues recent years, primarily focusing on model crops, wood. We then offered five databases that could facilitate identification distinct marker genes various cell types. Finally, analyzed problems, challenges, directions applying with aim providing theoretical foundation better use this technique future research.

Language: Английский

Citations

3
Comparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant DOI Creative Commons

Maria Borowska-Beszta,

Magdalena Smoktunowicz,

Daria Horoszkiewicz

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: March 21, 2024

Introduction Bacteria of genus Pectobacterium , encompassing economically significant pathogens affecting various plants, includes the species P. betavasculorum initially associated with beetroot infection. However, its host range is much broader. It causes diseases sunflower, potato, tomato, carrots, sweet radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic phenomic characterisation was performed. Methods Genomes strains isolated from artichoke were sequenced compared those sugar beet isolates. Metabolic profiling analyses conducted to assess virulence determinants adaptation potential. Pathogenicity assays performed on potato tubers chicory leaves confirm in silico predictions disease symptoms. Phenotypic also ability synthesise homoserine lactones siderophores. Results The genome size ranged 4.675 4.931 kbp, GC % between 51.0% 51.2%. pangenome open comprises, average, 4,220 gene families. Of these, 83% genes are core genome, 2% entire unique genes. Strains have smaller higher number than other plants. Interestingly, genomes sunflower share 391 common CDS that not present or potato. Those only one gene. All could use numerous sugars as building materials energy sources possessed high repertoire genomes. able cause symptoms leaves. They Discussion findings underscore adaptability diverse hosts environments. adapted plants content tissues different composition fatty acids membranes mechanism replenishing nitrogen case deficiency compound derived plant species. Extensive phenomics genomic study shown an agronomically relevant pathogen.

Language: Английский

Citations

2
Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches DOI Creative Commons

Sofía Cristina Somoza,

Paola Bonfante, Marco Antonio Giovannetti

et al.

Biology Direct, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 17, 2024

The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques roots sampled in bulk, with methods to capture subsets cells such as laser microdissection. These approaches revealed central regulators this complex relationship, yet the requisite level detail effectively untangle intricacies temporal spatial development remains elusive.The recent adoption single-cell (scRNA-seq) plant research is revolutionizing our ability dissect intricate transcriptional profiles plant-microbe interactions, offering unparalleled insights into diversity dynamics individual during symbiosis. isolation particularly challenging due presence walls, leading researchers widely adopt nuclei methods. Despite increased resolution that analyses offer, it also comes at cost perspective, hence, necessary integration these transcriptomics obtain comprehensive overview.To date, few studies on interactions published, most which provide high-resolution atlases will become fully deciphering symbiotic addressing future questions. In AM symbiosis research, key processes mutual recognition partners arbuscule within cortical cells, or senescence degeneration, remain poorly understood, advancements are expected shed light contribute deeper understanding interaction.

Language: Английский

Citations

1