Physiology and Molecular Biology of Plants, Journal Year: 2024, Volume and Issue: 30(7), P. 1185 - 1208
Published: July 1, 2024
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 1, 2025
Abstract Invasive plants can profoundly disrupt native biodiversity, yet the genetic mechanisms underpinning their success remain poorly understood. To date, genomic studies have been conducted on only a limited number of invasive species, and no single-cell level applied. This research investigates drivers behind behavior common reed ( Phragmites australis ), hardy grass species that became in North America following its introduction from Europe. By integrating whole-genome sequencing with spatial transcriptomics, we developed comprehensive atlas reed’s shoot system. UMAP analysis identified 19 distinct cell clusters within Gene Ontology (GO) enrichment enabled annotation key types, including mesophyll, epidermal, bundle sheath, xylem cells, as well apical lateral bud meristems, auxillary meristems. RNA velocity highlighted multipotent nature mesophyll chlorenchyma Cluster 3 progenitor cells capable differentiating into various tissues 1 progressing towards aerenchyma formation. Comparative between European American populations revealed significant differences transcriptional activity gene expression, particularly associated meristem. exhibited higher prevalence B chromosomes, three genes IMPA-3, SSC3, DDE family endonuclease consistently upregulated across nearly all clusters, notably near meristematic regions. The fast mutation IMPA-3 which functions major receptor Resistance (R) may strengthened adaptability population America. These findings provide critical insights cellular development diversity underlying invasiveness reed, offering valuable information to guide ecological management strategies.
Language: Английский
Citations
1
Developmental Cell, Journal Year: 2023, Volume and Issue: 58(8), P. 694 - 708.e4
Published: April 1, 2023
Language: Английский
Citations
22
Crop Design, Journal Year: 2023, Volume and Issue: 2(2), P. 100041 - 100041
Published: Aug. 1, 2023
High-throughput sequencing technologies at single-cell resolution have great potential to reveal a new landscape of plant cells. Single-cell/nucleus RNA (scRNA/snRNA), single-cell/nucleus assay for transposase accessible chromatin (scATAC/snATAC) and spatial transcriptome been applied in multiple tissues. Consequently, significant increase publications on transcriptomics was seen the recent two years. In this review, we will summarize advantages weaknesses these approaches, offer glimpse their developments cell biology, bioinformatic tools databases latest
Language: Английский
Citations
22
Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 74, P. 102378 - 102378
Published: May 10, 2023
Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden states, continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers distinguish between distinct plant populations, delineate cycle continuums, infer differentiation trajectories diverse types shoots, roots, floral vascular meristems with unprecedented resolution. We then highlight emerging power dissect heterogeneity regenerating tissues uncover cellular basis reprogramming stem commitment during regeneration. conclude by discussing related outstanding questions field.
Language: Английский
Citations
20
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: Aug. 11, 2023
Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to single-cell information. transcriptomes provide insights into transcriptome at level, whereas help preserve Although these two omics technologies are helpful mature, further research is needed ensure their widespread applicability in plant studies. Reviewing recent on or transcriptomics, we compared different experimental methods used various plants. The limitations challenges clear for both transcriptomic analyses, such as lack of applicability, information, high resolution. Subsequently, put forth applications, cross-species analysis roots idea that needs be combined with other analyses achieve superiority over individual analyses. Overall, results this review suggest combining element distribution can a promising direction, particularly research.
Language: Английский
Citations
20
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Jan. 11, 2024
The regulation of gene expression in plant responses to drought has been thoroughly investigated previous studies. Despite this, a detailed understanding the cell type-specific regulatory mechanisms, encompassing multi-layered biological processes, is lacking. In this study, we report use single-nucleus multiomic analysis Arabidopsis seedlings response stress. Our single-nuclei RNA (snRNA) delineated 14 distinct clusters representing major root and shoot types discovered new markers. Integration snRNA with ATAC (snATAC) data leaf epidermis, endodermis, guard cells revealed accessible chromatin regions (ACRs)-linked genes predominantly enriched pathways responsive drought, heat, light. Motif enrichment network (GRN) inference highlighted key transcription factors (TFs) networks related ethylene signaling endodermis as well circadian rhythms both cells. Pseudotime identified critical transcriptomic progression from metabolic process stress within three types. Overall, study elucidates drought-related mechanisms at single-cell resolution, providing valuable insights into fundamental events involved responses. It also serves reference for future investigations crop plants.
Language: Английский
Citations
7
Molecular Plant, Journal Year: 2024, Volume and Issue: 17(7), P. 1019 - 1037
Published: June 13, 2024
Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes floret single-cell of tassel, we revealed dynamics pathways inflorescence development sex differentiation. We identified 16 diverse gene clusters differential spatiotemporal expression patterns biased regulation redox, programmed cell death, hormone signals during differentiation between tassel. Notably, based on their dynamic patterns, roles two RNA-binding proteins in regulating activity axillary formation. Moreover, using transcriptional profiles 53 910 single cells, uncovered cellular heterogeneity florets. found that multiple associated either enhanced death or reduced growth are responsible for pistil suppression, while part gibberellic acid signal may act non-cell-autonomously to regulate stamen arrest further showed pistil-protection SILKLESS 1 (SK1) functions antagonistically known pistil-suppression genes common molecular pathways, constructed a network pistil-fate determination. Collectively, our study provides deep understanding maize, laying foundation identifying new regulators maize hybrid breeding improvement.
Language: Английский
Citations
7
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Jan. 9, 2024
Abstract Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas chromatin accessibility Oryza sativa , integrating data from 103,911 nuclei representing 126 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved between O. 57,552 four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum Urochloa fusca ). Accessible regions (ACRs) had different levels conservation depending on the degree specificity. found complex relationship ACRs with conserved noncoding sequences, specificity, conservation, tissue-specific switching. Additionally, that epidermal were less compared other types, potentially indicating more rapid regulatory has occurred L1-derived layer these species. Finally, identified characterized subset overlapped repressive histone modification H3K27me3, implicating them as silencer-like CREs maintained by evolution. Collectively, this approach highlights dynamics plant cell-type-specific
Language: Английский
Citations
6
Crop Design, Journal Year: 2024, Volume and Issue: 3(2), P. 100057 - 100057
Published: Feb. 24, 2024
Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made novel development, with two innovative methodologies being developed, single-cell (scRNA-seq) technology spatial transcriptome (ST) technology. The scRNA-seq allows researchers to analyze gene expression individual cells, providing more detailed information relative technologies. Meanwhile, ST overcomes limitations of terms loss information, enabling scientists better understand distribution within tissues. These advancements transcriptomics technologies revolutionize field genomics been widely used disease diagnosis medicine. However, they are less utilized plant research. This review describes advantage three technologies, presents their applications sciences.
Language: Английский
Citations
6
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 6, 2024
SUMMARY Stem cells in plant shoots are a rare population of that produce leaves, fruits and seeds, vital sources for food bioethanol. Uncovering regulators expressed these stem will inform crop engineering to boost productivity. Single-cell analysis is powerful tool identifying specific groups cells. However, accessing shoot challenging. Recent single-cell analyses have not captured cells, failed detect cell like CLAVATA3 WUSCHEL . In this study, we finely dissected cell-enriched tissues from both maize arabidopsis RNA-seq profiling. We optimized protocols efficiently recover thousands A cross-species comparison identified conserved between arabidopsis. also performed on overproliferation mutants find additional candidate regulators. Expression genes was validated using spatial transcriptomics, functionally confirmed roles development. These candidates include family ribosome-associated RNA-binding proteins, two families sugar kinase related hypoxia signaling cytokinin hormone homeostasis. large-scale profiling provide resource mining regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding development open avenues manipulating diverse crops enhance energy security.
Language: Английский
Citations
6