Summary Single‐cell RNA‐seq (scRNA‐seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were divided into eight cell clusters based on reported marker genes by applying scRNA‐seq. Further, a pseudo‐time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re‐investigation of the primordium‐driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA‐seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA‐seq values. Additionally, peanut AHL23 (AT‐HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA‐seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.
Plant cell proliferation associated with multiple layers of gene regulation, including modulation of transcriptome by changes in chromatin accessibility. However, cell proliferation is an asynchronous process precluding a temporal understanding of regulatory events leading to single-cell fate commitment. Here, a robust single nucleus RNA sequencing approach, where single nucleus employed for simultaneous investigation of transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same single-cell of Arachis hypogaea leaves. A total of 5,930 leaf cells with 10,793 expressed genes were used to construct development trajectory and characterized large-scale critical differentially expressed genes (DEGs). Additionally, uncovered extending insights of chromatin opening guided 5,315 DEGs expression involved biological pathway determines differentiation direction in distinct cell-types. But obtained members in each cell-clusters not exhibits obvious difference in distinct cell-cycling regulated genome duplication phases. Furthermore, snRNA-seq identified AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displays contrasting results to repress the leaf development by jasmonic acid pathway in ectopically expressed Arabidopsis. We concluded that, snRNA-seq combined with snATAC-seq is an extensible platform to explore association between the chromatin regulatory events and gene expression across diversity cell-types in peanut leaf, broadly application of this approach will enable significant advances in the functional research of tissues ontology in plant species.
Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of Arachis hypogaea. A total of 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. The developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insight for mesophyll and vascular cell development. Additionally, dual-omics described the epidermal progenitor cell development trajectory, primordium and palisade cells were able to convert into spongy cells, and bundle sheath cells developed earlier than other vascular-cells. Further cell-cycle analysis demonstrated that cytokinin biosynthesis promotes mesophyll cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified that the AT-hook transcription factor AhAHL11promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displaying contrasting results by repressing leaf development via the jasmonic acid pathway in ectopically expressed Arabidopsis. Conclusively, our study demonstrates that snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell types in peanut leaves. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species. Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of peanut. Totally 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. Developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insights for mesophyll and vascular cells development. Further ell-cycle demonstrated that cytokinin promotes mesophyll-cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 repressing leaf development via jasmonic acid pathway. Conclusively, snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell-types. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species.
Silicon (Si) has been shown to promote peanut growth and yield, but whether Si can enhance the resistance against peanut bacterial wilt (PBW) caused by Ralstonia solanacearum, identified as a soil-borne pathogen, is still unclear. A question regarding whether Si enhances the resistance of PBW is still unclear. Here, an in vitro R. solanacearum inoculation experiment was conducted to study the effects of Si application on the disease severity and phenotype of peanuts, as well as the microbial ecology of the rhizosphere. Results revealed that Si treatment significantly reduced the disease rate, with a decrement PBW severity of 37.50% as compared to non-Si treatment. The soil available Si (ASi) significantly increased by 13.62–44.87%, and catalase activity improved by 3.01–3.10%, which displayed obvious discrimination between non-Si and Si treatments. Furthermore, the rhizosphere soil bacterial community structures and metabolite profiles dramatically changed under Si treatment. Three significantly changed bacterial taxa were observed, which showed significant abundance under Si treatment, whereas the genus Ralstonia genus was significantly suppressed by Si. Similarly, nine differential metabolites were identified to involve into unsaturated fatty acids via a biosynthesis pathway. Significant correlations were also displayed between soil physiochemical properties and enzymes, the bacterial community, and the differential metabolites by pairwise comparisons. Overall, this study reports that Si application mediated the evolution of soil physicochemical properties, the bacterial community, and metabolite profiles in the soil rhizosphere, which significantly affects the colonization of the Ralstonia genus and provides a new theoretical basis for Si application in PBW prevention.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.