Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
5.6
Journals
IJMS
Special Issues
Single Cell Multiomics in Plants
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Single Cell Multiomics in Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 23959

Special Issue Editors

Prof. Dr. Xuwu Sun

E-Mail Website
Guest Editor
State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
Interests: single cell; RNA-seq; spatial transcriptomics; spatial metabolomics; mass spectrometry imaging; stomatal development; stress response; stem cell; arabidopsis; cotton
Prof. Dr. Weiqiang Li

E-Mail Website
Guest Editor
State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
Interests: plant hormones; development; Arabidopsis; drought stress; halophyte; strigolactone; meristem; stomata; rice
Prof. Dr. Hikmet Budak

E-Mail Website
Guest Editor
Montana BioAgriculture, Inc., Missoula, MT 59802, USA
Interests: plant genomics; next generation sequencing; small RNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A multicellular organism is essentially an interaction network composed of different cell types. In recent years, rapid development of single cell RNA sequencing (scRNA-Seq) technology and spatial transcriptomics (ST) technology has provided us with unparalleled insights and opportunities to analyze the deep operation mechanisms of this network. In addition to the spatial transcriptome, spatial metabolomics (SM), which has been developed based on mass spectrometry imaging (MSI) in recent years, provided us with rich research means to solve biological problems at a new omics level. ST and SM technology have been widely used in studies of medicine, pharmacy, animal developmental biology, plant developmental biology, etc.

This Special Issue focuses on Single cell Multiomics in Plants. The scope of this Special Issue includes:

(1) Single cell multiomics studies on the growth and development of plant specific tissues and organs (seeds, roots, stems, leaves, flowers, embryos, or fruits);

(2) Single cell multiomics studies on plant specific tissues and organs’ (seeds, roots, stems, leaves, flowers, or embryos) responses to biotic and abiotic stresses;

(3) Single cell multiomics studies on the dynamic regulation of plant meristems’ (apical, lateral, and intercalary meristems and callus) growth and development;

(4) Single cell multiomics studies on plant meristems’ (sapical, lateral, and intercalary meristems and callus) responses to biotic and abiotic stresses;

(5) Contributions on single cell and multiomics research related to crops, model plants, moss, lichen, algae, etc.

Prof. Dr. Xuwu Sun
Prof. Dr. Weiqiang Li
Prof. Dr. Hikmet Budak
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Single Cell RNA-seq
  • Spatial Transcriptomics
  • Spatial Metabolomics
  • Mass Spectrometry Imaging
  • Stem Cell
  • Arabidopsis
  • Rice
  • Maize
  • Wheat
  • Soybean
  • Lichen

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

13 pages, 18477 KiB  
Article
NAC1 Maintains Root Meristem Activity by Repressing the Transcription of E2Fa in Arabidopsis
by Chuantian Xie and Zhaojun Ding
Int. J. Mol. Sci. 2022, 23(20), 12258; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012258 - 14 Oct 2022
Cited by 4 | Viewed by 1963
Abstract
Root meristem is a reserve of undifferentiated cells which guide root development. To maintain root meristem identity and therefore continuous root growth, the rate of cell differentiation must coordinate with the rate of generation of new cells. The E2 promoter-binding factor a ( [...] Read more.
Root meristem is a reserve of undifferentiated cells which guide root development. To maintain root meristem identity and therefore continuous root growth, the rate of cell differentiation must coordinate with the rate of generation of new cells. The E2 promoter-binding factor a (E2Fa) has been shown to regulate root growth through controlling G1/S cell cycle transitions in Arabidopsis thaliana. Here, we found that NAC1, a member of the NAM/ATAF/CUC family of transcription factors, regulated root growth by directly repressing the transcription of E2Fa. Loss of NAC1 triggers an up-regulation of the E2Fa expression and causes a reduced meristem size and short-root phenotype, which are largely rescued by mutation of E2Fa. Further analysis showed that NAC1 was shown to regulate root meristem by controlling endopolyploidy levels in an E2Fa-dependent manner. This study provides evidence to show that NAC1 maintains root meristem size and root growth by directly repressing the transcription of E2Fa in Arabidopsis. Full article
(This article belongs to the Special Issue Single Cell Multiomics in Plants)
►▼ Show Figures

Figure 1

11 pages, 3544 KiB  
Article
An Efficient and Universal Protoplast Isolation Protocol Suitable for Transient Gene Expression Analysis and Single-Cell RNA Sequencing
by Juanjuan Wang, Yang Wang, Tianfeng Lü, Xia Yang, Jing Liu, Yang Dong and Yinzheng Wang
Int. J. Mol. Sci. 2022, 23(7), 3419; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073419 - 22 Mar 2022
Cited by 18 | Viewed by 5079
Abstract
The recent advent of single-cell RNA sequencing (scRNA-seq) has enabled access to the developmental landscape of a complex organ by monitoring the differentiation trajectory of every specialized cell type at the single-cell level. A main challenge in this endeavor is dissociating plant cells [...] Read more.
The recent advent of single-cell RNA sequencing (scRNA-seq) has enabled access to the developmental landscape of a complex organ by monitoring the differentiation trajectory of every specialized cell type at the single-cell level. A main challenge in this endeavor is dissociating plant cells from the rigid cell walls and some species are recalcitrant to such cellular isolation. Here, we describe the establishment of a simple and efficient protocol for protoplast preparation in Chirita pumila, which includes two consecutive digestion processes with different enzymatic buffers. Using this protocol, we generated viable cell suspensions suitable for an array of expression analyses, including scRNA-seq. The universal application of this protocol was further tested by successfully isolating high-quality protoplasts from multiple organs (petals, fruits, tuberous roots, and gynophores) from representative species on the key branches of the angiosperm lineage. This work provides a robust method in plant science, overcoming barriers to isolating protoplasts in diverse plant species and opens a new avenue to study cell type specification, tissue function, and organ diversification in plants. Full article
(This article belongs to the Special Issue Single Cell Multiomics in Plants)
►▼ Show Figures

Figure 1

17 pages, 8764 KiB  
Article
Identification of the Regulators of Epidermis Development under Drought- and Salt-Stressed Conditions by Single-Cell RNA-Seq
by Zhixin Liu, Chenxi Guo, Rui Wu, Jiajing Wang, Yaping Zhou, Xiaole Yu, Yixin Zhang, Zihao Zhao, Hao Liu, Susu Sun, Mengke Hu, Aizhi Qin, Yumeng Liu, Jincheng Yang, George Bawa and Xuwu Sun
Int. J. Mol. Sci. 2022, 23(5), 2759; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23052759 - 02 Mar 2022
Cited by 20 | Viewed by 3818
Abstract
As sessile organisms, plants constantly face challenges from the external environment. In order to meet these challenges and survive, plants have evolved a set of sophisticated adaptation strategies, including changes in leaf morphology and epidermal cell development. These developmental patterns are regulated by [...] Read more.
As sessile organisms, plants constantly face challenges from the external environment. In order to meet these challenges and survive, plants have evolved a set of sophisticated adaptation strategies, including changes in leaf morphology and epidermal cell development. These developmental patterns are regulated by both light and hormonal signaling pathways. However, our mechanistic understanding of the role of these signaling pathways in regulating plant response to environmental stress is still very limited. By applying single-cell RNA-Seq, we determined the expression pattern of PHYTOCHROME INTERACTING FACTOR (PIF) 1, PIF3, PIF4, and PIF5 genes in leaf epidermal pavement cells (PCs) and guard cells (GCs). PCs and GCs are very sensitive to environmental stress, and our previous research suggests that these PIFs may be involved in regulating the development of PCs, GCs, and leaf morphology under environmental stress. Growth analysis showed that pif1/3/4/5 quadruple mutant maintained tolerance to drought and salt stress, and the length to width ratio of leaves and petiole length under normal growth conditions were similar to those of wild-type (WT) plants under drought and salt treatment. Analysis of the developmental patterns of PCs and GCs, and whole leaf morphology, further confirmed that these PIFs may be involved in mediating the development of epidermal cells under drought and salt stress, likely by regulating the expression of MUTE and TOO MANY MOUTHS (TMM) genes. These results provide new insights into the molecular mechanism of plant adaptation to adverse growth environments. Full article
(This article belongs to the Special Issue Single Cell Multiomics in Plants)
►▼ Show Figures

Figure 1

Review

Jump to: Research

12 pages, 830 KiB  
Review
Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits
by George Bawa, Zhixin Liu, Xiaole Yu, Aizhi Qin and Xuwu Sun
Int. J. Mol. Sci. 2022, 23(9), 4497; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094497 - 19 Apr 2022
Cited by 18 | Viewed by 11145
Abstract
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 our analysis to single-cell resolution. Application of scRNA-seq to plants enables the comprehensive characterization of both common and [...] Read more.
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 our analysis to single-cell resolution. Application of scRNA-seq to plants enables the comprehensive characterization of both common and rare cell types and cell states, uncovering new cell types and revealing how cell types relate to each other spatially and developmentally. This review provides an overview of scRNA-seq methodologies, highlights the application of scRNA-seq in plant science, justifies why scRNA-seq is a master player of sequencing, and explains the role of single-cell transcriptomics technologies in environmental stress adaptation, alongside the challenges and prospects of single-cell transcriptomics. Collectively, we put forward a central role of single-cell sequencing in plant research. Full article
(This article belongs to the Special Issue Single Cell Multiomics in Plants)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop