Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis DOI Creative Commons
Jie Yao, Nianmin Shang, Hongyu Chen

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function development. However, plant cell’s rigid walls require protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq various tissues before after protoplasting. Cell-type specific effects were discovered in different tissues. Protoplasting-related biases found to distort clustering, marker identification, multi-omics integration. By calculating protoplasted scores based expression, identified mitigated effects, enabling the accurate clustering annotation tobacco BY-2 cells identification cell-cycle-related genes. Our findings underscore importance assessing correcting analysis, offering new insights more interpretation biological discovery.

Язык: Английский

Rewriting cellular fate: epigenetic interventions in obesity and cellular programming DOI Creative Commons
Ruilin Li, Sheng Kang

Molecular Medicine, Год журнала: 2024, Номер 30(1)

Опубликована: Окт. 10, 2024

External constraints, such as development, disease, and environment, can induce changes in epigenomic patterns that may profoundly impact the health trajectory of fetuses neonates into adulthood, influencing conditions like obesity. Epigenetic modifications encompass processes including DNA methylation, covalent histone modifications, RNA-mediated regulation. Beyond forward cellular differentiation (cell programming), terminally differentiated cells are reverted to a pluripotent or even totipotent state, is, reprogramming. modulators facilitate erase both vivo vitro during programming Noticeably, obesity is complex metabolic disorder driven by genetic environmental factors. Increasing evidence suggests epigenetic play critical role regulation gene expression involved adipogenesis, energy homeostasis, pathways. Hence, we discuss mechanisms which interventions influence obesity, focusing on non-coding RNAs. We also analyze methodologies have been pivotal uncovering these regulations, i.e., Large-scale screening has instrumental identifying genes pathways susceptible control, particularly context adipogenesis homeostasis; Single-cell RNA sequencing (scRNA-seq) provides high-resolution view at individual cell level, revealing heterogeneity dynamics reprogramming; Chromatin immunoprecipitation (ChIP) assays, focused candidate genes, crucial for characterizing transcription factor binding specific genomic loci, thereby elucidating govern programming; Somatic nuclear transfer (SCNT) fusion techniques employed study reprogramming accompanying cloning generation hybrid with characteristics, etc. These approaches marks implicated providing foundation developing targeted therapeutic interventions. Understanding dynamic interplay between advancing mechanism clinical management

Язык: Английский

Процитировано

4
Opportunities and challenges in the application of single-cell transcriptomics in plant tissue research DOI
Man Luo, Yunpeng Cao,

Jiayi Hong

и другие.

Physiology and Molecular Biology of Plants, Год журнала: 2025, Номер 31(2), С. 199 - 209

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

0
Screening for Resistant Germplasms and Quantitative Trait Locus Mapping of Resistance to Tomato Chlorosis Virus DOI Open Access
Wenzheng Gao, Zhirong Wang,

Chenchen Dong

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(5), С. 2060 - 2060

Опубликована: Фев. 26, 2025

Tomato chlorosis virus (ToCV) is an emerging plant that poses a substantial threat to the cultivation of economically vital vegetable crops, particularly tomato (Solanum lycopersicum). Despite its impact on crop yield, resistant or tolerant germplasms have not been well documented, and genetic basis resistance ToCV remains poorly understood. In this study, two wild accessions were immune five highly identified from 58 accessions. Additionally, novel method was developed for evaluating in tomatoes, it observed tomatoes exhibited typical pathological features days 15 30 after inoculation, referred as Stage 1 2, respectively. Using quantitative trait locus (QTL) sequencing conjunction with classical QTL approaches, loci F2 populations derived crosses between SG11 (susceptible) LA1028 (resistant) SP15 LA0444 (resistant). Genetic analysis indicated wild-type ToCV-resistant mainly governed by four (Qtc1.1 Qtc11.1 Qtc7.1 Qtc9.1 LA0444). Subsequently, transcriptome three (LA2157, LA0444, LA1028) susceptible (SG11 SP15) revealed unique differentially expressed genes specific biological processes stages infection. This study provides new potential resources resistance, which can be valuable molecular breeding programs obtaining varieties.

Язык: Английский

Процитировано

0
Single-nucleus transcriptome analysis reveals the cellular and molecular responses of tobacco roots to Ralstonia solanacearum invasion DOI Creative Commons
Meng Jia,

Xuanquan Zhu,

D. Y. Chen

и другие.

Industrial Crops and Products, Год журнала: 2025, Номер 226, С. 120752 - 120752

Опубликована: Фев. 27, 2025

Язык: Английский

Процитировано

0
Recent progress in single-cell transcriptomic studies in plants DOI Creative Commons
Yuhan Cho, Ulhas Sopanrao Kadam,

Bogun Park

и другие.

Plant Biotechnology Reports, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

Язык: Английский

Процитировано

0
Single-Cell Transcriptome Reveals the Cellular Response to PEG-Induced Stress in Wheat Leaves DOI

Xiaorui Guo,

Aiju Zhao,

Jeong-Ji Han

и другие.

Journal of Agricultural and Food Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Апрель 27, 2025

Drought is a major factor limiting the production and yield of wheat bread (Triticum aestivum). Therefore, investigating drought-related response mechanism an urgent priority. Here, single-cell transcriptome drought-nonsusceptible susceptible seedlings subjected to PEG-induced stress was systematically analyzed study at cellular level. We identified five cell types using known marker genes constructed leaf atlas. On this foundation, several potential specific for each type were identified, which provide reference further annotation. Moreover, we heterogeneity in mechanisms regulatory networks among types. Specifically, drought mesophyll cells correlated with photosynthetic pathway. Pseudotime trajectory analysis revealed transition epidermal from their normal function defense under stress. also characterized associated response. Notably, two transcription factors (TraesCS1D02G223600 TraesCS1D02G072900) as master regulators most Our provides detailed insights into The gene resources obtained our could be applied breed better crop plants improved tolerance.

Язык: Английский

Процитировано

0
Unveiling the Spatiotemporal Strategies of Plants in Response to Biotic and Abiotic Stresses:A Comprehensive Review DOI
Guo Yu, Jingyu Xiang,

Caixing Lai

и другие.

Plant Physiology and Biochemistry, Год журнала: 2025, Номер unknown, С. 109967 - 109967

Опубликована: Апрель 1, 2025

Язык: Английский

Процитировано

0
Single-cell transcriptomics: a new frontier in plant biotechnology research DOI
Shilpy Singh,

Afsana Praveen,

Namrata Dudha

и другие.

Plant Cell Reports, Год журнала: 2024, Номер 43(12)

Опубликована: Ноя. 25, 2024

Язык: Английский

Процитировано

1
Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement DOI Creative Commons
Yuzhao Hu,

Linkan Dash,

Gregory D. May

и другие.

Plants, Год журнала: 2024, Номер 13(24), С. 3476 - 3476

Опубликована: Дек. 11, 2024

Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on application these in improvement. The heterogeneity different cell populations within a tissue plays crucial role coordinated response organism to its environment. enables dissection this heterogeneity, offering insights into cell-specific transcriptomic responses plants various environmental stimuli. Spatial complement single-cell approaches by preserving context gene expression profiles, allowing for situ localization transcripts. Together, facilitate discovery novel genes regulatory networks that can be targeted genetic manipulation breeding strategies aimed at enhancing yield, quality, resilience. highlights significant findings from recent studies, discusses expanding roles technologies, explores future opportunities their

Язык: Английский

Процитировано

0
Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis DOI Creative Commons
Jie Yao, Nianmin Shang, Hongyu Chen

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function development. However, plant cell’s rigid walls require protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq various tissues before after protoplasting. Cell-type specific effects were discovered in different tissues. Protoplasting-related biases found to distort clustering, marker identification, multi-omics integration. By calculating protoplasted scores based expression, identified mitigated effects, enabling the accurate clustering annotation tobacco BY-2 cells identification cell-cycle-related genes. Our findings underscore importance assessing correcting analysis, offering new insights more interpretation biological discovery.

Язык: Английский

Процитировано

0