Xinyang Wang, Runfeng Wang, Xing Huo, Yueni Zhou, Muhammad J. Umer, Zihao Zheng, Weicai Jin, Lu Huang, Haifen Li, Qianxia Yu, Shaoxiong Li, Rajeev K Varshney, Wenyi Wang, Yuan Xiao, Yanbin Hong, Xiaoping Chen, Qing Lu, Hao Liu
{"title":"Integration of single‐nuclei transcriptome and bulk RNA‐seq to unravel the role of AhWRKY70 in regulating stem cell development in Arachis hypogaea L.","authors":"Xinyang Wang, Runfeng Wang, Xing Huo, Yueni Zhou, Muhammad J. Umer, Zihao Zheng, Weicai Jin, Lu Huang, Haifen Li, Qianxia Yu, Shaoxiong Li, Rajeev K Varshney, Wenyi Wang, Yuan Xiao, Yanbin Hong, Xiaoping Chen, Qing Lu, Hao Liu","doi":"10.1111/pbi.70009","DOIUrl":null,"url":null,"abstract":"SummaryPeanut stem is a vital organ to provide mechanical support and energy for aerial tissue development. However, the transcriptional regulatory mechanisms underlying stem development at a single‐cell resolution remain unclear. Herein, single‐nuclei isolation coupled with fluorescent‐activated cell sorting was employed to construct a cell atlas of peanut seedling stems using microdroplets‐based single‐nuclei RNA‐sequencing. This approach yielded 29 308 cells with 53 349 expressed genes underlying the identification of five cell types characterized by known marker genes. Additionally, 2053 differentially expressed genes (DEGs) were identified across different cell types. Furthermore, 3306 core‐DEGs involved in cell development trajectories were used to construct a transcription factor (TF) interaction network, providing insights into specific biological pathways and transcriptional regulation dynamics underlying cell‐type differentiation. Additionally, 1446 DEGs associated with different cell‐cycle profile were identified, revealing that peanut stem elongation and cell expansion are closely linked to auxin‐responsive pathway. This was supported by the examination of endogenous phytohormones and the identification of 10 hormone‐responsive DEGs. Moreover, <jats:italic>AhWRKY70</jats:italic> was localized in the nucleus and is highly enriched in stem cortex and xylem cells and exhibits a tissue‐specific expression pattern that regulates stem growth. Overexpression of <jats:italic>AhWRKY70</jats:italic> in <jats:italic>Arabidopsis</jats:italic> led to accelerated stem growth by modulating the phytohormone signalling pathway, influencing the expression of sixteen auxin and ethylene‐responsive genes as demonstrated by transcriptome sequencing. In conclusion, the single‐cell atlas provides a foundational dataset for understanding gene expression heterogeneity in peanut seedling stems. The elucidation of <jats:italic>AhWRKY70</jats:italic> function expands our understanding of the roles of <jats:italic>WRKY</jats:italic> family members in peanut.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"8 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Biotechnology Journal","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1111/pbi.70009","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
SummaryPeanut stem is a vital organ to provide mechanical support and energy for aerial tissue development. However, the transcriptional regulatory mechanisms underlying stem development at a single‐cell resolution remain unclear. Herein, single‐nuclei isolation coupled with fluorescent‐activated cell sorting was employed to construct a cell atlas of peanut seedling stems using microdroplets‐based single‐nuclei RNA‐sequencing. This approach yielded 29 308 cells with 53 349 expressed genes underlying the identification of five cell types characterized by known marker genes. Additionally, 2053 differentially expressed genes (DEGs) were identified across different cell types. Furthermore, 3306 core‐DEGs involved in cell development trajectories were used to construct a transcription factor (TF) interaction network, providing insights into specific biological pathways and transcriptional regulation dynamics underlying cell‐type differentiation. Additionally, 1446 DEGs associated with different cell‐cycle profile were identified, revealing that peanut stem elongation and cell expansion are closely linked to auxin‐responsive pathway. This was supported by the examination of endogenous phytohormones and the identification of 10 hormone‐responsive DEGs. Moreover, AhWRKY70 was localized in the nucleus and is highly enriched in stem cortex and xylem cells and exhibits a tissue‐specific expression pattern that regulates stem growth. Overexpression of AhWRKY70 in Arabidopsis led to accelerated stem growth by modulating the phytohormone signalling pathway, influencing the expression of sixteen auxin and ethylene‐responsive genes as demonstrated by transcriptome sequencing. In conclusion, the single‐cell atlas provides a foundational dataset for understanding gene expression heterogeneity in peanut seedling stems. The elucidation of AhWRKY70 function expands our understanding of the roles of WRKY family members in peanut.
期刊介绍:
Plant Biotechnology Journal aspires to publish original research and insightful reviews of high impact, authored by prominent researchers in applied plant science. The journal places a special emphasis on molecular plant sciences and their practical applications through plant biotechnology. Our goal is to establish a platform for showcasing significant advances in the field, encompassing curiosity-driven studies with potential applications, strategic research in plant biotechnology, scientific analysis of crucial issues for the beneficial utilization of plant sciences, and assessments of the performance of plant biotechnology products in practical applications.