Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses

Wu Liu; Yuyun Zhang; Xing Fang; Sorrel Tran; Ning Zhai; Zhengfei Yang; Fu Guo; Lyuqin Chen; Jie Yu; Madalene S Ison; Teng Zhang; Lijun Sun; Hongwu Bian; Yijing Zhang; Li Yang; Lin Xu

doi:10.1016/j.xplc.2022.100306

Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses

Plant Commun. 2022 Jul 11;3(4):100306. doi: 10.1016/j.xplc.2022.100306. Epub 2022 Feb 25.

Authors

Wu Liu¹, Yuyun Zhang², Xing Fang², Sorrel Tran³, Ning Zhai¹, Zhengfei Yang⁴, Fu Guo⁵, Lyuqin Chen², Jie Yu¹, Madalene S Ison³, Teng Zhang², Lijun Sun⁶, Hongwu Bian⁷, Yijing Zhang⁸, Li Yang⁹, Lin Xu¹⁰

Affiliations

¹ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
² National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.
³ Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA.
⁴ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
⁵ Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China.
⁶ School of Life Sciences, Nantong University, Nantong, China.
⁷ Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
⁸ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China. Electronic address: zhangyijing@fudan.edu.cn.
⁹ Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA. Electronic address: li.yang1@uga.edu.
¹⁰ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. Electronic address: xulin@cemps.ac.cn.

Abstract

Detached Arabidopsis thaliana leaves can regenerate adventitious roots, providing a platform for studying de novo root regeneration (DNRR). However, the comprehensive transcriptional framework of DNRR remains elusive. Here, we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR. Time-lapse RNA sequencing (RNA-seq) of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate, ethylene, and reactive oxygen species (ROS) pathways in response to wounding. Genetic analyses confirmed that ethylene and ROS may serve as wound signals to promote DNRR. Next, time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis, wound-induced regeneration, and resource allocation in the wounded region of detached leaves during adventitious rooting. Genetic studies showed that BLADE-ON-PETIOLE1/2, which control aboveground organs, PLETHORA3/5/7, which control root organogenesis, and ETHYLENE RESPONSE FACTOR115, which controls wound-induced regeneration, are involved in DNRR. Furthermore, single-cell RNA-seq data revealed gene expression patterns in the wounded region of detached leaves during adventitious rooting. Overall, our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.

Keywords: Arabidopsis thaliana; de novo root regeneration; plant regeneration; single-cell RNA-seq; time-lapse RNA-seq; wounding.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Arabidopsis* / metabolism
Ethylenes / metabolism
Plant Leaves / genetics
Plant Roots / genetics
Reactive Oxygen Species / metabolism
Sequence Analysis, RNA
Time-Lapse Imaging

Substances

Ethylenes
Reactive Oxygen Species