A cross-species co-functional gene network underlying leaf senescence

Moyang Liu; Chaocheng Guo; Kexuan Xie; Kai Chen; Jiahao Chen; Yudong Wang; Xu Wang

doi:10.1093/hr/uhac251

A cross-species co-functional gene network underlying leaf senescence

Hortic Res. 2022 Nov 10;10(1):uhac251. doi: 10.1093/hr/uhac251. eCollection 2023.

Authors

Moyang Liu^{1

2}, Chaocheng Guo^{1

2}, Kexuan Xie^{1

2}, Kai Chen^{1

2}, Jiahao Chen^{1

2}, Yudong Wang^{1

2}, Xu Wang^{1

2}

Affiliations

¹ Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
² Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.

Abstract

The complex leaf senescence process is governed by various levels of transcriptional and translational regulation. Several features of the leaf senescence process are similar across species, yet the extent to which the molecular mechanisms underlying the process of leaf senescence are conserved remains unclear. Currently used experimental approaches permit the identification of individual pathways that regulate various physiological and biochemical processes; however, the large-scale regulatory network underpinning intricate processes like leaf senescence cannot be built using these methods. Here, we discovered a series of conserved genes involved in leaf senescence in a common horticultural crop (Solanum lycopersicum), a monocot plant (Oryza sativa), and a eudicot plant (Arabidopsis thaliana) through analyses of the evolutionary relationships and expression patterns among genes. Our analyses revealed that the genetic basis of leaf senescence is largely conserved across species. We also created a multi-omics workflow using data from more than 10 000 samples from 85 projects and constructed a leaf senescence-associated co-functional gene network with 2769 conserved, high-confidence functions. Furthermore, we found that the mitochondrial unfolded protein response (UPR^mt) is the central biological process underlying leaf senescence. Specifically, UPR^mt responds to leaf senescence by maintaining mitostasis through a few cross-species conserved transcription factors (e.g. NAC13) and metabolites (e.g. ornithine). The co-functional network built in our study indicates that UPR^mt figures prominently in cross-species conserved mechanisms. Generally, the results of our study provide new insights that will aid future studies of leaf senescence.