Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research  Jeongsik Kim, Hye Ryun Woo, Hong Gil Nam  Molecular Plant  Volume 9, Issue 6, Pages 813-825 (June 2016) DOI: 10.1016/j.molp.2016.04.017 Copyright © 2016 The Author Terms and Conditions

Figure 1 Milestones in Leaf Senescence Research from a Multi-Omics Perspective. The timeline of leaf senescence research, beginning from 1866 when Mendel reported the I locus, is divided into three phases: pre-genomic, genomic, and multi-omics and systems eras. Below the timeline are the major breakthroughs in the development of “omics” technologies and their important contributions. Above the timeline are the major milestones of leaf senescence research using genetic/genomic, transcriptomic, epigenomic, proteomic, metabolomic, and mix-omics technologies described in the text. 2D gel & MALDI-TOF/MS, two-dimensional gel and matrix-assisted laser desorption/ionization time-of-flight/mass spectrometry; cDNA-AFLP, cDNA-amplified fragment-length polymorphism; DD, differential display; DIGE, differential gel electrophoresis; EST, expression sequence tag; LC-MS/MS, liquid chromatography–tandem mass spectrometry; LSD, leaf senescence database; seq, sequencing; smRNA, small RNA; SSH, suppression subtractive hybridization. Numbers in the symbols correspond to the references numbers in Supplemental References. Molecular Plant 2016 9, 813-825DOI: (10.1016/j.molp.2016.04.017) Copyright © 2016 The Author Terms and Conditions

Figure 2 Evolutionary Relationships between ORE1 and AtNAP Homologs and the miR164 Family. Shown is a schematic diagram of the green plant tree of life. The homologous proteins of ORE1 and AtNAP and the miR164 family in the indicated species, given in color-coded boxes, have been plotted on the tree. The homologous proteins of ORE1 and AtNAP and miR164 are shown in blue, yellow, and green boxes, respectively. The homologous proteins of ORE1 containing the miR164 recognition site are indicated in blue boxes with black lines. Branch lengths are arbitrary. The homologous proteins of ORE1 and AtNAP in each of the species were selected using Protein BLAST searches with ORE1 and AtNAP of Arabidopsis as the query against the species listed. All of the homologous proteins listed have expected P < 10−60 and 30% or higher coverage of the entire protein region except the NAC domain. The miR164 family was obtained from the Plant MicroRNA database (Zhang et al., 2010). The species are Arabidopsis thaliana, Brachypodium distachyon, Brassica rapa, Camellia sinensis, Chlamydomonas reinhardtii, Glycine max, Gossypium raimondii, Medicago truncatula, Ostreococcus lucimarinus, Oryza sativa, Picea abies, Physcomitrella patens, Prunus persica, Sorghum bicolor, Solanum lycopersicum, Selaginella moellendorffii, Vitis vinifera, and Zea mays. Molecular Plant 2016 9, 813-825DOI: (10.1016/j.molp.2016.04.017) Copyright © 2016 The Author Terms and Conditions

Figure 3 Multi-Dimensional Approaches to Systems Understanding of Leaf Senescence. Given the multifaceted nature of the leaf senescence process, multi-dimensional approaches are required for the systems understanding of the mechanistic principles governing leaf senescence. The “Age/environment” dimension includes internal (age) and external (environmental) factors that regulate leaf senescence. The “Organization” dimension refers to various analytic layers, including organelle, cell, organ, and organism. The “Analysis” dimension defines diverse high-throughput “omics” technologies. Efforts to integrate multi-omics data, including genomic, epigenomic, transcriptomic, proteomic, metabolomic, and phenomic data, on leaf senescence are essential for an in-depth understanding of the molecular nature of leaf senescence. Molecular Plant 2016 9, 813-825DOI: (10.1016/j.molp.2016.04.017) Copyright © 2016 The Author Terms and Conditions