Overview

Networks offer a reasonable means of describing complex life systems. Here, we generate a first-generation interactome of maize , a first-generation functional genome, which contains over 6 million edges for more than 4000 functional modules, covering the whole genetic transmission from genome, to transcriptome, to translatome, and to proteome. The first-generation interactome integrates genomic interactions by ChIA-PET, transcriptomic co-expression networks by mRNA-seq, lncRNA-seq, circRNA-seq, and small RNA-seq across root, leaf, tassel, SAM and other tissues or developmental stages (totally 26 different tissues/stages), translatomic co-expression networks by Ribo-seq across 20 different tissues/stages, and protein-protein interactions by high-throughput Yeast-2-hybridyzation across 8 distinct tissues for the maize reference inbred line B73. The first-generation interactome can trace the functional divergence of functional elements originated from different evolutionary time-points and classify distinct functional coherent sets of molecular interactions and pathway modules, indicative of evolutionary and biological senses. It can help to dig out the key genes from a subset of differentially expressed genes, assist mutant/QTL cloning, and systematically dissect the molecular mechanisms conferring the agronomic important traits. Importantly, this database presented here integrates state-of-the-art technologies such as machine-learning, network comparison for the network Big-Data mining. This interactome resource database paves the way for the complete era of functional genomics and offers an unprecedented chance for rapid gene cloning and network analyses.

Maize EMS induced Mutant Database (MEMD) is strongly recommended for the functional validation of genes, which are functionally predicted and systematically dissected for the molecular networks by the interactome big data.