A genome is a system: Interactions among the elements constituting the plant genomes

Genome sequencing has revealed that the genome of any organism, regardless of whether it is a prokaryote or a eukaryote, is made of a limited number of sequence-specialized fundamental function elements (FFE). For the genome of a higher organism, FFE consist of genes (GEN), retro-transposable elements (RTE), DNA-transposable elements (DTE), simple sequence repeats (SSR) and/or low complexity repeat (LCR). Our previous study showed that these elements are structured in a genome in an unambiguous and collaborative manner resembling a “Jigsaw Puzzle”, i.e., the DNA “Jigsaw Puzzle” structure (Wu, Wang and Zhang, 2006, Genomics 88:394-406). We previously also showed that the sizes of gene (GEN) families vary significantly not only among congeneric species, but also within a species (Zhang et al. 2011, Nucleic Acids Res. 38:6513-6525). Here we investigated the relationships of the family size variation among the families of GEN, DTE, RTE, SSR and LCR, and established their interaction networks. We show that the size of an FFE family in a genome, or the member loss or gain of an FFE family of a genome is not independent; it is significantly correlated with those of one or more other FFE families. Our study also shows that the interaction pattern or network of the FFE families is a unique characteristic of a genome, suggesting that a genome is a system; the interaction and collaboration of the FFE underlay the biology, variation and evolution of organisms. These findings provide a novel molecular basis of genetics, biology and physiology.