Liu, Yun-Hua (2008-12). The dna ?saw puzzle??ructure model: the case studies of the rice and yeast genomes. Master's Thesis.
How does DNA make the abundant and diverged life world? To address this question, a DNA "Jigsaw Puzzle" structure model was proposed and first tested by comprehensively analyzing the genome of the model dicot plant, Arabidopsis thaliana. However, it is unknown whether this model is held in other species. Here we report the studies of the DNA structure model using the monocot plant model species, rice (Oryza sativa), and the single-celled model species, yeast (Saccharomyces cerevisiae). Analyses of the genomes sequenced so far revealed that the genome of an organism consists of a limited number of sequence-specialized, so-called fundamental function elements. For a higher organism, these elements often include genes (GEN), retro-transposable elements (RTE), DNA transposable elements (DTE), simple sequence repeats (SSR) and low complex repeats (LCR). Datasets were developed for RTE, DTE, SSR, LCR and GEN as well as genes categorized into different function categories from the sequences of the rice and yeast genomes using appropriate window sizes. The datasets were subjected to statistical analyses to test the DNA "Jigsaw Puzzle" structure model in terms of the unambiguousness, correlation, uniqueness and selection of their genome-constituting element arrays. The analyses were conducted with a series of window sizes of the sequences at both the whole genome and individual chromosome levels, both including and excluding the centromeric regions. The results showed that all fundamental function elements of the genomes as well as the genes categorized into different function categories were arrayed in the genomes in an unambiguous manner resembling linear "Jigsaw Puzzles" at the whole genome and/or individual chromosome levels, no matter whether the centromeric regions were included or excluded. The analyses revealed that arraying of the genomic elements was correlated significantly and uniquely for each chromosome and each species. This further confirmed the non-random arraying characteristic of the genomic elements for the DNA "Jigsaw Puzzle" structure model and suggested that the DNA "Jigsaw Puzzle" structure is unique for an organism, which has probably resulted from natural selection. These results unambiguously support the hypothesis of the DNA "Jigsaw Puzzle" structure model. Since the content, arraying and interaction pattern of the fundamental function elements were shown to be unique for each organism, variations of an organism in its DNA "Jigsaw Puzzle" array would lead to phenotypic variations, thus resulting in different organisms. Moreover, the fundamental function elements constituting a genome, as the four nucleotides (A, T, G and C) of DNA, could be arrayed into an infinite number of DNA molecules, thus giving different forms of organisms. Therefore, the DNA "Jigsaw Puzzle" structure model would provide a novel, but convincing explanation for the abundance, diversity and complexity of living organisms in the world.