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.
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/ETD-TAMU-3228 |
| Date | 15 May 2009 |
| Creators | Liu, Yun-Hua |
| Contributors | Zhang, Hongbin |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | Book, Thesis, Electronic Thesis, text |
| Format | electronic, application/pdf, born digital |
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