Date of Award


Document Type


Degree Name

Master of Science (MS)


College of Science and Mathematics



Thesis Sponsor/Dissertation Chair/Project Chair

C. Du

Committee Member

Q. Vega

Committee Member

J. Gaynor


Rice has one of the simplest of the monocotyledonous genomes analyzed to date. The Oryza sativa genome is made of 12 chromosomes and has a total length of 430 MB. It is highly syntenic amongst other cereals. Therefore, genetic distances of these organisms are surprisingly very similar, meaning that genomic recombinations in each cereal occur at much the same frequency despite the differences in their genome size. The reason for this synchrony in recombinations may be due to similar lengths of gene-rich and gene-rare regions. This study focuses on the gene-rare repetitive centromeric region of rice chromosome 8. Although the centromeric functions are conserved across organisms of different species, DNA content, organization and complexity of centromeres significantly vary. This investigation involves comparative analysis of two rice species in terms of their genomic makeup within the centromeric heterochromatic regions: wild rice (rufipogon) and domesticated Japonica. It incorporates fragments of newly sequenced centromeric region of wild rice chromosome 8 and previously sequenced Japonica genome in the same region.

The analysis of wild rice contigs after their alignment revealed regions of significant homology over Japonica centromeric sequence ranging from 88 to 99% identity. The manual wild rice sequence alignment rendered the genome covering about 63% of the Japonica centromeric region. Automatic comparisons done with alignment softwares showed higher coverage due to relatively lenient parameters. All methods predicted the wild rice fragment placements over the second half of the Japonica centromeric sequence.

Annotation results of both genomes suggest that many of the structural aspects parallel in both species. For example, both wild rice fragments and Japonica centromere 8 sequence were found to share their GC content at 45.6% and 45.2% respectively. In addition, retrotransposable elements of RIRE family were also found in both species. Presence of this specific family of retroelements allows for an inference that they also share their G-C distribution patterns. Additional elements in the wild rice fragments were DNA transposons, simple repeats, SINEs and long terminal repeats. The two species of rice were found to have similar proportions of the repeat element. For example, the average LTR content of wild rice was calculated to be 57.2% and that of Japonica was 59.0%.

Despite the structural similarities, the study was inconclusive, however, about the genes coded by the regions of the two genome sequences compared. Wild rice fragments were found to code for seven genes. These included a tertiary structural protein, two ATPases, a retroviral aspartyl protease, an accessory protein and two chromatin organization modifiers. In comparison, the regions of Japonica centromere aligned with wild rice fragments were found to contain one sulfotransferase and two fatty acyl reductases.

Although the gene predictions, which greatly depend on the prediction softwares and databases, do not parallel in the two species, this study provides some important comparative links. Building on the structural similarities found in this study, additional sequencing of the wild rice genome and more detailed annotation of Japonica genome may provide additional insight into their genome analysis.

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