Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes

<p>With the availability of near-complete rice genome sequence,</p> <p>high-quality annotation data, and large expression profile datasets, we examined</p> <p>segmental duplication, intron turnover, and paralogous protein family</p> <p>composition in rice. These data suggest a large percentage of the rice genome</p> <p>was involved in segmental duplication creating a large number of paralogous</p> <p>families. We found that singleton and paralogous family genes differed</p> <p>substantially not only in their likelihood of encoding a protein of known or</p> <p>putative function but also in the distribution of specific gene function. We</p> <p>showed that a significant portion of the duplicated genes in rice show divergent</p> <p>expression although a correlation between sequence divergence and correlation of</p> <p>expression could be seen in very young genes. We observed that intron evolution</p> <p>within the rice genome following segmental duplication is dominated by intron</p> <p>loss rather than intron gain. In addition, with the availability of more</p> <p>complete or near-complete plant genomes and transcriptomes across a wide range</p> <p>of species, we identified and characterized conserved Brassicaceae-specific</p> <p>genes and Arabidopsis lineage-specific genes. Lineage specific genes in the</p> <p>Brassicaceae and within Arabidopsis were enriched in genes of no known function</p> <p>and appear to be fast evolving at the protein sequence level.</p>

Name thesis:degree_name

Doctor of Philosophy

Level thesis:degree_level

dissertation

Discipline thesis:degree_discipline

Bioinformatics and Computational Biology

Department dc:contributor.department

Department of Genetics, Development, and Cell Biology (LAS)

Year dc:date.issued

2009

Author dc:creator

• Lin, Haining

Advisors dc:contributor.advisor

• Carol R. Buell
• Xun Gu

Language dc:language.iso

en

DOI

https://doi.org/10.31274/etd-180810-4323

Identifier

archive/lib.dr.iastate.edu/etd/12194/

OAI identifier oai:identifier

oai:dr.lib.iastate.edu:20.500.12876/26385