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

dc.contributor.advisor Carol R. Buell
dc.contributor.advisor Xun Gu Lin, Haining
dc.contributor.department Genetics, Development and Cell Biology 2018-08-11T09:07:06.000 2020-06-30T02:40:59Z 2020-06-30T02:40:59Z Thu Jan 01 00:00:00 UTC 2009 2013-06-05 2009-01-01
dc.description.abstract <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>
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dc.identifier.articleid 3143
dc.identifier.contextkey 2808341
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/12194
dc.language.iso en
dc.source.bitstream archive/|||Fri Jan 14 19:14:54 UTC 2022
dc.subject.disciplines Cell and Developmental Biology
dc.subject.disciplines Genetics and Genomics
dc.title Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes
dc.type article
dc.type.genre dissertation
dspace.entity.type Publication
relation.isOrgUnitOfPublication 9e603b30-6443-4b8e-aff5-57de4a7e4cb2 Bioinformatics and Computational Biology dissertation Doctor of Philosophy
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