With the availability of near-complete rice genome sequence,
high-quality annotation data, and large expression profile datasets, we examined
segmental duplication, intron turnover, and paralogous protein family
composition in rice. These data suggest a large percentage of the rice genome
was involved in segmental duplication creating a large number of paralogous
families. We found that singleton and paralogous family genes differed
substantially not only in their likelihood of encoding a protein of known or
putative function but also in the distribution of specific gene function. We
showed that a significant portion of the duplicated genes in rice show divergent
expression although a correlation between sequence divergence and correlation of
expression could be seen in very young genes. We observed that intron evolution
within the rice genome following segmental duplication is dominated by intron
loss rather than intron gain. In addition, with the availability of more
complete or near-complete plant genomes and transcriptomes across a wide range
of species, we identified and characterized conserved Brassicaceae-specific
genes and Arabidopsis lineage-specific genes. Lineage specific genes in the
Brassicaceae and within Arabidopsis were enriched in genes of no known function
and appear to be fast evolving at the protein sequence level.
","abstract_html":"<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>","abstract_has_math":false,"creators":["Lin, Haining"],"institution":null,"degree_name":"Doctor of Philosophy","degree_level":"dissertation","degree_discipline":"Bioinformatics and Computational Biology","degree_department":"Department of Genetics, Development, and Cell Biology (LAS)","school":null,"contributors":[],"advisors":["Carol R. Buell","Xun Gu"],"committee_chairs":[],"committee_members":[],"year":2009,"date_issued":"2009-01-01","date_published":"2009-01-01","updated_at":"2026-07-24T02:38:34Z","subjects":[],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.31274/etd-180810-4323"],"render_values":[{"text":"https://doi.org/10.31274/etd-180810-4323","href":"https://doi.org/10.31274/etd-180810-4323","code":true}]},{"key":"dc:identifier","label":"Identifier","values":["archive/lib.dr.iastate.edu/etd/12194/"],"render_values":[{"text":"archive/lib.dr.iastate.edu/etd/12194/","href":null,"code":true}]}]},"links":{"outbound_url":"https://dr.lib.iastate.edu/handle/20.500.12876/26385","outbound_label":"Repository record","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Carol R. Buell","Xun Gu"]},{"key":"dc:contributor.department","label":"Department","values":["Department of Genetics, Development, and Cell Biology (LAS)"]},{"key":"dc:creator","label":"Author","values":["Lin, Haining"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2018-08-11T09:07:06.000"]},{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2020-06-30T02:40:59Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2020-06-30T02:40:59Z"]},{"key":"dc:date.issued","label":"Date","values":["2009-01-01"]},{"key":"dc:type","label":"Dc Type","values":["dissertation"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioinformatics and Computational Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["archive/lib.dr.iastate.edu/etd/12194/"]},{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.31274/etd-180810-4323"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://dr.lib.iastate.edu/handle/20.500.12876/26385"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["With the availability of near-complete rice genome sequence,
high-quality annotation data, and large expression profile datasets, we examined
segmental duplication, intron turnover, and paralogous protein family
composition in rice. These data suggest a large percentage of the rice genome
was involved in segmental duplication creating a large number of paralogous
families. We found that singleton and paralogous family genes differed
substantially not only in their likelihood of encoding a protein of known or
putative function but also in the distribution of specific gene function. We
showed that a significant portion of the duplicated genes in rice show divergent
expression although a correlation between sequence divergence and correlation of
expression could be seen in very young genes. We observed that intron evolution
within the rice genome following segmental duplication is dominated by intron
loss rather than intron gain. In addition, with the availability of more
complete or near-complete plant genomes and transcriptomes across a wide range
of species, we identified and characterized conserved Brassicaceae-specific
genes and Arabidopsis lineage-specific genes. Lineage specific genes in the
Brassicaceae and within Arabidopsis were enriched in genes of no known function
and appear to be fast evolving at the protein sequence level.
"]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes"]}]}],"canonical_facts":{"dc:contributor.advisor":["Carol R. Buell","Xun Gu"],"dc:contributor.department":["Department of Genetics, Development, and Cell Biology (LAS)"],"dc:creator":["Lin, Haining"],"dc:date":["2018-08-11T09:07:06.000"],"dc:date.accessioned":["2020-06-30T02:40:59Z"],"dc:date.available":["2020-06-30T02:40:59Z"],"dc:date.issued":["2009-01-01"],"dc:description.abstract":["With the availability of near-complete rice genome sequence,
high-quality annotation data, and large expression profile datasets, we examined
segmental duplication, intron turnover, and paralogous protein family
composition in rice. These data suggest a large percentage of the rice genome
was involved in segmental duplication creating a large number of paralogous
families. We found that singleton and paralogous family genes differed
substantially not only in their likelihood of encoding a protein of known or
putative function but also in the distribution of specific gene function. We
showed that a significant portion of the duplicated genes in rice show divergent
expression although a correlation between sequence divergence and correlation of
expression could be seen in very young genes. We observed that intron evolution
within the rice genome following segmental duplication is dominated by intron
loss rather than intron gain. In addition, with the availability of more
complete or near-complete plant genomes and transcriptomes across a wide range
of species, we identified and characterized conserved Brassicaceae-specific
genes and Arabidopsis lineage-specific genes. Lineage specific genes in the
Brassicaceae and within Arabidopsis were enriched in genes of no known function
and appear to be fast evolving at the protein sequence level.
"],"dc:format.mimetype":["application/pdf"],"dc:identifier":["archive/lib.dr.iastate.edu/etd/12194/"],"dc:identifier.doi":["https://doi.org/10.31274/etd-180810-4323"],"dc:identifier.uri":["https://dr.lib.iastate.edu/handle/20.500.12876/26385"],"dc:language.iso":["en"],"dc:title":["Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes"],"dc:type":["dissertation"],"thesis:degree_discipline":["Bioinformatics and Computational Biology"],"thesis:degree_level":["dissertation"],"thesis:degree_name":["Doctor of Philosophy"]},"updated_at":"2026-07-24T02:38:34Z"}