Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Finally, a comparative phylogenetic approach compared the gene families between Prochlorococcus and Synechococcus and concluded that Prochlorococcus evolved towards genome reduction. Mapping various overlapping patterns to the ancestral genomes along the Prochlorococcus phylogeny, we found that formation of overlapping genes has evolved faster than their degradation, which could be a mechanism of reductive genome evolution of Prochlorococcus.
","abstract_html":"<p>Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Finally, a comparative phylogenetic approach compared the gene families between Prochlorococcus and Synechococcus and concluded that Prochlorococcus evolved towards genome reduction. Mapping various overlapping patterns to the ancestral genomes along the Prochlorococcus phylogeny, we found that formation of overlapping genes has evolved faster than their degradation, which could be a mechanism of reductive genome evolution of Prochlorococcus.</p>","abstract_has_math":false,"creators":["Luo, Haiwei"],"institution":null,"degree_name":"Ph.D.","degree_level":"Campus Access Dissertation","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":["Robert Friedman"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2010,"date_issued":"2010-01-01T08:00:00Z","date_published":"2010-01-01T08:00:00Z","updated_at":"2026-07-24T04:37:14Z","subjects":["Life Sciences","Medicine and Health Sciences","Physical Sciences and Mathematics","gene order","genome reduction","mammal","phylogeny","Prochlorococcus","rearrangement"],"languages":[],"rights":["© 2010, Haiwei Luo"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarcommons.sc.edu/etd/216","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Robert Friedman"]},{"key":"dc:creator","label":"Author","values":["Luo, Haiwei"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Campus Access Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Life Sciences","Medicine and Health Sciences","Physical Sciences and Mathematics","gene order","genome reduction","mammal","phylogeny","Prochlorococcus","rearrangement"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["© 2010, Haiwei Luo"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://scholarcommons.sc.edu/etd/216"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Finally, a comparative phylogenetic approach compared the gene families between Prochlorococcus and Synechococcus and concluded that Prochlorococcus evolved towards genome reduction. Mapping various overlapping patterns to the ancestral genomes along the Prochlorococcus phylogeny, we found that formation of overlapping genes has evolved faster than their degradation, which could be a mechanism of reductive genome evolution of Prochlorococcus.
"]},{"key":"dc:title","label":"Title","values":["Evolutionary Analysis of Large-Scale Genomic Changes"]}]}],"canonical_facts":{"dc:contributor":["Robert Friedman"],"dc:creator":["Luo, Haiwei"],"dc:description.abstract":["Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Finally, a comparative phylogenetic approach compared the gene families between Prochlorococcus and Synechococcus and concluded that Prochlorococcus evolved towards genome reduction. Mapping various overlapping patterns to the ancestral genomes along the Prochlorococcus phylogeny, we found that formation of overlapping genes has evolved faster than their degradation, which could be a mechanism of reductive genome evolution of Prochlorococcus.
"],"dc:identifier":["https://scholarcommons.sc.edu/etd/216"],"dc:rights":["© 2010, Haiwei Luo"],"dc:subject":["Life Sciences","Medicine and Health Sciences","Physical Sciences and Mathematics","gene order","genome reduction","mammal","phylogeny","Prochlorococcus","rearrangement"],"dc:title":["Evolutionary Analysis of Large-Scale Genomic Changes"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Campus Access Dissertation"],"thesis:degree_name":["Ph.D."]},"updated_at":"2026-07-24T04:37:14Z"}