Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates
Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for con...
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MDPI AG
2017-02-01
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| Series: | Life |
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| Online Access: | http://www.mdpi.com/2075-1729/7/1/9 |
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| author | Roman A. Gershgorin Konstantin Yu. Gorbunov Oleg A. Zverkov Lev I. Rubanov Alexandr V. Seliverstov Vassily A. Lyubetsky |
| author_facet | Roman A. Gershgorin Konstantin Yu. Gorbunov Oleg A. Zverkov Lev I. Rubanov Alexandr V. Seliverstov Vassily A. Lyubetsky |
| author_sort | Roman A. Gershgorin |
| collection | DOAJ |
| description | Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome. |
| first_indexed | 2024-04-11T13:57:37Z |
| format | Article |
| id | doaj.art-f760835d9b764ec4bb8d1a2171f5298b |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T13:57:37Z |
| publishDate | 2017-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-f760835d9b764ec4bb8d1a2171f5298b2022-12-22T04:20:13ZengMDPI AGLife2075-17292017-02-0171910.3390/life7010009life7010009Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in CiliatesRoman A. Gershgorin0Konstantin Yu. Gorbunov1Oleg A. Zverkov2Lev I. Rubanov3Alexandr V. Seliverstov4Vassily A. Lyubetsky5Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, RussiaRecent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome.http://www.mdpi.com/2075-1729/7/1/9Ciliophoramitochondriahighly conserved elementsproteins clusteringchromosome structureevolution |
| spellingShingle | Roman A. Gershgorin Konstantin Yu. Gorbunov Oleg A. Zverkov Lev I. Rubanov Alexandr V. Seliverstov Vassily A. Lyubetsky Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates Life Ciliophora mitochondria highly conserved elements proteins clustering chromosome structure evolution |
| title | Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates |
| title_full | Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates |
| title_fullStr | Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates |
| title_full_unstemmed | Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates |
| title_short | Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates |
| title_sort | highly conserved elements and chromosome structure evolution in mitochondrial genomes in ciliates |
| topic | Ciliophora mitochondria highly conserved elements proteins clustering chromosome structure evolution |
| url | http://www.mdpi.com/2075-1729/7/1/9 |
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