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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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Autores principales: Gershgorin, Roman A., Gorbunov, Konstantin Yu., Zverkov, Oleg A., Rubanov, Lev I., Seliverstov, Alexandr V., Lyubetsky, Vassily A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370409/
https://www.ncbi.nlm.nih.gov/pubmed/28264444
http://dx.doi.org/10.3390/life7010009
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author Gershgorin, Roman A.
Gorbunov, Konstantin Yu.
Zverkov, Oleg A.
Rubanov, Lev I.
Seliverstov, Alexandr V.
Lyubetsky, Vassily A.
author_facet Gershgorin, Roman A.
Gorbunov, Konstantin Yu.
Zverkov, Oleg A.
Rubanov, Lev I.
Seliverstov, Alexandr V.
Lyubetsky, Vassily A.
author_sort Gershgorin, Roman A.
collection PubMed
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.
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spelling pubmed-53704092017-04-05 Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates Gershgorin, Roman A. Gorbunov, Konstantin Yu. Zverkov, Oleg A. Rubanov, Lev I. Seliverstov, Alexandr V. Lyubetsky, Vassily A. Life (Basel) Article 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. MDPI 2017-02-27 /pmc/articles/PMC5370409/ /pubmed/28264444 http://dx.doi.org/10.3390/life7010009 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gershgorin, Roman A.
Gorbunov, Konstantin Yu.
Zverkov, Oleg A.
Rubanov, Lev I.
Seliverstov, Alexandr V.
Lyubetsky, Vassily A.
Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370409/
https://www.ncbi.nlm.nih.gov/pubmed/28264444
http://dx.doi.org/10.3390/life7010009
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