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Life 2017, 7(1), 9; doi:10.3390/life7010009

Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates

1
Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia
2
Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskiye Gory 1, Main Building, Moscow 119991, Russia
*
Author to whom correspondence should be addressed.
Academic Editor: David Deamer
Received: 1 December 2016 / Revised: 19 February 2017 / Accepted: 24 February 2017 / Published: 27 February 2017
(This article belongs to the Section Life Sciences)
View Full-Text   |   Download PDF [1260 KB, uploaded 27 February 2017]   |  

Abstract

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. View Full-Text
Keywords: Ciliophora; mitochondria; highly conserved elements; proteins clustering; chromosome structure; evolution Ciliophora; mitochondria; highly conserved elements; proteins clustering; chromosome structure; evolution
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Gershgorin, R.A.; Gorbunov, K.Y.; Zverkov, O.A.; Rubanov, L.I.; Seliverstov, A.V.; Lyubetsky, V.A. Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates. Life 2017, 7, 9.

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