title: Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates.
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.
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. gershr@mail.ru.
authors.forename: Roman A
authors.initials: RA
authors.lastname: Gershgorin
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. gorbunov@iitp.ru.
authors.forename: Konstantin Yu
authors.initials: KY
authors.lastname: Gorbunov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. zverkov@iitp.ru.
authors.forename: Oleg A
authors.initials: OA
authors.lastname: Zverkov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. rubanov@iitp.ru.
authors.forename: Lev I
authors.initials: LI
authors.lastname: Rubanov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. slvstv@iitp.ru.
authors.forename: Alexandr V
authors.initials: AV
authors.lastname: Seliverstov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia. lyubetsk@iitp.ru.|Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskiye Gory 1, Main Building, Moscow 119991, Russia. lyubetsk@iitp.ru.
authors.forename: Vassily A
authors.initials: VA
authors.lastname: Lyubetsky
keywords: Ciliophora; chromosome structure; evolution; highly conserved elements; mitochondria; proteins clustering