High evolutionary turnover of satellite families in Caenorhabditis

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  • dc.contributor.author Subirana, Juan A.ca
  • dc.contributor.author Albà Soler, Marca
  • dc.contributor.author Messeguer, Xavierca
  • dc.date.accessioned 2015-11-25T14:46:54Z
  • dc.date.available 2015-11-25T14:46:54Z
  • dc.date.issued 2015ca
  • dc.description.abstract Background. The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. We take advantage of the previously developed SATFIND program to study the satellites in four Caenorhabditis species and investigate these questions./nMethods. The identification and comparison of satellites is carried out in three steps. First we find all the satellites present in each species with the SATFIND program. Each satellite is defined by its length, number of repeats, and repeat sequence. Only satellites with at least ten repeats are considered. In the second step we build satellite families with a newly developed alignment program. Satellite families are defined by a consensus sequence and the number of satellites in the family. Finally we compare the consensus sequence of satellite families in different species./nResults. We give a catalog of individual satellites in each species. We have also identified satellite families with a related sequence and compare them in different species. We analyze the turnover of satellites: they increased in size through duplications of fragments of 100-300 bases. It appears that in many cases they have undergone an explosive expansion. In C. elegans we have identified a subset of large satellites that have strong affinity for the centromere protein CENP-A. We have also compared our results with those obtained from other species, including one nematode and three mammals./nConclusions. Most satellite families found in Caenorhabditis are species-specific; in particular those with long repeats. A subset of these satellites may facilitate the formation of kinetochores in mitosis. Other satellite families in C. elegans are either related to Helitron transposons or to meiotic pairing centers.
  • dc.description.sponsorship We are thankful to Dr. Lourdes Campos for valuable suggestions. Also to Messrs. W. Blevins and F. Acosta-Reyes for help in the preparation of the manuscript and figures. This work was funded by Ministerio de Economía y Competitividad (TIN2010-21062-C02-01, TIN2013-45732-C4-3-P, BFU2012-36820 and 2009–10380) with additional Feder funds.
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Subirana J, Albà M, Messeguer X. High evolutionary turnover of satellite families in Caenorhabditis. BMC Evol Biol. 2015;15:218. DOI: 10.1186/s12862-015-0495-xca
  • dc.identifier.doi http://dx.doi.org/10.1186/s12862-015-0495-x
  • dc.identifier.issn 1471-2148ca
  • dc.identifier.uri http://hdl.handle.net/10230/25217
  • dc.language.iso engca
  • dc.publisher BioMed Centralca
  • dc.relation.ispartof BMC Evolutionary Biology. 2015;15:218
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/TIN2010-21062
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/TIN2013-45732
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2012-36820
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009–10380
  • dc.rights © 2015 Subirana et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were madeca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Nematodes
  • dc.subject.keyword Satellite DNA
  • dc.subject.keyword Tandem repeat sequences
  • dc.subject.keyword Caenorhabditis elegans
  • dc.subject.keyword Mitosis
  • dc.subject.keyword DNA elimination
  • dc.subject.other Mitosi
  • dc.title High evolutionary turnover of satellite families in Caenorhabditisca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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