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dc.creatorMisas E. 
dc.creatorMuñoz J.F. 
dc.creatorGallo J.E. 
dc.creatorMcEwen J.G. 
dc.creatorClay O.K. 
dc.date.accessioned2020-05-26T00:05:10Z
dc.date.available2020-05-26T00:05:10Z
dc.date.created2016
dc.identifier.issn14769271
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/23762
dc.description.abstract"The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention. © 2016 Elsevier Ltd."
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.relation.ispartof"Computational Biology and Chemistry, ISSN:14769271, Vol.61,(2016); pp. 258-269"
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84960122132&doi=10.1016%2fj.compbiolchem.2016.02.016&partnerID=40&md5=8386bf3b7527458187c667fa03422601
dc.sourceinstname:Universidad del Rosario
dc.sourcereponame:Repositorio Institucional EdocUR
dc.titleFrom NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity
dc.typearticle
dc.publisherElsevier Ltd
dc.subject.keyword"Dna
dc.subject.keywordFungi
dc.subject.keywordGene encoding
dc.subject.keywordMitochondria
dc.subject.keywordNucleic acids
dc.subject.keywordScreening
dc.subject.keywordDe novo assemblies
dc.subject.keywordDna secondary structures
dc.subject.keywordEukaryotic genome
dc.subject.keywordGenome assembly
dc.subject.keywordMitochondrial genomes
dc.subject.keywordNext-generation sequencing
dc.subject.keywordPremature termination
dc.subject.keywordRegions of interest
dc.subject.keywordGenes
dc.subject.keywordFungal genome
dc.subject.keywordMetabolism
dc.subject.keywordMitochondrion
dc.subject.keywordGenome, fungal
dc.subject.keywordMitochondria
dc.subject.keywordDna secondary structure
dc.subject.keywordFungal mitochondria
dc.subject.keywordGenome assembly
dc.subject.keywordNext generation sequencing
dc.subject.keywordRepetitive dna"
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.type.spaArtículo
dc.rights.accesoAbierto (Texto Completo)
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doihttps://doi.org/10.1016/j.compbiolchem.2016.02.016


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