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From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity

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dc.creatorMisas E.spa
dc.creatorMuñoz J.F.spa
dc.creatorGallo J.E.spa
dc.creatorMcEwen J.G.spa
dc.creatorClay O.K.spa
dc.date.accessioned2020-05-26T00:05:10Z
dc.date.available2020-05-26T00:05:10Z
dc.date.created2016spa
dc.description.abstractThe 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.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1016/j.compbiolchem.2016.02.016
dc.identifier.issn14769271
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/23762
dc.language.isoengspa
dc.publisherElsevier Ltdspa
dc.relation.citationEndPage269
dc.relation.citationStartPage258
dc.relation.citationTitleComputational Biology and Chemistry
dc.relation.citationVolumeVol. 61
dc.relation.ispartofComputational Biology and Chemistry, ISSN:14769271, Vol.61,(2016); pp. 258-269spa
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=8386bf3b7527458187c667fa03422601spa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subject.keywordDnaspa
dc.subject.keywordFungispa
dc.subject.keywordGene encodingspa
dc.subject.keywordMitochondriaspa
dc.subject.keywordNucleic acidsspa
dc.subject.keywordScreeningspa
dc.subject.keywordDe novo assembliesspa
dc.subject.keywordDna secondary structuresspa
dc.subject.keywordEukaryotic genomespa
dc.subject.keywordGenome assemblyspa
dc.subject.keywordMitochondrial genomesspa
dc.subject.keywordNext-generation sequencingspa
dc.subject.keywordPremature terminationspa
dc.subject.keywordRegions of interestspa
dc.subject.keywordGenesspa
dc.subject.keywordFungal genomespa
dc.subject.keywordMetabolismspa
dc.subject.keywordMitochondrionspa
dc.subject.keywordGenomeeng
dc.subject.keywordMitochondriaspa
dc.subject.keywordDna secondary structurespa
dc.subject.keywordFungal mitochondriaspa
dc.subject.keywordGenome assemblyspa
dc.subject.keywordNext generation sequencingspa
dc.subject.keywordRepetitive dnaspa
dc.titleFrom NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexityspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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