From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.
Identifieur interne : 001211 ( PubMed/Corpus ); précédent : 001210; suivant : 001212From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.
Auteurs : Elizabeth Misas ; José Fernando Mu Oz ; Juan Esteban Gallo ; Juan Guillermo Mcewen ; Oliver Keatinge ClaySource :
- Computational biology and chemistry [ 1476-928X ] ; 2016.
English descriptors
- KwdEn :
- MESH :
- metabolism : Mitochondria.
- Genome, Fungal.
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.
DOI: 10.1016/j.compbiolchem.2016.02.016
PubMed: 26970210
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Electronic address: oliver.clay@gmail.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Computational biology and chemistry</title><idno type="eISSN">1476-928X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Fungal</term><term>Mitochondria (metabolism)</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Mitochondria</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Fungal</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26970210</PMID><DateCompleted><Year>2016</Year><Month>12</Month><Day>23</Day></DateCompleted><DateRevised><Year>2016</Year><Month>12</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1476-928X</ISSN><JournalIssue CitedMedium="Internet"><Volume>61</Volume><PubDate><Year>2016</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Computational biology and chemistry</Title><ISOAbbreviation>Comput Biol Chem</ISOAbbreviation></Journal><ArticleTitle>From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.</ArticleTitle><Pagination><MedlinePgn>258-69</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.compbiolchem.2016.02.016</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1476-9271(15)30101-8</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2016 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Misas</LastName><ForeName>Elizabeth</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Muñoz</LastName><ForeName>José Fernando</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gallo</LastName><ForeName>Juan Esteban</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McEwen</LastName><ForeName>Juan Guillermo</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clay</LastName><ForeName>Oliver Keatinge</ForeName><Initials>OK</Initials><AffiliationInfo><Affiliation>Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia. Electronic address: oliver.clay@gmail.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Comput Biol Chem</MedlineTA><NlmUniqueID>101157394</NlmUniqueID><ISSNLinking>1476-9271</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008928" MajorTopicYN="N">Mitochondria</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DNA secondary structure</Keyword><Keyword MajorTopicYN="N">Fungal mitochondria</Keyword><Keyword MajorTopicYN="N">Genome assembly</Keyword><Keyword MajorTopicYN="N">Next generation sequencing</Keyword><Keyword MajorTopicYN="N">Repetitive DNA</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>07</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>02</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>02</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>3</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>3</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>12</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26970210</ArticleId><ArticleId IdType="pii">S1476-9271(15)30101-8</ArticleId><ArticleId IdType="doi">10.1016/j.compbiolchem.2016.02.016</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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