Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.
Identifieur interne : 001E06 ( PubMed/Curation ); précédent : 001E05; suivant : 001E07Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.
Auteurs : Jennifer Monson-Miller [États-Unis] ; Diana C. Sanchez-Mendez ; Joseph Fass ; Isabelle M. Henry ; Thomas H. Tai ; Luca ComaiSource :
- BMC genomics [ 1471-2164 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Arabidopsis, Oryza.
- métabolisme : Type II site-specific deoxyribonuclease.
- normes : Analyse de séquence d'ADN.
- Analyse de séquence d'ADN, Génome végétal, Génotype, Mutation, Polymorphisme de nucléotide simple, Valeurs de référence.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Deoxyribonucleases, Type II Site-Specific.
- genetics : Arabidopsis, Oryza.
- methods : Sequence Analysis, DNA.
- standards : Sequence Analysis, DNA.
- Genome, Plant, Genotype, Mutation, Polymorphism, Single Nucleotide, Reference Values.
Abstract
The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference.
DOI: 10.1186/1471-2164-13-72
PubMed: 22333298
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Sanchez-Mendez</name></author><author><name sortKey="Fass, Joseph" sort="Fass, Joseph" uniqKey="Fass J" first="Joseph" last="Fass">Joseph Fass</name></author><author><name sortKey="Henry, Isabelle M" sort="Henry, Isabelle M" uniqKey="Henry I" first="Isabelle M" last="Henry">Isabelle M. Henry</name></author><author><name sortKey="Tai, Thomas H" sort="Tai, Thomas H" uniqKey="Tai T" first="Thomas H" last="Tai">Thomas H. Tai</name></author><author><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22333298</idno><idno type="pmid">22333298</idno><idno type="doi">10.1186/1471-2164-13-72</idno><idno type="wicri:Area/PubMed/Corpus">001E06</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E06</idno><idno type="wicri:Area/PubMed/Curation">001E06</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E06</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.</title><author><name sortKey="Monson Miller, Jennifer" sort="Monson Miller, Jennifer" uniqKey="Monson Miller J" first="Jennifer" last="Monson-Miller">Jennifer Monson-Miller</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology and Genome Center, UC Davis, Davis, California 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Biology and Genome Center, UC Davis, Davis, California 95616</wicri:regionArea></affiliation></author><author><name sortKey="Sanchez Mendez, Diana C" sort="Sanchez Mendez, Diana C" uniqKey="Sanchez Mendez D" first="Diana C" last="Sanchez-Mendez">Diana C. Sanchez-Mendez</name></author><author><name sortKey="Fass, Joseph" sort="Fass, Joseph" uniqKey="Fass J" first="Joseph" last="Fass">Joseph Fass</name></author><author><name sortKey="Henry, Isabelle M" sort="Henry, Isabelle M" uniqKey="Henry I" first="Isabelle M" last="Henry">Isabelle M. Henry</name></author><author><name sortKey="Tai, Thomas H" sort="Tai, Thomas H" uniqKey="Tai T" first="Thomas H" last="Tai">Thomas H. Tai</name></author><author><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Deoxyribonucleases, Type II Site-Specific (metabolism)</term><term>Genome, Plant</term><term>Genotype</term><term>Mutation</term><term>Oryza (genetics)</term><term>Polymorphism, Single Nucleotide</term><term>Reference Values</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Analysis, DNA (standards)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Analyse de séquence d'ADN (normes)</term><term>Arabidopsis (génétique)</term><term>Génome végétal</term><term>Génotype</term><term>Mutation</term><term>Oryza (génétique)</term><term>Polymorphisme de nucléotide simple</term><term>Type II site-specific deoxyribonuclease (métabolisme)</term><term>Valeurs de référence</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Deoxyribonucleases, Type II Site-Specific</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Type II site-specific deoxyribonuclease</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Analyse de séquence d'ADN</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Genotype</term><term>Mutation</term><term>Polymorphism, Single Nucleotide</term><term>Reference Values</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génome végétal</term><term>Génotype</term><term>Mutation</term><term>Polymorphisme de nucléotide simple</term><term>Valeurs de référence</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22333298</PMID><DateCompleted><Year>2012</Year><Month>05</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><PubDate><Year>2012</Year><Month>Feb</Month><Day>14</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.</ArticleTitle><Pagination><MedlinePgn>72</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-13-72</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide) were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to NlaIII restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15×. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This de novo "genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The combination of a simple and cost-effective library construction method, with Illumina sequencing, and the use of a bioinformatic pipeline allows practical SNP discovery regardless of whether a genomic reference is available.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Monson-Miller</LastName><ForeName>Jennifer</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Plant Biology and Genome Center, UC Davis, Davis, California 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sanchez-Mendez</LastName><ForeName>Diana C</ForeName><Initials>DC</Initials></Author><Author ValidYN="Y"><LastName>Fass</LastName><ForeName>Joseph</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Henry</LastName><ForeName>Isabelle M</ForeName><Initials>IM</Initials></Author><Author ValidYN="Y"><LastName>Tai</LastName><ForeName>Thomas H</ForeName><Initials>TH</Initials></Author><Author ValidYN="Y"><LastName>Comai</LastName><ForeName>Luca</ForeName><Initials>L</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>EC 3.1.21.-</RegistryNumber><NameOfSubstance UI="C048422">endodeoxyribonuclease NlaIII</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.21.4</RegistryNumber><NameOfSubstance UI="D015252">Deoxyribonucleases, Type II Site-Specific</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015252" MajorTopicYN="N">Deoxyribonucleases, Type II Site-Specific</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012016" MajorTopicYN="N">Reference Values</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName><QualifierName UI="Q000592" MajorTopicYN="N">standards</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2011</Year><Month>09</Month><Day>09</Day></PubMedPubDate><PubMedPubDate 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