Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
Identifieur interne : 001C29 ( PubMed/Corpus ); précédent : 001C28; suivant : 001C30Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
Auteurs : David Williams ; William L. Trimble ; Meghan Shilts ; Folker Meyer ; Howard OchmanSource :
- BMC genomics [ 1471-2164 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
Abstract
The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.
DOI: 10.1186/1471-2164-14-537
PubMed: 23924250
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pubmed:23924250Le document en format XML
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<author><name sortKey="Williams, David" sort="Williams, David" uniqKey="Williams D" first="David" last="Williams">David Williams</name>
<affiliation><nlm:affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</nlm:affiliation>
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<author><name sortKey="Trimble, William L" sort="Trimble, William L" uniqKey="Trimble W" first="William L" last="Trimble">William L. Trimble</name>
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<author><name sortKey="Shilts, Meghan" sort="Shilts, Meghan" uniqKey="Shilts M" first="Meghan" last="Shilts">Meghan Shilts</name>
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<author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name>
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<author><name sortKey="Ochman, Howard" sort="Ochman, Howard" uniqKey="Ochman H" first="Howard" last="Ochman">Howard Ochman</name>
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<author><name sortKey="Williams, David" sort="Williams, David" uniqKey="Williams D" first="David" last="Williams">David Williams</name>
<affiliation><nlm:affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</nlm:affiliation>
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<author><name sortKey="Trimble, William L" sort="Trimble, William L" uniqKey="Trimble W" first="William L" last="Trimble">William L. Trimble</name>
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<author><name sortKey="Shilts, Meghan" sort="Shilts, Meghan" uniqKey="Shilts M" first="Meghan" last="Shilts">Meghan Shilts</name>
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<author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name>
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<series><title level="j">BMC genomics</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Escherichia coli (genetics)</term>
<term>Gene Dosage (genetics)</term>
<term>Genome Size</term>
<term>Genome, Bacterial (genetics)</term>
<term>Genomics</term>
<term>Repetitive Sequences, Nucleic Acid (genetics)</term>
<term>Sequence Analysis</term>
<term>Time Factors</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term>
<term>Gene Dosage</term>
<term>Genome, Bacterial</term>
<term>Repetitive Sequences, Nucleic Acid</term>
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<keywords scheme="MESH" xml:lang="en"><term>Genome Size</term>
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<front><div type="abstract" xml:lang="en">The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.</div>
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<Month>Aug</Month>
<Day>08</Day>
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<Title>BMC genomics</Title>
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<ArticleTitle>Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Application of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.</AbstractText>
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<AffiliationInfo><Affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</Affiliation>
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<MeshHeading><DescriptorName UI="D012091" MajorTopicYN="N">Repetitive Sequences, Nucleic Acid</DescriptorName>
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<MeshHeading><DescriptorName UI="D017421" MajorTopicYN="Y">Sequence Analysis</DescriptorName>
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<ReferenceList><Reference><Citation>J Bacteriol. 1992 Jul;174(14):4525-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">1624445</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genetics. 1992 May;131(1):9-20</Citation>
<ArticleIdList><ArticleId IdType="pubmed">1317318</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Bacteriol. 1995 Oct;177(20):5784-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">7592324</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Comput Biol. 1995 Summer;2(2):291-306</Citation>
<ArticleIdList><ArticleId IdType="pubmed">7497130</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Microbiology. 1996 Aug;142 ( Pt 8):2087-95</Citation>
<ArticleIdList><ArticleId IdType="pubmed">8760921</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 1997 Sep 5;277(5331):1453-62</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9278503</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2005 Mar 1;21(5):582-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15374857</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plasmid. 2005 Jul;54(1):86-91</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15907542</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Biol Evol. 2006 Apr;23(4):723-33</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16373392</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Microbiol. 2006 Jun;60(5):1136-51</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16689791</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Biol Evol. 2006 Jun;23(6):1156-68</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16533821</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS Genet. 2007 Aug;3(8):e142</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17784789</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2007;8:321</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17868451</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2007;8:456</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18070355</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2008 Feb 15;24(4):462-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18202027</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Bacteriol. 2008 Oct;190(20):6881-93</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18676672</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2008;9:517</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18976482</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS Genet. 2009 Jan;5(1):e1000344</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19165319</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2677-82</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19188606</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Methods. 2009 Sep;6(9):673-6</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19648916</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17939-44</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19815525</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS Comput Biol. 2009 Dec;5(12):e1000593</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20011103</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):133-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20018669</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Bioinformatics. 2010;11:485</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20875133</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2010;11(11):R116</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21114842</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Comput Biol. 2011 Mar;18(3):523-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21385052</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2012 Mar;22(3):549-56</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22156294</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Ind Microbiol Biotechnol. 2012 Apr;39(4):629-39</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22075923</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2012;13:92</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22417298</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22847406</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Microbiol. 2012 Sep;10(9):599-606</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22864262</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genomics. 2012 Sep;100(3):167-75</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22750556</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2013 Jan 7;41(1):e3</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22941634</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2001;17 Suppl 1:S225-33</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11473013</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2002 Apr 15;30(8):1826-33</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11937637</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2003 Aug;13(8):1916-22</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12902383</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2003 Oct;13(10):2306-15</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12975312</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2004 Sep 1;20(13):2067-74</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15059830</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 1982 Aug 19;298(5876):760-2</Citation>
<ArticleIdList><ArticleId IdType="pubmed">7110312</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Cell. 1984 Jul;37(3):1015-26</Citation>
<ArticleIdList><ArticleId IdType="pubmed">6378385</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation>
<ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Res Microbiol. 1991 Feb-Apr;142(2-3):217-22</Citation>
<ArticleIdList><ArticleId IdType="pubmed">1656494</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genetics. 1993 Mar;133(3):449-54</Citation>
<ArticleIdList><ArticleId IdType="pubmed">8384142</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
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