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dc.contributor.author
Schmid, Michael
dc.contributor.author
Frei, Daniel
dc.contributor.author
Patrignani, Andrea
dc.contributor.author
Schlapbach, Ralph
dc.contributor.author
Frey, Jürg E.
dc.contributor.author
Remus-Emsermann, Mitja N.P.
dc.contributor.author
Ahrens, Christian H.
dc.date.accessioned
2019-03-27T16:00:04Z
dc.date.available
2018-12-05T16:22:46Z
dc.date.available
2018-12-10T14:52:45Z
dc.date.available
2019-03-27T16:00:04Z
dc.date.issued
2018-09-28
dc.identifier.other
10.1093/nar/gky726
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/309039
dc.identifier.doi
10.3929/ethz-b-000309039
dc.description.abstract
Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this ‘dark matter’ for de novo genome assembly of prokaryotes. Several of these ‘dark matter’ genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Oxford University Press (OUP)
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.title
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2018-08-23
ethz.journal.title
Nucleic acids research
ethz.journal.volume
46
en_US
ethz.journal.issue
17
en_US
ethz.pages.start
8953
en_US
ethz.pages.end
8965
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.publication.place
Oxford
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung / Domain VP Research::02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::08828 - Schlapbach, Ralph (Tit.-Prof.)
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung / Domain VP Research::02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
ethz.date.deposited
2018-12-05T16:22:47Z
ethz.source
WOS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-12-10T14:52:54Z
ethz.rosetta.lastUpdated
2020-02-15T18:07:20Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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