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dc.contributor.authorKaramitros, Timokratis
dc.contributor.authorvan Wilgenburg, Bonnie
dc.contributor.authorWills, Mark
dc.contributor.authorKlenerman, Paul
dc.contributor.authorMagiorkinis, Gkikas
dc.date.accessioned2018-11-07T00:31:21Z
dc.date.available2018-11-07T00:31:21Z
dc.date.issued2018-08-02
dc.identifier.issn1471-2164
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/284714
dc.description.abstractBACKGROUND: Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies. RESULTS: The MinION run of the HCMV (strain TB40/E) library resulted in ~ 47,000 reads from a single R9 flowcell and in ~ 100× average read depth across the virus genome. We developed a novel, self-correcting bioinformatics algorithm to assemble the pooled HCMV genomes in three stages. In the first stage of the bioinformatics algorithm, long contigs (N50 = 21,892) of lower accuracy were reconstructed. In the second stage, short contigs (N50 = 5686) of higher accuracy were assembled, while in the final stage the high quality contigs served as template for the correction of the longer contigs resulting in a high-accuracy, full genome assembly (N50 = 41,056). We were able to reconstruct a single representative haplotype without employing any scaffolding steps. The majority (98.8%) of the genomic features from the reference strain were accurately annotated on this full genome construct. Our method also allowed the detection of multiple alternative sub-genomic fragments and non-canonical structures suggesting rearrangement events between the unique (UL /US) and the repeated (T/IRL/S) genomic regions. CONCLUSIONS: Third generation high-throughput sequencing technologies can accurately reconstruct full-length HCMV genomes including their low-complexity and highly repetitive regions. Full-length HCMV genomes could prove crucial in understanding the genetic determinants and viral evolution underpinning drug resistance, virulence and pathogenesis.
dc.format.mediumElectronic
dc.languageeng
dc.publisherSpringer Science and Business Media LLC
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectCell Line
dc.subjectHumans
dc.subjectCytomegalovirus
dc.subjectSequence Analysis, DNA
dc.subjectEvolution, Molecular
dc.subjectGenome, Viral
dc.subjectAlgorithms
dc.subjectNanopores
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectGenome Size
dc.titleNanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.
dc.typeArticle
prism.issueIdentifier1
prism.publicationDate2018
prism.publicationNameBMC Genomics
prism.startingPage577
prism.volume19
dc.identifier.doi10.17863/CAM.32086
dcterms.dateAccepted2018-07-19
rioxxterms.versionofrecord10.1186/s12864-018-4949-6
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2018-08-02
dc.contributor.orcidKaramitros, Timokratis [0000-0003-0841-9159]
dc.contributor.orcidWills, Mark [0000-0001-8548-5729]
dc.identifier.eissn1471-2164
rioxxterms.typeJournal Article/Review
pubs.funder-project-idMedical Research Council (G0701279)
pubs.funder-project-idMedical Research Council (G9202171)
pubs.funder-project-idMedical Research Council (MR/K021087/1)
cam.issuedOnline2018-08-02


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International