Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
PublisherNature Publishing Group
MetadataShow full item record
AbstractLateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16). Using a sequencing depth threshold of two or three standard deviations above the mean, 96.9% or 96.7% of positions, respectively, are predicted in the same manner between the two datasets, with 24.7% or 42.5% of the known 49.0 kbp of LGT sequence predicted correctly, respectively. Prior qPCR results for nuwts showed similar correlations for both datasets supporting our conclusion that oligonucleotide-based capture methods can be used to obtain sequences from Wolbachia-host LGT. However, at least 121 positions had a minority of the reads supporting the endosymbiont reference base call using the capture data, illustrating that sequence reads from endosymbiont-host LGTs can confound endosymbiont genome projects, erroneously altering the called consensus genome, a problem that is irrespective to the sequencing technology or platform. Copyright 2017 The Author(s).
SponsorsThis work was funded by the National Institutes of Health through the NIH Director's New Innovator Award Program (1-DP2-OD007372), National Institute of Allergy and Infectious Diseases (U19AI110820), and internal funding from New England Biolabs, Inc.
Illumina paired-end data
Gene Transfer, Horizontal
High-Throughput Nucleotide Sequencing
Real-Time Polymerase Chain Reaction
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85018268181&doi=10.1038%2fs41598-017-00814-4&partnerID=40&md5=fd934a4087ce516fa729c91ffa1729ad; http://hdl.handle.net/10713/11062
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- Authors: Luck AN, Slatko BE, Foster JM
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- Issue date: 2007 Sep 21
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