Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

Abstract Lateral 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...

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Autores principales:	Julie C. Dunning Hotopp, Barton E. Slatko, Jeremy M. Foster
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/615865d84e6d43a0b823249be7faf09c
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spelling	oai:doaj.org-article:615865d84e6d43a0b823249be7faf09c2021-12-02T15:05:48ZTargeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers10.1038/s41598-017-00814-42045-2322https://doaj.org/article/615865d84e6d43a0b823249be7faf09c2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00814-4https://doaj.org/toc/2045-2322Abstract Lateral 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.Julie C. Dunning HotoppBarton E. SlatkoJeremy M. FosterNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Julie C. Dunning Hotopp Barton E. Slatko Jeremy M. Foster Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
description	Abstract Lateral 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.
format	article
author	Julie C. Dunning Hotopp Barton E. Slatko Jeremy M. Foster
author_facet	Julie C. Dunning Hotopp Barton E. Slatko Jeremy M. Foster
author_sort	Julie C. Dunning Hotopp
title	Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
title_short	Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
title_full	Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
title_fullStr	Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
title_full_unstemmed	Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers
title_sort	targeted enrichment and sequencing of recent endosymbiont-host lateral gene transfers
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/615865d84e6d43a0b823249be7faf09c
work_keys_str_mv	AT juliecdunninghotopp targetedenrichmentandsequencingofrecentendosymbionthostlateralgenetransfers AT bartoneslatko targetedenrichmentandsequencingofrecentendosymbionthostlateralgenetransfers AT jeremymfoster targetedenrichmentandsequencingofrecentendosymbionthostlateralgenetransfers
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Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

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