Target enrichment of metazoan mitochondrial DNA with hybridization capture probes

High-throughput DNA sequencing studies allow rapid and widescale investigations into complex assemblages of organisms that would otherwise remain infeasible. Recently scientists have begun to apply metagenomic sequencing (sequencing of the complete pool of DNA from a sample) to investigate microscop...

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Autores principales:	Joseph Sevigny, Francesca Leasi, Stephen Simpson, Maikon Di Domenico, Katharina M. Jörger, Jon L. Norenburg, W. Kelley Thomas
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Biodiversity Sequencing Metagenomics Meiofauna Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/d51790eeae4644a6af68375263c27686
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spelling	oai:doaj.org-article:d51790eeae4644a6af68375263c276862021-12-01T04:31:20ZTarget enrichment of metazoan mitochondrial DNA with hybridization capture probes1470-160X10.1016/j.ecolind.2020.106973https://doaj.org/article/d51790eeae4644a6af68375263c276862021-02-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1470160X20309122https://doaj.org/toc/1470-160XHigh-throughput DNA sequencing studies allow rapid and widescale investigations into complex assemblages of organisms that would otherwise remain infeasible. Recently scientists have begun to apply metagenomic sequencing (sequencing of the complete pool of DNA from a sample) to investigate microscopic animal communities. Mitochondrial genomes are an important locus for such studies; however, current databases of complete mitochondrial genomes remain incomplete, and many important meiofaunal clades are underrepresented or missing entirely. This underrepresentation is likely due to the low amount of input DNA acquired from meiofaunal individuals, the impossibility of pooling animals because of high levels of cryptic speciation, and the paucity of researchers collecting and studying these animals. Here we help to alleviate the first two barriers by developing a method of enriching animal mtDNA from next-generation sequencing libraries by using hybridization capture probes. These hybrid-capture probes were designed based on the complete collection of mitochondrial genomes available from GenBank and are suitable for enrichment of diverse animal lineages. We demonstrate the protocol on forty-seven meiofaunal specimens spanning four different phyla. Overall, we observed an average of ~450× fold enrichment over standard NGS sequencing library preparation. In addition, we were able to enrich the mtDNA from taxa distantly related to those in the database, indicating that even animals that were not directly targeted by the probe design can be enriched with this method.Joseph SevignyFrancesca LeasiStephen SimpsonMaikon Di DomenicoKatharina M. JörgerJon L. NorenburgW. Kelley ThomasElsevierarticleBiodiversitySequencingMetagenomicsMeiofaunaEcologyQH540-549.5ENEcological Indicators, Vol 121, Iss , Pp 106973- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biodiversity Sequencing Metagenomics Meiofauna Ecology QH540-549.5
spellingShingle	Biodiversity Sequencing Metagenomics Meiofauna Ecology QH540-549.5 Joseph Sevigny Francesca Leasi Stephen Simpson Maikon Di Domenico Katharina M. Jörger Jon L. Norenburg W. Kelley Thomas Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
description	High-throughput DNA sequencing studies allow rapid and widescale investigations into complex assemblages of organisms that would otherwise remain infeasible. Recently scientists have begun to apply metagenomic sequencing (sequencing of the complete pool of DNA from a sample) to investigate microscopic animal communities. Mitochondrial genomes are an important locus for such studies; however, current databases of complete mitochondrial genomes remain incomplete, and many important meiofaunal clades are underrepresented or missing entirely. This underrepresentation is likely due to the low amount of input DNA acquired from meiofaunal individuals, the impossibility of pooling animals because of high levels of cryptic speciation, and the paucity of researchers collecting and studying these animals. Here we help to alleviate the first two barriers by developing a method of enriching animal mtDNA from next-generation sequencing libraries by using hybridization capture probes. These hybrid-capture probes were designed based on the complete collection of mitochondrial genomes available from GenBank and are suitable for enrichment of diverse animal lineages. We demonstrate the protocol on forty-seven meiofaunal specimens spanning four different phyla. Overall, we observed an average of ~450× fold enrichment over standard NGS sequencing library preparation. In addition, we were able to enrich the mtDNA from taxa distantly related to those in the database, indicating that even animals that were not directly targeted by the probe design can be enriched with this method.
format	article
author	Joseph Sevigny Francesca Leasi Stephen Simpson Maikon Di Domenico Katharina M. Jörger Jon L. Norenburg W. Kelley Thomas
author_facet	Joseph Sevigny Francesca Leasi Stephen Simpson Maikon Di Domenico Katharina M. Jörger Jon L. Norenburg W. Kelley Thomas
author_sort	Joseph Sevigny
title	Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
title_short	Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
title_full	Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
title_fullStr	Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
title_full_unstemmed	Target enrichment of metazoan mitochondrial DNA with hybridization capture probes
title_sort	target enrichment of metazoan mitochondrial dna with hybridization capture probes
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/d51790eeae4644a6af68375263c27686
work_keys_str_mv	AT josephsevigny targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT francescaleasi targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT stephensimpson targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT maikondidomenico targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT katharinamjorger targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT jonlnorenburg targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes AT wkelleythomas targetenrichmentofmetazoanmitochondrialdnawithhybridizationcaptureprobes
_version_	1718405871315189760

Target enrichment of metazoan mitochondrial DNA with hybridization capture probes

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