Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.

DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequenci...

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Autores principales:	Nathan Wales, J Alberto Romero-Navarro, Enrico Cappellini, M Thomas P Gilbert
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/00fd7538cd974b0b9fd60f084943320a
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spelling	oai:doaj.org-article:00fd7538cd974b0b9fd60f084943320a2021-11-18T07:04:42ZChoosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.1932-620310.1371/journal.pone.0045644https://doaj.org/article/00fd7538cd974b0b9fd60f084943320a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029156/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.Nathan WalesJ Alberto Romero-NavarroEnrico CappelliniM Thomas P GilbertPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45644 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nathan Wales J Alberto Romero-Navarro Enrico Cappellini M Thomas P Gilbert Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
description	DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.
format	article
author	Nathan Wales J Alberto Romero-Navarro Enrico Cappellini M Thomas P Gilbert
author_facet	Nathan Wales J Alberto Romero-Navarro Enrico Cappellini M Thomas P Gilbert
author_sort	Nathan Wales
title	Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
title_short	Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
title_full	Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
title_fullStr	Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
title_full_unstemmed	Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
title_sort	choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/00fd7538cd974b0b9fd60f084943320a
work_keys_str_mv	AT nathanwales choosingthebestplantforthejobacosteffectiveassaytoprescreenancientplantremainsdestinedforshotgunsequencing AT jalbertoromeronavarro choosingthebestplantforthejobacosteffectiveassaytoprescreenancientplantremainsdestinedforshotgunsequencing AT enricocappellini choosingthebestplantforthejobacosteffectiveassaytoprescreenancientplantremainsdestinedforshotgunsequencing AT mthomaspgilbert choosingthebestplantforthejobacosteffectiveassaytoprescreenancientplantremainsdestinedforshotgunsequencing
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Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.

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