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Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of a...

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Autores principales: Pratas, Diogo, Hosseini, Morteza, Grilo, Gonçalo, Pinho, Armando J., Silva, Raquel M., Caetano, Tânia, Carneiro, João, Pereira, Filipe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162538/
https://www.ncbi.nlm.nih.gov/pubmed/30200636
http://dx.doi.org/10.3390/genes9090445
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author Pratas, Diogo
Hosseini, Morteza
Grilo, Gonçalo
Pinho, Armando J.
Silva, Raquel M.
Caetano, Tânia
Carneiro, João
Pereira, Filipe
author_facet Pratas, Diogo
Hosseini, Morteza
Grilo, Gonçalo
Pinho, Armando J.
Silva, Raquel M.
Caetano, Tânia
Carneiro, João
Pereira, Filipe
author_sort Pratas, Diogo
collection PubMed
description The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.
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spelling pubmed-61625382018-10-10 Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard Pratas, Diogo Hosseini, Morteza Grilo, Gonçalo Pinho, Armando J. Silva, Raquel M. Caetano, Tânia Carneiro, João Pereira, Filipe Genes (Basel) Article The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination. MDPI 2018-09-06 /pmc/articles/PMC6162538/ /pubmed/30200636 http://dx.doi.org/10.3390/genes9090445 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pratas, Diogo
Hosseini, Morteza
Grilo, Gonçalo
Pinho, Armando J.
Silva, Raquel M.
Caetano, Tânia
Carneiro, João
Pereira, Filipe
Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title_full Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title_fullStr Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title_full_unstemmed Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title_short Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
title_sort metagenomic composition analysis of an ancient sequenced polar bear jawbone from svalbard
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162538/
https://www.ncbi.nlm.nih.gov/pubmed/30200636
http://dx.doi.org/10.3390/genes9090445
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