The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.

The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies bas...

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Autores principales:	Chih-Ming Hung, Rong-Chien Lin, Jui-Hua Chu, Chia-Fen Yeh, Chiou-Ju Yao, Shou-Hsien Li
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6e6259309db64d98b4f84cb52115305b
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spelling	oai:doaj.org-article:6e6259309db64d98b4f84cb52115305b2021-11-18T07:56:56ZThe de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.1932-620310.1371/journal.pone.0056301https://doaj.org/article/6e6259309db64d98b4f84cb52115305b2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23437111/?tool=EBIhttps://doaj.org/toc/1932-6203The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.Chih-Ming HungRong-Chien LinJui-Hua ChuChia-Fen YehChiou-Ju YaoShou-Hsien LiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e56301 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chih-Ming Hung Rong-Chien Lin Jui-Hua Chu Chia-Fen Yeh Chiou-Ju Yao Shou-Hsien Li The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
description	The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
format	article
author	Chih-Ming Hung Rong-Chien Lin Jui-Hua Chu Chia-Fen Yeh Chiou-Ju Yao Shou-Hsien Li
author_facet	Chih-Ming Hung Rong-Chien Lin Jui-Hua Chu Chia-Fen Yeh Chiou-Ju Yao Shou-Hsien Li
author_sort	Chih-Ming Hung
title	The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
title_short	The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
title_full	The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
title_fullStr	The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
title_full_unstemmed	The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
title_sort	de novo assembly of mitochondrial genomes of the extinct passenger pigeon (ectopistes migratorius) with next generation sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/6e6259309db64d98b4f84cb52115305b
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The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.

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