Cargando…
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...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577829/ https://www.ncbi.nlm.nih.gov/pubmed/23437111 http://dx.doi.org/10.1371/journal.pone.0056301 |
_version_ | 1782259982470742016 |
---|---|
author | Hung, Chih-Ming Lin, Rong-Chien Chu, Jui-Hua Yeh, Chia-Fen Yao, Chiou-Ju Li, Shou-Hsien |
author_facet | Hung, Chih-Ming Lin, Rong-Chien Chu, Jui-Hua Yeh, Chia-Fen Yao, Chiou-Ju Li, Shou-Hsien |
author_sort | Hung, Chih-Ming |
collection | PubMed |
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 | Online Article Text |
id | pubmed-3577829 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35778292013-02-22 The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing Hung, Chih-Ming Lin, Rong-Chien Chu, Jui-Hua Yeh, Chia-Fen Yao, Chiou-Ju Li, Shou-Hsien PLoS One Research Article 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. Public Library of Science 2013-02-20 /pmc/articles/PMC3577829/ /pubmed/23437111 http://dx.doi.org/10.1371/journal.pone.0056301 Text en © 2013 Hung et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Hung, Chih-Ming Lin, Rong-Chien Chu, Jui-Hua Yeh, Chia-Fen Yao, Chiou-Ju Li, Shou-Hsien The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577829/ https://www.ncbi.nlm.nih.gov/pubmed/23437111 http://dx.doi.org/10.1371/journal.pone.0056301 |
work_keys_str_mv | AT hungchihming thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT linrongchien thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT chujuihua thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT yehchiafen thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT yaochiouju thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT lishouhsien thedenovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT hungchihming denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT linrongchien denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT chujuihua denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT yehchiafen denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT yaochiouju denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing AT lishouhsien denovoassemblyofmitochondrialgenomesoftheextinctpassengerpigeonectopistesmigratoriuswithnextgenerationsequencing |