Unknown

Dataset Information

0

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


ABSTRACT: 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.

SUBMITTER: Hung CM 

PROVIDER: S-EPMC3577829 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Hung Chih-Ming CM   Lin Rong-Chien RC   Chu Jui-Hua JH   Yeh Chia-Fen CF   Yao Chiou-Ju CJ   Li Shou-Hsien SH  

PloS one 20130220 2


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 pa  ...[more]

Similar Datasets

| S-EPMC4402509 | biostudies-literature
| S-EPMC2945192 | biostudies-literature
| S-EPMC2997550 | biostudies-literature
| S-EPMC3137213 | biostudies-literature
| S-EPMC3526293 | biostudies-literature
| S-EPMC3726674 | biostudies-literature
| S-EPMC3639258 | biostudies-literature
| S-EPMC3767511 | biostudies-literature
| S-EPMC3056720 | biostudies-literature
| S-EPMC3708500 | biostudies-literature