Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 8 (2), e56301

The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes Migratorius) With Next Generation Sequencing


The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes Migratorius) With Next Generation Sequencing

Chih-Ming Hung et al. PLoS One.


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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. Average sequence coverage of contigs against their lengths (bp) for the de novo assemblies based on Illumina paired-end reads of (A) BMNH1149 and (B) BMNH1389.
Arrows indicate the contigs that were annotated as the mitogenomes of passenger pigeons.
Figure 2
Figure 2. Sequence coverage (in red) and frequency of the major allele (in green) of each base pair along the mitogenomes of BMNH1149 (upper) and BMNH1389 (lower).
Both mitogenomes start from the first base of tRNA-Phe.
Figure 3
Figure 3. Metagenomic composition of the Illumina sequence reads from the toe pads of two passenger pigeons, BMNH1149 and BMNH1389.
Percentage of non-duplicate reads blasted to chicken, human bacterial and fungal genome references downloaded from the NCBI genome database.
Figure 4
Figure 4. Frequency for 12 categories of sequence mismatches for raw read sequences against the consensus sequence of mitogenomes of BMNH1149 (in green) and BMNH1389 (in red).

Similar articles

See all similar articles

Cited by 5 PubMed Central articles


    1. Nee S, May RM (1997) Extinction and the loss of evolutionary history. Science 278: 692–694. - PubMed
    1. Pääbo S, Poinar H, Serre D, Jaenicke-Després, Hebler J, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645–679. - PubMed
    1. Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM (2008) New developments in ancient genomics. Trends Ecol Evol 23: 386–393. - PubMed
    1. Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, et al. (2002) Flight of the Dodo. Science 295: 1683. - PubMed
    1. Gilbert MTP, Drautz DI, Lesk AM, Ho SYW, Qi J, et al. (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci USA 105: 8327–8332. - PMC - PubMed

Publication types

Grant support

This project is funded by the National Science Council of Taiwan to SHL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.