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, 8 (2), e56301

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

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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.

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.

Conflict of interest statement

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

Figures

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).

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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.
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