ArticlePloS one2013
The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 34 citations in OpenAlex.
- Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples.Zoological research · 2021Article
- Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.Scientific reports · 2021Article
- The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon,ZooKeys · 2021Article
- Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens.Genome biology and evolution · 2020Article
- Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens.PloS one · 2020Article
- The complete mitochondrial genomes of two vent squat lobsters,Ecology and evolution · 2019Article
- Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics.Frontiers in genetics · 2019Review
- The use of museum specimens with high-throughput DNA sequencers.Journal of human evolution · 2015Article
- Pleistocene range dynamics and episodic rarity in an extinct bird.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.