Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. / Vieira, Filipe Garrett; Castruita, Jose Alfredo Samaniego; Gilbert, M. Thomas P.

In: Ecology and Evolution, Vol. 10, No. 23, 2020, p. 12700-12709.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Vieira, FG, Castruita, JAS & Gilbert, MTP 2020, 'Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction', Ecology and Evolution, vol. 10, no. 23, pp. 12700-12709. https://doi.org/10.1002/ece3.6925

APA

Vieira, F. G., Castruita, J. A. S., & Gilbert, M. T. P. (2020). Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. Ecology and Evolution, 10(23), 12700-12709. https://doi.org/10.1002/ece3.6925

Vancouver

Vieira FG, Castruita JAS, Gilbert MTP. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. Ecology and Evolution. 2020;10(23):12700-12709. https://doi.org/10.1002/ece3.6925

Author

Vieira, Filipe Garrett ; Castruita, Jose Alfredo Samaniego ; Gilbert, M. Thomas P. / Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. In: Ecology and Evolution. 2020 ; Vol. 10, No. 23. pp. 12700-12709.

Bibtex

@article{c064046398cf41da95e138e04e535ce1,
title = "Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction",
abstract = "Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.",
keywords = "ancestral genome reconstruction, paleogenomics, ANCIENT DNA, MISCODING LESIONS, MITOCHONDRIAL-DNA, EVOLUTION, SEQUENCES, INSIGHTS, HISTORY, ORIGIN, DAMAGE",
author = "Vieira, {Filipe Garrett} and Castruita, {Jose Alfredo Samaniego} and Gilbert, {M. Thomas P.}",
year = "2020",
doi = "10.1002/ece3.6925",
language = "English",
volume = "10",
pages = "12700--12709",
journal = "Ecology and Evolution",
issn = "2045-7758",
publisher = "Wiley",
number = "23",

}

RIS

TY - JOUR

T1 - Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction

AU - Vieira, Filipe Garrett

AU - Castruita, Jose Alfredo Samaniego

AU - Gilbert, M. Thomas P.

PY - 2020

Y1 - 2020

N2 - Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.

AB - Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.

KW - ancestral genome reconstruction

KW - paleogenomics

KW - ANCIENT DNA

KW - MISCODING LESIONS

KW - MITOCHONDRIAL-DNA

KW - EVOLUTION

KW - SEQUENCES

KW - INSIGHTS

KW - HISTORY

KW - ORIGIN

KW - DAMAGE

U2 - 10.1002/ece3.6925

DO - 10.1002/ece3.6925

M3 - Journal article

C2 - 33304488

VL - 10

SP - 12700

EP - 12709

JO - Ecology and Evolution

JF - Ecology and Evolution

SN - 2045-7758

IS - 23

ER -

ID: 252475666