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

Filipe Garrett Vieira,M Thomas P Gilbert,José Alfredo Samaniego Castruita

doi:10.1002/ece3.6925

Filipe Garrett Vieira, M Thomas P Gilbert + Show 1 more

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https://doi.org/10.1002/ece3.6925

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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.

Highlights

The number and quality of sequenced genomes is rapidly increasing as DNA sequencing technologies become increasingly faster and cheaper per base sequence (Mardis, 2011)
The sequencing of genomes from ancient DNA within historic, ancient, or otherwise degraded samples has started to become of growing interest, and these so-called paleogenomic studies have helped us better understand the history of ancient species and populations (Brunson & Reich, 2019; MacHugh et al, 2017; Nielsen et al, 2017; Przelomska et al, 2020)
We explore the potential use of ancestral sequence reconstruction (ASR) to reconstruct ancestral genomes and test their potential use as reference genomes, so as to improve the mapping of ancient samples

Summary

Introduction

The number and quality of sequenced genomes is rapidly increasing as DNA sequencing technologies become increasingly faster and cheaper per base sequence (Mardis, 2011). This has been revolutionary across the fields of biology, enabling researchers to introduce genomic approaches to model organisms, but across the tree of life (Ellegren, 2014). The sequencing of genomes from ancient DNA (aDNA) within historic, ancient, or otherwise degraded samples has started to become of growing interest, and these so-called paleogenomic studies have helped us better understand the history of ancient species and populations (Brunson & Reich, 2019; MacHugh et al, 2017; Nielsen et al, 2017; Przelomska et al, 2020).

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