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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
FPSAC: fast phylogenetic scaffolding of ancient contigs
Ashok Rajaraman1, Eric Tannier, Cedric Chauve
1Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, INRIA Grenoble Rhône-Alpes, Montbonnot 38334, France, Université de Lyon 1, Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR5558 F-69622 Villeurbanne, France and LaBRI, Université Bordeaux I, 33405 Talence, France.
Motivations:
Recent progress in ancient DNA sequencing technologies and protocols has lead to the sequencing of whole ancient bacterial genomes, as illustrated by the recent sequence of the Yersinia pestis strain that caused the Black Death pandemic. However, sequencing ancient genomes raises specific problems, because of the decay and fragmentation of ancient DNA among others, making the scaffolding of ancient contigs challenging.
Results:
We show that computational paleogenomics methods aimed at reconstructing the organization of ancestral genomes from the comparison of extant genomes can be adapted to correct, order and orient ancient bacterial contigs. We describe the method FPSAC (fast phylogenetic scaffolding of ancient contigs) and apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome. We obtain a unique scaffold for the whole chromosome of this ancient genome that allows to gain precise insights into the structural evolution of the Yersinia clade.
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