Abstract
BackgroundWe propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging.ResultsWe use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids.ConclusionThe comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison.
Highlights
We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA
The shape of the ancestral genome We perform the whole process of ancestral gene order reconstruction for three data sets: the whole set of filtered families, the set of D free families, without duplication and the DL free families, without duplication nor loss
In conclusion, we report here the reconstructed ancestral bacterial genome of an ancestral Yersinia pestis
Summary
We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. Extant species are derived from a process of evolution and diversification from species disappeared These species are called ancient in general and ancestral if they left a descendant. While originally used to study proteins or Obtaining ancestral sequences can allow, through the study of physical properties of the reconstructed molecules, the inference of the paleoenvironnements in which these molecules evolved [9]. These methods allow access to an oriented and ordered view of molecular events along the history of life. They offer a better understanding of this history and can further our knowledge of the mechanisms linking organic sequences to their functions [10]
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