Skip to Main content Skip to Navigation
Journal articles

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

Wandrille Duchemin 1, 2 Vincent Daubin 3 Eric Tannier 2, 1 
1 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Background: We 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. Results: We 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. Conclusion: The 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.
Complete list of metadata

Cited literature [42 references]  Display  Hide  Download
Contributor : Anne Jaigu Connect in order to contact the contributor
Submitted on : Thursday, October 15, 2015 - 4:40:20 PM
Last modification on : Monday, May 16, 2022 - 3:00:06 PM
Long-term archiving on: : Thursday, April 27, 2017 - 4:26:13 AM


Publication funded by an institution



Wandrille Duchemin, Vincent Daubin, Eric Tannier. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S9. ⟨10.1007/978-3-319-19048-8_16⟩. ⟨hal-01179197v3⟩



Record views


Files downloads