Biology subjects

Cedric Chauve

Publications and source records attributed to Cedric Chauve.

3 recordsLinked to original sources

bioRxiv2016

Improved assemblies and comparison of two ancient Yersinia pestis genomes

Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Yersinia pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and prevents in many cases a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Yersinia pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (Ancestral Gap Estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We apply our method to two data sets from the London and Marseilles outbreaks of the bubonic plague. We obtain highly improved genome assemblies for both the London strain and Marseille strain genomes, comprised of respectively five and six scaffolds, with 95% of the assemblies supported by ancient reads. We analyze the genome evolution between both ancient genomes in terms of genome rearrangements, and observe a high level of synteny conservation between these two strains.

Bioinformatics↗

bioRxiv2015

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

ContextThe reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Berard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.\n\nContributionWe extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.\n\nResultsWe apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.

Bioinformatics↗

bioRxiv2015

Ancestral gene synteny reconstruction improves extant species scaffolding

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARO_SCPCAPTC_SCPCAP-DO_SCPCAPEC_SCPCAPCO_SCPCAPOC_SCPCAP that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARO_SCPCAPTC_SCPCAP-DO_SCPCAPEC_SCPCAPCO_SCPCAPOC_SCPCAP by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.

Bioinformatics↗