Biology subjects

Gauthier, J.

Publications and source records attributed to Gauthier, J..

3 recordsLinked to original sources

bioRxiv2017

DiscoSnp-RAD: de novo detection of small variants for population genomics

We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.\n\nLicenseGNU Affero general public license\n\nAvailabilityhttps://github.com/GATB/DiscoSnp\n\nContactjeremy.gauthier@inria.fr

bioinformatics↗

bioRxiv2017

Genomic divergence footprints in the bracovirus of Cotesia sesamiae identified by targeted re-sequencing approach

The African parasitoid wasp Cotesia sesamiae is structured in contrasted populations showing differences in host range and the recent discovery of a specialist related species, C. typhae, provide a good framework to study the mechanisms that link the parasitoid and their host range. To investigate the genomic bases of divergence between these populations, we used a targeted sequencing approach on 24 samples. We targeted a specific genomic region encoding the bracovirus, which is deeply involved in the interaction with the host. High sequencing coverage was obtained for all samples allowing the study of genetic variations between wasp populations and species. Combining population genetic estimations, the diversity ({pi}), the relative differentiation (FST) and the absolute differentiation (dxy), and branch-site dN/dS measures, we identified six divergent genes impacted by positive selection belonging to different gene families. These genes are potentially involved in host adaptation and in the specialization process. Fine scale analyses of the genetic variations also revealed deleterious mutations and large deletions on certain genes inducing pseudogenization and loss of function. These results highlight the crucial role of the bracovirus in the molecular interactions between the wasp and its hosts and in the evolutionary processes of specialization.

evolutionary biology↗

bioRxiv2017

Determinants of genetic structure of the Sub-Saharan parasitic wasp Cotesia sesamiae

Parasitoid life style represents one of the most diversified life history strategies on earth. There are however very few studies on the variables associated with intraspecific diversity of parasitoid insects, especially regarding the relationship with spatial, biotic and abiotic ecological factors. Cotesia sesamiae is a Sub-Saharan stenophagous parasitic wasp that parasitizes several African stemborer species with variable developmental success. The different host-specialized populations are infected with different strains of Wolbachia, an endosymbiotic bacterium widespread in arthropods that is known for impacting life history traits notably reproduction, and consequently species distribution. In this study, first we analyzed the genetic structure of C. sesamiae across Sub-Saharan Africa, using 8 microsatellite markers, and 3 clustering software. We identified five major population clusters across Sub-Saharan Africa, which probably originated in East African Rift region and expanded throughout Africa in relation to host genus and abiotic factors such as climatic classifications. Using laboratory lines, we estimated the incompatibility between the different strains of Wolbachia infecting C. sesamiae. We observed an incompatibility between Wolbachia strains was asymmetric; expressed in one direction only. Based on these results, we assessed the relationships between direction of gene flow and Wolbachia infections in the genetic clusters. We found that Wolbachia-induced reproductive incompatibility was less influential than host specialization in the genetic structure. Both Wolbachia and host were more influential than geography and current climatic conditions. These results are discussed in the context of African biogeography, and co-evolution between Wolbachia, virus parasitoid and host, in the perspective of improving biological control efficiency through a better knowledge of the biodiversity of biological control agents.

evolutionary biology↗