Biology subjects

Namias, A.

Publications and source records attributed to Namias, A..

3 recordsLinked to original sources

bioRxiv2023

Intra-lineage microevolution of Wolbachia leads to the emergence of new cytoplasmic incompatibility patterns

Mosquitoes of the Culex pipiens complex are worldwide vectors of arbovirus, filarial nematode, and avian malaria agents. In these hosts, the endosymbiotic bacteria Wolbachia induce cytoplasmic incompatibility (CI), that is, reduced embryo viability in so-called incompatible crosses. Wolbachia infecting Culex pipiens (wPip) cause CI patterns of unparalleled complexity, associated with the amplification and diversification of cidA and cidB genes, with up to six different gene copies described in a single wPip genome. By repeating crosses between Culex isofemale lines over 17 years, we documented the emergence of a new compatibility type. Using a new sequencing method adapted to multigene families to acquire cid genes, we showed that some wPip genomes lost specific cidA gene copies, thus giving rise to several sub-lineages segregating in the same cage. By linking phenotypic changes to their underlying genotypic bases, we showed that gene copies that are key for CI phenotypes originated from recombinations, not point mutations. We revealed how new CI patterns could emerge as part of a two-step process: first, local changes take place in the CI repertoires while maintaining compatibility with the surrounding mosquitoes, and then migration and secondary contact occur with the incompatible lines.

evolutionary biology↗

bioRxiv2023

Striking allelic diversity despite structural homogeneity of ace-1 duplications in Anopheles mosquitoes

A. gambiae s.l. has been the target of intense insecticide treatment since the mid-XXth century to try and control malaria, and a substitution in the ace-1 locus allowing resistance to organophosphate and carbamates insecticides has been rapidly selected for. Since then, several duplications of the ace-1 locus have been found in A. gambiae s.l. populations. They associate either several resistance copies (homogeneous duplications) or both resistance and susceptible copies (heterogeneous duplications). Heterogeneous duplications confer an intermediate trade-off between resistance in presence of insecticide and disadvantage in their absence. So far, and in striking contrast with C. pipiens mosquitoes, a single heterogeneous duplication had been describe in A. gambiae populations. We use an innovative approach, combining information from long and short read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications in A. gambiae. We further show that these alleles share the exact same structure than the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds a new light on the origin and maintenance of these alleles in A. gambiae populations, and pushes one step further the striking evolutionary convergence with C. pipiens mosquitoes.

evolutionary biology↗

bioRxiv2022

Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination

This study developed a new bioinformatics pipeline to acquire all the different copies of multi-copy gene families based on Oxford Nanopore Technologies sequencing of PCR products. We used this pipeline to acquire the sequences of highly similar copies of the cidA and cidB genes present in the genomes of Wolbachia pipientis (wPip) bacteria infecting the cells of Culex pipiens mosquitoes. The approach is based on read mapping, SNP calling and haplotyping, using our already wide existing reference database for the cid genes obtained by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants (or haplotypes). In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the pipeline through a combination of analyses of simulated reads and of gene sequence acquisitions through cloning and Sanger sequencing. For genes of which the haplotype cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.

genomics↗