Résumé
Structural variations (SVs) play pivotal roles genome architecture, potentially involved in adaptation and speciation, yet they are often overlooked. Here, we delved into the genomic landscape of SVs within Anopheles gambiae and Anopheles coluzzii, principal African malaria vectors. We used a «map-then- assemble» pangenomic strategy with short-read sequencing data, validated with samples for which short- and long-read data were available. Then we assessed pangenomic diversity and divergence in the two sister species by screening 200 samples across Africa from the Ag1000g consortium. Our study revealed strong disparities in read mapping efficiency accros five reference genomes available in the litterature. Using the Ngousso reference as a backbone for building the panreference, we identified substantial SVs within the reference, with ~10% (23Mb) as dispensable. De novo assembled SVs further augmented the reference genome with 1.5M new variants, totalling 521.4Mb (223% larger than Ngousso) across the 200 genomes. However, only 15% (234k SVs; 82.1Mb) of these SVs uniquely anchored into the reference, and 3% (46k SVs; 15.4Mb) with high confidence. Notably, our analysis delineated distinct pangenomic dynamics between autosomes and the X chromosome, particularly within heterochromatic regions. In particular, low-recombining regions previously identified as «genomic islands of differentiation» between An. gambiae and An. coluzzii were enriched in diagnostic pangenomic variations, dominated by young transposable elements. Moreover, SVs captured the key axes of ancestry variation along the genome previously identified with single nucleotide polymorphisms (SNPs), including well-known chromosomal inversions and islands of species differentiation, implying that SVs are impacted by the same evolutionary forces. This study offers critical insights into the genetic diversity and evolutionary trajectories of An. gambiae and An. coluzzii, highlighting SVs, particularly transposable elements, as pivotal drivers in their adaptive and speciation processes.