Genomic richness enables worldwide invasive success

Biological invasions are a major threat to biodiversity. Therefore, monitoring genomic features of invasive species is crucial to understand their population structure and adaptive processes. However, genomic resources of invasive species are scarce, compromising the study of their invasive success. Here, we present the reference genome of Styela plicata , one of the most widespread marine invasive species, combined with genomic data of 24 individuals from 6 populations distributed worldwide. We characterized large inversions in four chromosomes, accounting for ~ 15% of the genome size. These inversions are polymorphic through the species’ distribution area, and are enriched with genes enhancing fitness in estuary and harbor environments. Nonetheless, inversions mask detection of S. plicata population structure. When these structural variants are removed, we successfully identify the main oceanographic barriers and accurately characterize population differentiation between and within ocean basins. Several genes located in chromosome 3 are showcased as the main adaptive drivers between biogeographic regions. Moreover, we recover three major mitogenomic clades, involving structural rearrangements leading to cyto-nuclear coevolution likely involved in mitochondrion distribution during cell division. Our results suggest that genomic and structural variants contribute to S. plicata population structuring and adaptation processes, potentially enhancing the species success when colonizing new habitats.