Abstract
Biological invasions are a major threat to biodiversity. However, genomic resources of invasive species are scarce, compromising the study of their invasive success and our ability to mitigate their effects. Here, we assemble and annotate the reference chromosome-level genome of the invasive ascidian Styela plicata, and complement it with whole genome sequencing data from 24 individuals worldwide. We developed and validated the novel method "individual Detection of linkage by Genotyping" (iDlG), that allowed identifying four large chromosomal inversions and assigning karyotypes at the individual level. The four inversions are polymorphic throughout the species' distribution range and are enriched with genes that potentially influence fitness in estuarine and harbor environments, where Styela plicata thrives. It was only after we removed the inversions that we could detect clear population structuring, both between and within oceans, driven by several candidate adaptive genes involved in osmoregulation and other functions. Moreover, we recovered three major mitogenomic lineages, two of them globally sympatric and one specific to a single population. Interestingly, mitochondrial lineages show associations with nuclear genes likely involved in correct mitochondrion distribution during cell division. Our study highlights the importance of generating annotated reference genomes and combining them with whole genome sequencing data across whole distribution ranges to identify species' structural and sequence variation for understanding complex evolutionary processes.