Chromosomal Inversions in Chromosome U of Drosophila subobscura: A Story from Population Studies to Molecular Level.

Drosophila subobscura is a Palearctic species that colonized the west coast of South and North America in the last quarter of the 20th century. This species stands out for its large chromosomal inversion polymorphism that affects its five long chromosomes. Studies of natural populations revealed that the inversion polymorphism has an adaptive character and while the arrangement U_st was classified as adapted to cold, other arrangements, such as U₁₊₂₊₆ and U₁₊₈₊₂, were considered warm adapted. Characterization of the inversion breakpoints will allow a first approach to the genes included in the inversions and to find candidates to be affected by selection. In this work, we take advantage of the existence of a reference genomic sequence carrying the U₁₊₂ arrangement to locate the breakpoints of the U₆ and U₈ inversions, mapping paired-end Illumina reads from two homokaryotypic strains to U₁₊₂₊₆ and U₁₊₈₊₂, respectively. To date, most of the characterized inversion breakpoints in D. subobscura have been generated by non-homologous end-joining. In contrast, the U₆ and U₈ inversions seem to have originated by transposons, and, at the distal breakpoint of inversion U₈, we describe a new fold-back-like element characteristic of the suboscura species group that we have named Ziga-Zaga.