Maulana, A.; Bliznina, A.; Ebdon, S.; Thorpe, J. T.; Gries, J.; Nasvall, K.; McKenna, D. D.; Krasheninnikova, K.; Santos, C. A.; Brooks, K.; Absolon, D. E.; Zilov, D.; Darwin Tree of Life Consortium, ; Jaron, K. S.; Meier, J. I.

Chromosomal rearrangements reshape genome architecture, but rate variation across the tree of life remains poorly understood. Analysing 338 beetle (Coleoptera) genomes, we inferred eight ancestral linkage groups. No species retained these linkage groups, whereas the most frequent karyotypes of 10 or 11 chromosomes evolved at least 65 times through independent rearrangements. Rearrangement rates vary widely across lineages, with exceptionally high rates associated with major species radiations. Comparisons to 340 fly and 210 butterfly and moth genomes reveal the highest rates of long-term persistent rearrangements in beetles and that the beetle X chromosome traces back to the ancestor of Holometabola. We identified frequent X chromosome changes, mostly representing recent autosomal-X fusions, but no fissions. For autosomes, key rearrangement predictors include chromosome size, repeats and centromere position.