Abstract
Taxonomic orders vary in their degree of chromosomal conservation with some having high rates of chromosome number turnover despite maintaining some core sets of ordered genes (e.g. Mammalia) and others exhibiting rapid rates of gene-order reshuffling without changing chromosomal count (e.g. Diptera). However few clades exhibit as much conservation as the Lepidoptera for which both chromosomal count and gene colinearity (synteny) are very high over the past 140 MY. In contrast, here we report extensive chromosomal rearrangements in the genome of the green-veined white butterfly (Pieris napi, Pieridae, Linnaeus, 1758). This unprecedented reshuffling is cryptic: microsynteny and chromosome number do not indicate the extensive rearrangement revealed by a chromosome level assembly and high-resolution linkage map. Furthermore, the rearrangement blocks themselves appear to be non-random, as they are significantly enriched for clustered groups of functionally annotated genes revealing that the evolutionary dynamics acting on Lepidopteran genome structure are more complex than previously envisioned.