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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 gene order (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 where both chromosomal count and gene collinearity (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, micro-synteny 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 then previously envisioned.