Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly

Chromosomal arrangements are important for processes including genetic recombination, adaptation, and speciation. Related taxa often possess similar numbers of chromosomes, but some groups show remarkable variation in chromosome numbers. Most Lepidoptera, the butterflies and moths, have 31 or 32 chromosomes, but some species deviate from this norm. We present a chromosome-level genome assembly of a heterogametic female Atlas blue butterfly (Polyommatus atlantica; Lycaenidae) and find that it has 227 pairs of autosomes and four sex chromosomes, the highest recorded chromosome number in non-polyploid Metazoa. We show that the 227 autosomes, exceptionally small even for Lepidoptera, are derived from extensive fragmentation of the 24 ancestral lycaenid autosomes. We predict that autosomal fissions mostly occurred in euchromatic, lightly packed regions of chromosomes. We assemble two large Z chromosomes, one of which comprises the ancestral Z fused with an autosome and retains its ancestral length, while the other is a neo-Z, formed from the fusion and sex linkage of an intact ancestral autosome with a fragment of a second autosome. We find two large W chromosomes, derived from copies of the Z-linked, ancestrally autosomal sequences. In contrast to the autosomes, the sex chromosomes have not experienced fission. We observe the frequent presence of chromosome-internal arrays of the telomeric repeat motif in P. atlantica. Such arrays are not observed in the genomes of close relatives that have not undergone fission and suggest a possible mechanism for rapid, viable fragmentation. Altogether, our findings in P. atlantica suggest several constraints that govern karyotypic change, a key component of eukaryotic genome evolution.