A neo-sex chromosome in the Monarch butterfly , Danaus plexippus

We report the discovery of a neo-sex chromosome in Monarch butterfly, Danaus plexippus, and several of its close relatives. Z-linked scaffolds in the D. plexippus genome assembly were identified via sex-specific differences in Illumina sequencing coverage. Additionally, a majority of the D. plexippus genome assembly was assigned to chromosomes based on counts of 1-to-1 orthologs relative to the butterfly Melitaea cinxia (with replication using two other Lepidopteran species), where genome scaffolds have been robustly mapped to linkage groups. Combining sequencing-coverage based Z-linkage with homology based chromosomal assignments provided strong evidence for a Z-autosome fusion in the Danaus lineage, involving the autosome homologous to chromosome 21 in M. cinxia. Coverage analysis also identified three notable assembly errors resulting in chimeric Z-autosome scaffolds. The timing of this Z-autosome fusion event currently remains ambiguous due to incomplete sampling of karyotypes in the Danaini tribe of butterflies. The discovery of a neo-Z and the provisional assignment of chromosome linkage for >90% of D. plexippus genes lays the foundation for novel insights concerning sex chromosome evolution in this increasingly prominent female-heterogametic model species for functional and evolutionary genomics. Background Major rearrangements of karyotype and chromosome structure often have substantial evolutionary impacts on both the organisms carrying such mutations and the genes linked to such genomic reorganization [1, 2] . Additionally, such large-scale chromosomal mutations often present novel opportunities to investigate molecular evolutionary and functional genetic processes. One prominent example of this is the evolution of neo-sex chromosomes, which can arise from the fusion of an autosome with an existing and well-differentiated allosome. This effectively instantaneous transformation of a formerly autosomal set of genes into sex-linked loci is fertile ground for comparative analyses aimed at understanding the distinct set of evolutionary forces acting on sex chromosomes relative to autosomes [3-6]. Furthermore, when the relevant taxa also happen to be tractable genetic model systems, there is opportunity to explore the functional and mechanistic changes associated with sex chromosome evolution. The congruence of neo-sex chromosomes existing in a model system is relatively rare, although there are some notable examples. Numerous independent origins of neo-sex chromosomes are known in Drosophila fruit flies, where recent work has revealed much about the evolutionary and functional dynamics of these unusual sequences [3, 7-11]. Substantial insights have also come from stickleback fish, where neo-sex chromosomes appear to play an important role in reproductive isolation between incipient species [12-14]. Looking beyond these established model systems, the rapid expansion of genomic technologies has allowed extensive analyses of gene content, sex-biased gene expression, dosage compensation, and sequence divergence for recently evolved sex chromosomes among a very diverse set of organisms. This includes, for example, several insect lineages [Teleopsid flies, a grasshopper, and Strepsiptera [15-17]], vertebrates [mammals and . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/036483 doi: bioRxiv preprint first posted online Jan. 12, 2016;