Supporting data for "Chromosome-level echidna genome illuminates evolution of multiple-sex-chromosome system in monotremes"

A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology but the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex. <br>Here, we present a new long-reads-based chromosome-level short-beaked echidna (<i>Tachyglossus aculeatus</i>) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between one Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes. <br>The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.