Sex Chromosome Evolution Of The Pekin Duck And Monotremes

Pekin duck(Anas platyrhyachos)has a typical avian karyotype that consists of macro-and micro-chromosomes,but a pair of much less differentiated ZW sex chromosomes compared to chicken.To elucidate the evolution of chromosome architectures between Pekin duck and chicken,and between birds and mammals,we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques.The major improvement of genome assembly and annotation quality resulted in successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly.We found that the Pekin duck topologically associated domains(TAD)are demarcated by putative binding sites of the insulator protein CTCF,housekeeping genes,or transitions of active/inactive chromatin compartments,indicating the conserved mechanisms of spatial chromosome folding with mammals.There are extensive overlaps of TAD boundaries between Pekin duck and chicken,and also between the TAD boundaries and chromosome inversion breakpoints.This suggests strong natural selection on maintaining regulatory domain integrity,or vulnerability of TAD boundaries to DNA double-strand breaks.The Pekin duck W chromosome contains 2.5-fold more genes relative to chicken.Parallel to the independently evolved human Y chromosome,the Pekin duck W evolved massive dispersed palindromic structures,and a sequence divergence pattern with the Z chromosome that reflects stepwise suppression of homologous recombination.Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals,and also importantly add to the genomic resources for poultry studies.Egg-laying mammals were the first to diverge from the common ancestor of modern mammals and provide key insights into mammalian evolution and the innovations that have occurred in the three mammalian lineages present on earth today.Here we report the generation and analyses of high-quality reference genomes for two monotreme species,platypus(Ornithorhynchus anatinus)and echidna(Tachyglossus aculeatus).The new platypus genome assembly anchors almost the entire genome onto chromosomes,dramatically improving the previous draft genome and gene annotation.The two monotreme genomes allowed us to reconstruct genomic innovations at the time of mammalian diversification.We provide evidence that the extraordinary monotreme sex chromosome complex originated from an ancestral chromosome ring configuration.The formation of such a unique chromosome complex may have been facilitated by the unusual extensive interactions between the multi-X and-Y chromosomes that are shared by their human autosomal homologues.The monotremes are belonging to one important clade of mammals.However,their sex chromosomes are not homologous to human chrX,but homologous to chicken chrZ.The eutherian sex determining gene SRY is also missing in monotremes.In addition,like birds,the monotremes lack dosage compensation as well.Overall,my analyses of the Pekin duck and monotremes provide new insights into the transition of sex chromosome evolution between mammals and birds.