Golden pheasant diploid genome

Whether and how the patterns of structural variation of avian genomes are different from other vertebrate lineages is poorly explored. Here, we generated a diploid genome assembly for the golden pheasant (Chrysolophus pictus), a bird with gorgeous plumage in males.

Each haploid genome assembly contains complete chromosomal models, including all microchromosomes. We discovered tandem amplification of immune genes across the smallest microchromosomes (dot chromosomes), with an average copy number of 54. We further discovered that the landscape of structural variation between the two haploid genomes is primarily shaped by large indels, with little impact from inversions or duplications.