Transposable elements shape the landscape of heterozygous structural variation of a bird genome

Avian genomes are characterized by streamlined organization and stable chromosomes. 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. About ~28% of the large indels are associated with recent insertions of transposable elements whose activities are usually infrequent in bird genomes. We however find little evidence for the role of transposable elements in altering gene expression. Finally, we identified evolutionary strata on the sex chromosomes and characterized the drastic rearrangement of the W chromosome. Our analyses on the high-quality diploid genome of golden pheasant provide insights into the evolutionary patterns of structural variation of avian genomes.