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

Avian genomes exhibit compact organization and remarkable chromosomal stability. However, the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored. This study generated a diploid genome assembly for the golden pheasant ( Chrysolophus pictus), a species distinguished by the vibrant plumage of males. Each haploid genome assembly included complete chromosomal models, incorporating all microchromosomes. Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes (dot chromosomes), with an average copy number of 54. Structural variation between the haploid genomes was primarily shaped by large insertions and deletions (indels), with minimal contributions from inversions or duplications. Approximately 28% of these large indels were associated with recent insertions of transposable elements, despite their typically low activity in bird genomes. Evidence for significant effects of transposable elements on gene expression was minimal. Evolutionary strata on the sex chromosomes were identified, along with a drastic rearrangement of the W chromosome. These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.