Abstract
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots.
Highlights
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots
Some microchromosomes were missing in the genome assemblies of blue-fronted amazon and budgerigar, so we may have underestimated the frequency of chromosomal changes if the microchromosomes experienced any rearrangements
Apart from the frequent chromosomal changes, the parrot genomes have a slightly higher proportion of transposable elements (TEs) than songbirds (9.6% vs. 7.8%) due to recent chicken repeat 1 (CR1) proliferation, and we speculate that recent CR1-psi accumulation may have provided substrates for ectopic recombination events leading to the loss of at least some of the 74 conserved genes
Summary
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. Our previous cytogenetic work characterizing the karyotype of monk parakeet (Myiopsitta monachus) and blue-fronted amazon (Amazona aestiva) revealed their diploid numbers of 48 and 70, respectively[21], suggesting that chromosome rearrangements in birds can occur frequently in less than 30 million years (My)[22]. It is unclear, how and why some bird groups have more frequent chromosome rearrangements than others. We identified one satellite sequence that plays a role in the enlargement of the W chromosome in the monk parakeet
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