Chromosome Evolution and Genome Reconstruction in Falcon Species

Falcons and falconry have become an essential part of life in the Middle East since

ancient times. In the United Arab Emirates (UAE) itself, the number of trained falcons ranges from 8,000 to 10,000. Over the last five years, falcon racing, a traditional sport, has gained momentum in the UAE where captive falcons are competing for huge prizemoney. A proportion of the UAE economy goes into their care and conservation e.g. through establishing falcon hospitals with modern facilities for disease treatment and breeding as well as centers for diagnosis and research. Being the national bird of the UAE, any research on falcons is of significant interest for the country. Most of the world's falcon species are in decline. Moreover, Saker falcons are classified as 'endangered' according to the IUCN Red List of Threatened Species. From the chromosomal perspective falcons are very interesting, as they represent birds that have undergone significant genome rearrangement compared to the "norm" of 2n=~80. 'Molecular cytogenomics' in birds includes karyotyping, cross species comparisons, nuclear organization, BAC mapping, physical mapping and telomeric DNA profiling. This thesis makes use of the above approaches to define chromosome evolution and genome organization in falcon species with the following results:

Firstly, successful conventional characterization of the Saker, Peregrine and Gyr falcon karyotypes (2n=50-52) was achieved producing improved karyotypes and ideograms than those previously published. Comparative genomic analyses among these three species using molecular cytogenetic approaches revealed differences between Peregrine and the other two species, but none between Saker falcon and Gyrfalcon. Also, this study has supported upgrading the fragmented Saker genome assembly to chromosome level using a novel approach hitherto only published for the Peregrine falcon (and pigeon).

Secondly, a comparison of genome-wide BAC-based studies and bioinformatic analysis Multiple Genomes Rearrangement Algorithm 2 (MGRA2) revealed the chromosomal changes (inter- and intra-) that led to the falcon lineage. Also, the present study established that common mechanisms of chromosomal fusion do not recur in two different groups of species with rearranged karyotypes (falcons and parrots).

This thesis also provided an overview of the telomeric DNA profile in the three species of interest. It established that the highly rearranged karyotypes studied (plus those of the budgerigar and crocodile) do not appear to possess interstitial telomeres at evolutionary fusion points. Also, this study demonstrated the existence of megatelomeres in falcon species, their nature differing between the Peregrine and the other two species studied.

Finally, this thesis produced the first detailed description of nuclear organization in a bird species (Peregrine falcon) other than the Galloanserae. Non-fused macro and microchromosomes behave the same way in chickens and falcons. This implies that the same general nuclear organization mechanisms are present in falcons as well as in chickens, ducks and turkeys whose last common ancestor existed around 89 million years ago. Most notably, fused microchromosomes in the Peregrine falcon retain the same nuclear organization pattern despite being fused to a larger chromosome. The findings from this study give insight into the basic nature of chromosome territory patterns in bird species with highly rearranged karyotypes.

Overall, results presented in this thesis provide significant insight into genome

organization and evolution in the Falco genus, revealing previously undetected levels of chromosomal synteny between three species important to the UAE. Results generated here have also made a significant contribution to the chromosome-level genome assembly of the Saker falcon, providing tools for further study of avian species both within and beyond the falcon group.