Assemblies of the gyr falcon : Chromosome level genome assembly and comparative genomics between three falcon species reveals a pattern of genome organization not typical for birds

• Main Author: Unkn Unknown
• Format: Other/Unknown Material
• Language: English
• Published: University of Edinburgh. University of Kent 2018
• Subjects: Genome; falcon; Veterinary Sciences Agriculture and related subjects; peregrine falcon
• Online Access: https://dx.doi.org/10.7488/ds/2379; https://datashare.ed.ac.uk/handle/10283/3120

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology including morphology, ecology and physiology and thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, the arrangement of its chromosomes, which can then be linked to the whole genome sequence to generate a so-called chromosome level assembly. Chromosome level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes as well as determining patterns of gross genomic evolution. To date only two falcon species have been sequenced and neither initially to chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date however published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purpose of this study was to generate analyzable karyotypes and ideograms of peregrine, saker and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n=50 for peregrine falcon and 2n=52 for saker and gyr through high quality banded chromosomes. Standard ideograms generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by 1 interchromosomal and 7 intrachromosomal rearrangements (a fusion plus 7 inversions) whereas peregrine and saker/gyr differ from the reference chicken genomes by 14/13 fusions (11 microchromosomal) and 6 fissions. The chromosomal differences between the species could possibly provide the basis of a screening test for hybrid animals. We have preserved these partial assemblies here for future use. The final assemblies for this genome will be submitted to the nucleotide archives GenBank/ENA. : falcon.contig.fasta.gz - version 0.1 of the assembly (contigs) falcon_contigs_260911.fasta.gz - version 0.2 of the assembly (contigs) falcon_scaffolds_260911.fasta.gz - version 0.2 of the assembly (scaffolds)