Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Abstract

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, 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 were assembled to the 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 purposes of this study were 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 that are 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 one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.

A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes)

“…The G-banding was performed for ten Columbidae species with a combination of DAPI and propidium iodide [19] in order to detect intrachromosomal rearrangements not observed by chromosome painting. Images were captured by an Olympus BX61 epifluorescence microscope with a cooled CCD camera and SmartCapture (Digital Scientific UK) system.…”

Falcon genomics in the context of conservation, speciation, and human culture

“…The common kestrel ( Falco tinnunculus ) genome was sequenced more recently using similar methods, but with a very high depth of approximately 500× and achieved a scaffold N50 of 21 Mb (Cho et al, ). Less complete and lower coverage draft genomes have also recently been produced for two additional falcon species: A gyrfalcon ( Falco rusticolus ) draft genome has been assembled with a scaffold N50 of 32.8 kb (Joseph et al, ), and a prairie falcon ( Falco mexicanus ) draft genome has been assembled with a scaffold N50 of 3.7 kb (Doyle et al, ). As in most birds, the sizes of falcon genomes are relatively small (Kapusta, Suh, & Feschotte, ; Zhang et al, ), and the assemblies of the genomes of the five falcon species sequenced to date are consistent with genome size of ~1.2 Gb.…”

Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren (Malurus cyaneus)

“…Upgrading genome assemblies from scaffold‐level to chromosome‐level superscaffolds provides additional genomic context by orienting genes relative to each other and other genomic features such as centromeres, telomeres, various repeat elements and regulatory regions. Knowledge of this organization aids in understanding how genome architecture can influence variation in evolution within the genome but also provide insight into genome evolution between populations and species (Joseph et al, ; Sävilammi et al, ; Thind et al, ). To date, there are only 16 bird species with genome assemblies classified as ‘chromosome’ level in GenBank (as of August 19, 2019).…”