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

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.

Sex ratio of White Stork Ciconia ciconia in different environments of Poland

The aim of this study was to analyze the variation in sex ratio of White Stork Ciconia ciconia chicks from differentiated Poland environments. We took under a consideration the impact of Cd and Pb for establish differences among sex ratio in chicks. We also study multiplex PCR employment for establish gender considerations. We collected blood samples via venipuncture of brachial vein of chicks during 2006-2008 breeding seasons at the Odra meadows (SW-Poland; control), which were compared with those from suburbs (SW-Poland), and from copper smelter (S-Poland; polluted) and from swamps near Baltic Sea. We found differences among sex ratio in White Stork chicks from types of environment. Male participation in sex structure is importantly higher in each type of environment excluded suburban areas. Differences in White Stork sex ratio according to the degree of environmental degradation expressed by Cd and Pb and sex-environment-metal interactions testify about the impact of these metals upon sex ratios in storks. Simultaneously, as a result of multiplex PCR, 18S ribosome gene, which served as internal control of PCR, was amplified in male and female storks. It means that it is possible to use primers designed for chicken in order to replicate this fragment of genome in White Stork. Moreover, the use of Oriental White Stork Ciconia boyciana W- chromosome specific primers makes it possible to determine the sex of C. ciconia chicks. Many factors make sex ratio of White Stork changes in subsequent breeding seasons, which depend significantly on specific environmental parameters that shape individual detailed defense mechanisms.