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 ge...
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| Format: | Article |
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MDPI AG
2018-10-01
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| Series: | Diversity |
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| Online Access: | http://www.mdpi.com/1424-2818/10/4/113 |
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| author | Sunitha Joseph Rebecca E. O’Connor Abdullah F. Al Mutery Mick Watson Denis M. Larkin Darren K. Griffin |
| author_facet | Sunitha Joseph Rebecca E. O’Connor Abdullah F. Al Mutery Mick Watson Denis M. Larkin Darren K. Griffin |
| author_sort | Sunitha Joseph |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T11:52:26Z |
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| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-04-11T11:52:26Z |
| publishDate | 2018-10-01 |
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| spelling | doaj.art-ceb9c18306bc45668d254ab09963597e2022-12-22T04:25:18ZengMDPI AGDiversity1424-28182018-10-0110411310.3390/d10040113d10040113Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome OrganisationSunitha Joseph0Rebecca E. O’Connor1Abdullah F. Al Mutery2Mick Watson3Denis M. Larkin4Darren K. Griffin5School of Biosciences, University of Kent, Canterbury CT2 7NJ, UKSchool of Biosciences, University of Kent, Canterbury CT2 7NJ, UKSchool of Biosciences, University of Kent, Canterbury CT2 7NJ, UKDepartment of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UKSchool of Biosciences, University of Kent, Canterbury CT2 7NJ, UKWhole 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.http://www.mdpi.com/1424-2818/10/4/113falconsgenomechromosomeskaryotypeavian |
| spellingShingle | Sunitha Joseph Rebecca E. O’Connor Abdullah F. Al Mutery Mick Watson Denis M. Larkin Darren K. Griffin Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation Diversity falcons genome chromosomes karyotype avian |
| title | Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
| title_full | Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
| title_fullStr | Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
| title_full_unstemmed | Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
| title_short | Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
| title_sort | chromosome level genome assembly and comparative genomics between three falcon species reveals an unusual pattern of genome organisation |
| topic | falcons genome chromosomes karyotype avian |
| url | http://www.mdpi.com/1424-2818/10/4/113 |
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