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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ftmdpi:oai:mdpi.com:/1424-2818/10/4/113/ 2023-08-20T04:09:07+02:00 Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation Sunitha Joseph Rebecca O’Connor Abdullah Al Mutery Mick Watson Denis Larkin Darren Griffin agris 2018-10-18 application/pdf https://doi.org/10.3390/d10040113 EN eng Multidisciplinary Digital Publishing Institute Animal Diversity https://dx.doi.org/10.3390/d10040113 https://creativecommons.org/licenses/by/4.0/ Diversity; Volume 10; Issue 4; Pages: 113 falcons genome chromosomes karyotype avian Text 2018 ftmdpi https://doi.org/10.3390/d10040113 2023-07-31T21:47:13Z 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 ... Text peregrine falcon MDPI Open Access Publishing Diversity 10 4 113 |
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falcons genome chromosomes karyotype avian |
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falcons genome chromosomes karyotype avian Sunitha Joseph Rebecca O’Connor Abdullah Al Mutery Mick Watson Denis Larkin Darren Griffin Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation |
topic_facet |
falcons genome chromosomes karyotype avian |
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 ... |
format |
Text |
author |
Sunitha Joseph Rebecca O’Connor Abdullah Al Mutery Mick Watson Denis Larkin Darren Griffin |
author_facet |
Sunitha Joseph Rebecca O’Connor Abdullah Al Mutery Mick Watson Denis Larkin Darren Griffin |
author_sort |
Sunitha Joseph |
title |
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_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_sort |
chromosome level genome assembly and comparative genomics between three falcon species reveals an unusual pattern of genome organisation |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2018 |
url |
https://doi.org/10.3390/d10040113 |
op_coverage |
agris |
genre |
peregrine falcon |
genre_facet |
peregrine falcon |
op_source |
Diversity; Volume 10; Issue 4; Pages: 113 |
op_relation |
Animal Diversity https://dx.doi.org/10.3390/d10040113 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/d10040113 |
container_title |
Diversity |
container_volume |
10 |
container_issue |
4 |
container_start_page |
113 |
_version_ |
1774721859299835904 |