Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture and Chromosome Preparation
2.2. Preparation of BAC Probes for FISH
2.3. Fluorescence In Situ Hybridisation (FISH)
2.4. Karyotype Analysis and Ideogram Generation
2.5. MLGO (Maximum Likelihood for Gene Order Analysis) Analysis for Ancestral Genome Reconstruction
2.6. GRIMM (Genome Rearrangements In Man and Mouse) Analysis for Chromosome Rearrangement
2.7. Mathematical Analyses
3. Results
3.1. Karyotypes and Ideograms for Eight Avian Species
3.2. Application of a Panel of 74 Selected Chicken BACs for the Fine Mapping of Macrochromosome Homologs 1–9 and Z
3.3. Reconstructing the Neognathae Ancestor and Rearrangements
4. Discussion
4.1. Comparative Macrochromosome Maps
4.2. Chromosome Paints vs. BAC Mapping
4.3. Centromere Position
4.4. A Potential Tool for Genome Assembly
4.5. Phylogenetics
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Infraclass | Order | Common Name | 2n | Divergence 1 (Mya 2) | Hybridisation Success Rate (%) |
---|---|---|---|---|---|
Neognathae | Galliformes | chicken | 78 3 | – | 100 |
Galliformes | helmeted guinea fowl | 78 3 | 47 | 100 | |
Anseriformes | duck (mallard) | 80 4 | 80 | 85.1 | |
Columbiformes | rock dove (pigeon) | 80 5 | 98 | 93.2 | |
Otidiformes | houbara bustard | 76 6 | 98 | 87.8 | |
Passeriformes | common blackbird | 80 7 | 98 | 78.4 | |
Passeriformes | Atlantic canary | 80 8 | 98 | 73.0 | |
Charadriiformes | Eurasian woodcock | 96 6 | 98 | 73.0 | |
Palaeognathae | Struthioniformes | ostrich 9 | 80 6 | 140 | 83.8 |
Species | Inversions | Duplications | Intra-Chromosomal Translocations | Inter-Chromosomal Translocations | Fusions | Fissions | Total |
---|---|---|---|---|---|---|---|
Chicken | 3 | 1 | 4 | ||||
Guinea fowl | 4 | 2 | 6 | ||||
Duck | 8 | 8 | |||||
Houbara | 9 | 9 | |||||
Pigeon | 11 | 11 | |||||
Blackbird | 9 | 1 | 10 | ||||
Canary | 4 | 2 | 2 | 2 | 1 | 11 | |
Woodcock | 8 | 3 | 5 | 16 |
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Kiazim, L.G.; O’Connor, R.E.; Larkin, D.M.; Romanov, M.N.; Narushin, V.G.; Brazhnik, E.A.; Griffin, D.K. Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021, 10, 362. https://doi.org/10.3390/cells10020362
Kiazim LG, O’Connor RE, Larkin DM, Romanov MN, Narushin VG, Brazhnik EA, Griffin DK. Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells. 2021; 10(2):362. https://doi.org/10.3390/cells10020362
Chicago/Turabian StyleKiazim, Lucas G., Rebecca E. O’Connor, Denis M. Larkin, Michael N. Romanov, Valery G. Narushin, Evgeni A. Brazhnik, and Darren K. Griffin. 2021. "Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution" Cells 10, no. 2: 362. https://doi.org/10.3390/cells10020362