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Sazanov AA, Sazanova AL, Nefedov MD, Griffin DK, Romanov MN. A pair of gametologous genes provides further insights into avian comparative cytogenomics. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
AbstractExploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative cytogenomic studies. Using bioinformatic, molecular (overgo BAC library scanning), and cytogenetic (BAC-based FISH) techniques, we have investigated in detail a pair of UBE2R2/UBE2R2L gametologs. By screening a gridded genomic jungle fowl BAC library, CHORI-261, with a short labeled UBE2R2L gene fragment called overgo probe, we detected seven specific clones. For three of them, CH261-019I23, CH261-105E16, and CH261-114G22, we identified their precise cytogenetic location on the Gallus gallus W chromosome (GGAW). They also co-localized with the UBAP2L2 gene on the, as was shown previously, along with the CH261-053P09 BAC clone also containing the GGAW-specific UBE2R2L DNA sequence. The fine mapping of the UBE2R2/UBE2R2L homologs in the chicken genome also shed the light on comparative cytogenetic aspects in birds. Our findings provided further evidence that bird genomes moderately changed only during evolution and are suitable for successful use of interspecies hybridization using both overgo-based BAC library screen and BAC-based FISH.
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Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions. Genetica 2023:10.1007/s10709-023-00185-x. [PMID: 36940055 DOI: 10.1007/s10709-023-00185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/14/2023] [Indexed: 03/21/2023]
Abstract
Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.
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Griffin DK, Larkin DM, O’Connor RE, Romanov MN. Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants. Animals (Basel) 2022; 13:ani13010106. [PMID: 36611715 PMCID: PMC9817885 DOI: 10.3390/ani13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species. The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine-Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
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Affiliation(s)
- Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
| | - Denis M. Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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Romanov MN, Da Y, Chemnick LG, Thomas SM, Dandekar SS, Papp JC, Ryder OA. Towards a Genetic Linkage Map of the California Condor, an Endangered New World Vulture Species. Animals (Basel) 2022; 12:ani12233266. [PMID: 36496789 PMCID: PMC9739316 DOI: 10.3390/ani12233266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
The development of a linkage map is an important component for promoting genetic and genomic studies in California condors, an endangered New World vulture species. Using a set of designed anonymous microsatellite markers, we genotyped a reference condor population involving 121 individuals. After marker validation and genotype filtering, the genetic linkage analysis was performed using 123 microsatellite loci. This resulted in the identification of 15 linkage groups/subgroups that formed a first-generation condor genetic map, while no markers linked to a lethal chondrodystrophy mutation were found. A panel of polymorphic markers that is instrumental in molecular parentage diagnostics and other genetic studies in the California condor was selected. Further condor conservation genomics research will be focused on updating the linkage map and integrating it with cytogenetic and BAC-based physical maps and ultimately with the genome sequence assembly.
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Affiliation(s)
- Michael N. Romanov
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Correspondence:
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Leona G. Chemnick
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Steven M. Thomas
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Sugandha S. Dandekar
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Jeanette C. Papp
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Oliver A. Ryder
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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Ryder OA, Thomas S, Judson JM, Romanov MN, Dandekar S, Papp JC, Sidak-Loftis LC, Walker K, Stalis IH, Mace M, Steiner CC, Chemnick LG. Facultative Parthenogenesis in California Condors. J Hered 2021; 112:569-574. [PMID: 34718632 PMCID: PMC8683835 DOI: 10.1093/jhered/esab052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Abstract
Parthenogenesis is a relatively rare event in birds, documented in unfertilized eggs from columbid, galliform, and passerine females with no access to males. In the critically endangered California condor, parentage analysis conducted utilizing polymorphic microsatellite loci has identified two instances of parthenogenetic development from the eggs of two females in the captive breeding program, each continuously housed with a reproductively capable male with whom they had produced offspring. Paternal genetic contribution to the two chicks was excluded. Both parthenotes possessed the expected male ZZ sex chromosomes and were homozygous for all evaluated markers inherited from their dams. These findings represent the first molecular marker-based identification of facultative parthenogenesis in an avian species, notably of females in regular contact with fertile males, and add to the phylogenetic breadth of vertebrate taxa documented to have reproduced via asexual reproduction.
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Affiliation(s)
- Oliver A Ryder
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Steven Thomas
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,SGI-DNA, La Jolla, CA 92037, USA
| | - Jessica Martin Judson
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - Michael N Romanov
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Sugandha Dandekar
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Lindsay C Sidak-Loftis
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,Department of Veterinary Microbiology and Pathology, Program in Vector-borne Diseases, Washington State University, Pullman, WA, USA
| | | | - Ilse H Stalis
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Michael Mace
- San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Cynthia C Steiner
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Leona G Chemnick
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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Robinson JA, Bowie RCK, Dudchenko O, Aiden EL, Hendrickson SL, Steiner CC, Ryder OA, Mindell DP, Wall JD. Genome-wide diversity in the California condor tracks its prehistoric abundance and decline. Curr Biol 2021; 31:2939-2946.e5. [PMID: 33989525 DOI: 10.1016/j.cub.2021.04.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/05/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America's largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.
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Affiliation(s)
- Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Rauri C K Bowie
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA; Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China; Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA, Australia
| | | | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA; Department of Evolution, Behavior, and Ecology, University of California, San Diego, San Diego, CA, USA
| | - David P Mindell
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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Ryder OA, Onuma M. Viable Cell Culture Banking for Biodiversity Characterization and Conservation. Annu Rev Anim Biosci 2018; 6:83-98. [DOI: 10.1146/annurev-animal-030117-014556] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Because living cells can be saved for indefinite periods, unprecedented opportunities for characterizing, cataloging, and conserving biological diversity have emerged as advanced cellular and genetic technologies portend new options for preventing species extinction. Crucial to realizing the potential impacts of stem cells and assisted reproductive technologies on biodiversity conservation is the cryobanking of viable cell cultures from diverse species, especially those identified as vulnerable to extinction in the near future. The advent of in vitro cell culture and cryobanking is reviewed here in the context of biodiversity collections of viable cell cultures that represent the progress and limitations of current efforts. The prospects for incorporating collections of frozen viable cell cultures into efforts to characterize the genetic changes that have produced the diversity of species on Earth and contribute to new initiatives in conservation argue strongly for a global network of facilities for establishing and cryobanking collections of viable cells.
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Affiliation(s)
- Oliver A. Ryder
- San Diego Institute for Conservation Research, San Diego Zoo Global, Escondido, California 92027-7000, USA
| | - Manabu Onuma
- Ecological Risk Assessment and Control Section, Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies, 16-2, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
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Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 2016; 27:875-884. [PMID: 27903645 PMCID: PMC5411781 DOI: 10.1101/gr.213660.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Vasileios Panagiotis E Lenis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Henry J Martell
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Anjali Mandawala
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom.,School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Katie Fowler
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Ishijima J, Uno Y, Nishida C, Matsuda Y. Genomic structures of the kW1 loci on the Z and W chromosomes in ratite birds: structural changes at an early stage of W chromosome differentiation. Cytogenet Genome Res 2014; 142:255-67. [PMID: 24820528 DOI: 10.1159/000362479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2014] [Indexed: 11/19/2022] Open
Abstract
The W chromosome of ratite birds shows minimal morphological differentiation and retains homology of genetic linkage and gene order with a substantial stretch of the Z chromosome; however, the molecular structure in the differentiated region is still not well known. The kW1 sequence was isolated from the kiwi as a W-specific DNA marker for PCR-based molecular sexing of ratite birds. In ratite W chromosomes, this sequence commonly contains a ∼200-bp deletion. To characterize the very early event of avian sex chromosome differentiation, we performed molecular cytogenetic analyses of kW1 and its flanking sequences in paleognathous and neognathous birds and reptiles. Female-specific repeats were found in the kW1-flanking sequence of the cassowary (Casuarius casuarius), and the repeats have been amplified in the pericentromeric region of the W chromosomes of ratites, which may have resulted from the cessation of meiotic recombination between the Z and W chromosomes at an early stage of sex chromosome differentiation. The presence of the kW1 sequence in neognathous birds and a crocodilian species suggests that the kW1 sequence was present in the ancestral genome of Archosauria; however, it disappeared in other reptilian taxa and several lineages of neognathous birds.
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Affiliation(s)
- Junko Ishijima
- Laboratory of Animal Cytogenetics, Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
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Comparison of the Chromosome Structures between the Chicken and Three Anserid Species, the Domestic Duck ( Anas platyrhynchos), Muscovy Duck ( Cairina moschata), and Chinese Goose ( Anser cygnoides), and the Delineation of their Karyotype Evolution by Comparative Chromosome Mapping. J Poult Sci 2014. [DOI: 10.2141/jpsa.0130090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Romanov MN, Dodgson JB, Gonser RA, Tuttle EM. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization. BMC Res Notes 2011; 4:211. [PMID: 21693052 PMCID: PMC3155834 DOI: 10.1186/1756-0500-4-211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 06/21/2011] [Indexed: 12/23/2022] Open
Abstract
Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.
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Affiliation(s)
- Michael N Romanov
- Dept, of Biology, Indiana State University, Terre Haute, Indiana 47809, USA.
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