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Souza GM, Kretschmer R, Toma GA, de Oliveira AM, Deon GA, Setti PG, Zeni Dos Santos R, Goes CAG, Del Valle Garnero A, Gunski RJ, de Oliveira EHC, Porto-Foresti F, Liehr T, Utsunomia R, de Bello Cioffi M. Satellitome analysis on the pale-breasted thrush Turdus leucomelas (Passeriformes; Turdidae) uncovers the putative co-evolution of sex chromosomes and satellite DNAs. Sci Rep 2024; 14:20656. [PMID: 39232109 PMCID: PMC11375038 DOI: 10.1038/s41598-024-71635-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/29/2024] [Indexed: 09/06/2024] Open
Abstract
Do all birds' sex chromosomes follow the same canonical one-way direction of evolution? We combined cytogenetic and genomic approaches to analyze the process of the W chromosomal differentiation in two selected Passeriform species, named the Pale-breasted Thrush Turdus leucomelas and the Rufous-bellied thrush T. rufiventris. We characterized the full catalog of satellite DNAs (satellitome) of T. leucomelas, and the 10 TleSatDNA classes obtained together with 16 microsatellite motifs were in situ mapped in both species. Additionally, using Comparative Genomic Hybridization (CGH) assays, we investigated their intragenomic variations. The W chromosomes of both species did not accumulate higher amounts of both heterochromatin and repetitive sequences. However, while T. leucomelas showed a heterochromatin-poor W chromosome with a very complex evolutionary history, T. rufiventris showed a small and partially heterochromatic W chromosome that represents a differentiated version of its original autosomal complement (Z chromosome). The combined approach of CGH and sequential satDNA mapping suggest the occurrence of a former W-autosomal translocation event in T. leucomelas, which had an impact on the W chromosome in terms of sequence gains and losses. At the same time, an autosome, which is present in both males and females in a polymorphic state, lost sequences and integrated previously W-specific ones. This putative W-autosomal translocation, however, did not result in the emergence of a multiple-sex chromosome system. Instead, the generation of a neo-W chromosome suggests an unexpected evolutionary trajectory that deviates from the standard canonical model of sex chromosome evolution.
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Affiliation(s)
- Guilherme Mota Souza
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS, 96010-610, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Alan Moura de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Princia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | | | | | | | - Ricardo José Gunski
- Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, RS, 97307-020, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, PA, 67030-000, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Fabio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru, SP, 17033-360, Brazil
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Friedrich-Schiller Universität, 07747, Jena, Germany.
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru, SP, 17033-360, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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2
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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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3
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Kretschmer R, Rodrigues BS, Barcellos SA, Costa AL, Cioffi MDB, Garnero ADV, Gunski RJ, de Oliveira EHC, Griffin DK. Karyotype Evolution and Genomic Organization of Repetitive DNAs in the Saffron Finch, Sicalis flaveola (Passeriformes, Aves). Animals (Basel) 2021; 11:ani11051456. [PMID: 34069485 PMCID: PMC8160697 DOI: 10.3390/ani11051456] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022] Open
Abstract
The Saffron finch (Sicalis flaveola), a semi-domestic species, is tolerant of human proximity and nesting in roof spaces. Considering the importance of cytogenomic approaches in revealing different aspects of genomic organization and evolution, we provide detailed cytogenetic data for S. flaveola, including the standard Giemsa karyotype, C- and G-banding, repetitive DNA mapping, and bacterial artificial chromosome (BAC) FISH. We also compared our results with the sister groups, Passeriformes and Psittaciformes, bringing new insights into the chromosome and genome evolution of birds. The results revealed contrasting rates of intrachromosomal changes, highlighting the role of SSR (simple short repetition probes) accumulation in the karyotype reorganization. The SSRs showed scattered hybridization, but brighter signals were observed in the microchromosomes and the short arms of Z chromosome in S. flaveola. BACs probes showed conservation of ancestral syntenies of macrochromosomes (except GGA1), as well as the tested microchromosomes. The comparison of our results with previous studies indicates that the great biological diversity observed in Passeriformes was not likely accompanied by interchromosomal changes. In addition, although repetitive sequences often act as hotspots of genome rearrangements, Passeriformes species showed a higher number of signals when compared with the sister group Psittaciformes, indicating that these sequences were not involved in the extensive karyotype reorganization seen in the latter.
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Affiliation(s)
| | | | - Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (S.A.B.); (A.L.C.); (A.d.V.G.); (R.J.G.)
| | - Alice Lemos Costa
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (S.A.B.); (A.L.C.); (A.d.V.G.); (R.J.G.)
| | - Marcelo de Bello Cioffi
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil;
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (S.A.B.); (A.L.C.); (A.d.V.G.); (R.J.G.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (S.A.B.); (A.L.C.); (A.d.V.G.); (R.J.G.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, Brazil
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- Correspondence: ; Tel.: +44-1227-823022
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Ribas TFA, Pieczarka JC, Griffin DK, Kiazim LG, Nagamachi CY, O Brien PCM, Ferguson-Smith MA, Yang F, Aleixo A, O'Connor RE. Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype. BMC Ecol Evol 2021; 21:34. [PMID: 33653261 PMCID: PMC7927240 DOI: 10.1186/s12862-021-01768-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. RESULTS The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. CONCLUSIONS Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.
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Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- School of Biosciences, University of Kent, Canterbury, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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6
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Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes). BMC Ecol Evol 2021; 21:8. [PMID: 33514318 PMCID: PMC7853317 DOI: 10.1186/s12862-020-01737-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/14/2020] [Indexed: 11/12/2022] Open
Abstract
Background The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes. Conclusion Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.
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Affiliation(s)
- Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Cristovam Guerreiro Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal do Pará, Campus de Bragança, Avenida dos Bragançanos s/nº, Bragança, Pará, 68600-000, Brazil
| | - Patricia Caroline Mary O Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridgeshire, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil.
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7
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Kretschmer R, Furo IDO, Cioffi MDB, Gunski RJ, Garnero ADV, O’Brien PCM, Ferguson-Smith MA, de Freitas TRO, de Oliveira EHC. Extensive chromosomal fissions and repetitive DNA accumulation shaped the atypical karyotypes of two Ramphastidae (Aves: Piciformes) species. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In contrast to the ‘avian-like’ diploid number (2n = 80), most toucans and aracaris (Piciformes: Ramphastidae) have divergent karyotypes, exhibiting a higher 2n. To identify the chromosomal rearrangements that shaped the karyotype of these species, we applied chicken macrochromosome paints 1–10 and 11 microsatellite sequences to the chromosomes of two representative species, Pteroglossus inscriptus and Ramphastos tucannus tucannus. Paints of chicken chromosomes revealed that at least the first five ancestral chromosomes have undergone fissions, and a fusion between a segment of chicken chromosome 1 and a segment from chromosome 3 occurred in both species. The microsatellite sequences were accumulated mainly in the Z chromosome and in several microchromosomes in both species. These results suggest that the genomes of the Ramphastidae have been shaped by extensive fissions and repetitive DNA accumulation as the main driving forces leading to the higher 2n as found in these species. Furthermore, our results suggest that the putative ancestral karyotype of Ramphastidae already had a high diploid number, probably close to 2n = 112, similar to that observed in P. inscriptus and R. t. tucannus.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ivanete De Oliveira Furo
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, PA, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Marcelo De Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, RS, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, RS, Brazil
| | - Patricia C M O’Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, UK
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, Brazil
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8
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Furo IDO, Kretschmer R, O'Brien PC, Pereira JC, Garnero ADV, Gunski RJ, O'Connor RE, Griffin DK, Gomes AJB, Ferguson-Smith MA, de Oliveira EHC. Chromosomal Evolution in the Phylogenetic Context: A Remarkable Karyotype Reorganization in Neotropical Parrot Myiopsitta monachus (Psittacidae). Front Genet 2020; 11:721. [PMID: 32754200 PMCID: PMC7366516 DOI: 10.3389/fgene.2020.00721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Myiopsitta monachus is a small Neotropical parrot (Psittaciformes: Arini Tribe) from subtropical and temperate regions of South America. It has a diploid chromosome number 2n = 48, different from other members of the Arini Tribe that have usually 70 chromosomes. The species has the lowest 2n within the Arini Tribe. In this study, we combined comparative chromosome painting with probes generated from chromosomes of Gallus gallus and Leucopternis albicollis, and FISH with bacterial artificial chromosomes (BACs) selected from the genome library of G. gallus with the aim to shed light on the dynamics of genome reorganization in M. monachus in the phylogenetic context. The homology maps showed a great number of fissions in macrochromosomes, and many fusions between microchromosomes and fragments of macrochromosomes. Our phylogenetic analysis by Maximum Parsimony agree with molecular data, placing M. monachus in a basal position within the Arini Tribe, together with Amazona aestiva (short tailed species). In M. monachus many chromosome rearrangements were found to represent autopomorphic characters, indicating that after this species split as an independent branch, an intensive karyotype reorganization took place. In addition, our results show that M. monachus probes generated by flow cytometry provide novel cytogenetic tools for the detection of avian chromosome rearrangements, since this species presents breakpoints that have not been described in other species.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Brazil.,Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Patricia Caroline O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Jorge C Pereira
- Animal and Veterinary Research Centre (CEVAV), University of Tràs-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | | | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | | | | | | | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Edivaldo Herculano Correa de Oliveira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Brazil.,Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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9
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de Oliveira TD, Kretschmer R, Bertocchi NÁ, O’Brien PC, Ferguson-Smith MA, Garnero ADV, de Oliveira EHC, Gunski RJ. The molecular cytogenetic characterization of Conopophaga lineata indicates a common chromosome rearrangement in the Parvorder Furnariida (Aves, Passeriformes). Genet Mol Biol 2020; 43:e20200018. [PMID: 32542304 PMCID: PMC7295152 DOI: 10.1590/1678-4685-gmb-2020-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/12/2020] [Indexed: 11/26/2022] Open
Abstract
Cytogenetic analyses of the Suboscines species are still scarce, and so far, there is no karyotype description of any species belonging to the family Conopophagidae. Thus, the aim of this study is to describe and analyze the karyotype of Conopophaga lineata by chromosome painting using Gallus gallus (GGA) probes and to identify the location of the 18/28S rDNA cluster. Metaphases were obtained from fibroblast culture from two individuals of C. lineata. We observed a diploid number of 2n=78. GGA probes showed that most ancestral syntenies are conserved, except for the fission of GGA1 and GGA2, into two distinct pairs each. We identified the location of 18S rDNA genes in a pair of microchromosomes. The fission of the syntenic group corresponding to GGA2 was observed in other Furnariida, and hence may correspond to a chromosomal synapomorphy for the species of Parvorder Furnariida.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Natasha Ávila Bertocchi
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Patricia C.M. O’Brien
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
| | | | - Analía del Valle Garnero
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Instituto Evandro Chagas, Seção Meio Ambiente (SAMAM), Ananindeua, PA, Brazil
- Universidade Federal do Pará, Belém, Instituto de Ciências Exatas e Naturais, Belém, PA, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
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10
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Kretschmer R, Furo IDO, Gomes AJB, Kiazim LG, Gunski RJ, Garnero ADV, Pereira JC, Ferguson-Smith MA, de Oliveira EHC, Griffin DK, de Freitas TRO, O’Connor RE. A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes). Genes (Basel) 2020; 11:genes11060632. [PMID: 32521831 PMCID: PMC7349364 DOI: 10.3390/genes11060632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 11/18/2022] Open
Abstract
The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68-86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil;
- Correspondence:
| | - Ivanete de Oliveira Furo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, Brazil;
| | | | - Lucas G. Kiazim
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, Brazil; (R.J.G.); (A.d.V.G.)
| | - Jorge C. Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge CB3 0ES, UK;
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
| | | | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (L.G.K.); (D.K.G.);
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11
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Barcellos SA, Kretschmer R, Souza MSD, Costa AL, Degrandi TM, Lopes CF, Ferguson-Smith MA, Pereira J, Oliveira EHCD, Gunski RJ, Garnero ADV. Comparative analyses of three swallow species (Aves, Passeriformes, Hirundinidae): Insights on karyotype evolution and genomic organization. Genet Mol Biol 2020; 43:e20190232. [PMID: 32162650 PMCID: PMC7197979 DOI: 10.1590/1678-4685-gmb-2019-0232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/19/2019] [Indexed: 11/21/2022] Open
Abstract
Despite the richness of species in the Hirudinidae family, little is known about the genome organization of swallows. The Progne tapera species presents genetic and morphological difference when compared to other members of the same genus. Hence, the aims of this study were to analyze the chromosomal evolution of three species Progne tapera, Progne chalybea and Pygochelidon cyanoleuca - by comparative chromosome painting using two sets of probes, Gallus gallus and Zenaida auriculata, in order to determine chromosome homologies and the relationship between these species. All karyotypes exhibited 76 chromosomes with similar morphology, except for the 5th, 6th and 7th chromosome pairs in P. cyanoleuca. Additionally, comparative chromosome painting demonstrated the same hybridization pattern in the two Progne, which was similar to the putative avian ancestral karyotype, except for the centric fission in the first pair, as found in other Passeriformes. Thus, these data display a close relationship between the Progne species. Although P. cyanoleuca demonstrated the same fission in the first pair of the ancestral syntenic (GGA1), it also showed an additional chromosomal rearrangement for this species, namely a fusion with a microchromosome in the seventh pair.
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Affiliation(s)
- Suziane Alves Barcellos
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Genética e Biologia Molecular - PPGBM, Porto Alegre, RS, Brazil
| | - Marcelo Santos de Souza
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
| | - Alice Lemos Costa
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
| | - Tiago Marafiga Degrandi
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, PPGG, Curitiba, PR, Brazil
| | - Cassiane Furlan Lopes
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
| | - Malcolm A Ferguson-Smith
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Jorge Pereira
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Edivaldo Herculano Correa de Oliveira
- Universidade Federal do Pará, Instituto de Ciências Exatas e Naturais, Belém, PA, Brazil.,Instituto Evandro Chagas, Laboratório de Cultura de Tecidos e Citogenética, Ananindeua, PA, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
| | - Analía Del Valle Garnero
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, RS, Brazil
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13
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Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species. PLoS One 2019; 14:e0214028. [PMID: 30913221 PMCID: PMC6435179 DOI: 10.1371/journal.pone.0214028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 01/22/2023] Open
Abstract
The highly repetitive DNA sequence of centromeric heterochromatin is an effective molecular cytogenetic marker for investigating genomic compartmentalization between macrochromosomes and microchromosomes in birds. We isolated four repetitive sequence families of centromeric heterochromatin from three Anseriformes species, viz., domestic duck (Anas platyrhynchos, APL), bean goose (Anser fabalis, AFA), and whooper swan (Cygnus cygnus, CCY), and characterized the sequences by molecular cytogenetic approach. The 190-bp APL-HaeIII and 101-bp AFA-HinfI-S sequences were localized in almost all chromosomes of A. platyrhynchos and A. fabalis, respectively. However, the 192-bp AFA-HinfI-L and 290-bp CCY-ApaI sequences were distributed in almost all microchromosomes of A. fabalis and in approximately 10 microchromosomes of C. cygnus, respectively. APL-HaeIII, AFA-HinfI-L, and CCY-ApaI showed partial sequence homology with the chicken nuclear-membrane-associated (CNM) repeat families, which were localized primarily to the centromeric regions of microchromosomes in Galliformes, suggesting that ancestral sequences of the CNM repeat families are observed in the common ancestors of Anseriformes and Galliformes. These results collectively provide the possibility that homogenization of centromeric heterochromatin occurred between microchromosomes in Anseriformes and Galliformes; however, homogenization between macrochromosomes and microchromosomes also occurred in some centromeric repetitive sequences.
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14
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Mahiddine-Aoudjit L, Boucekkine O, Ladjali-Mohammedi K. Banding cytogenetics of the vulnerable species Houbara bustard (Otidiformes) and comparative analysis with the Domestic fowl. COMPARATIVE CYTOGENETICS 2019; 13:1-17. [PMID: 30701036 PMCID: PMC6351704 DOI: 10.3897/compcytogen.v13i1.30660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
The Houbara bustard Chlamydotisundulata (Jacquin, 1784) is an emblematic and endangered bird of steppes and desert spaces of North Africa. This species belonging to Otidiformes is recognized as vulnerable by the International Union for Nature Conservation. The critical situation of this species and the revision of its classification on the tree of birds encouraged the authors to start accumulating chromosome data. For that, we propose the GTG- and RBG-banded karyotypes of the Houbara bustard prepared from primary fibroblast cell cultures. The first eight autosomal pairs and sex chromosomes have been described and compared to those of the domestic fowl Gallusdomesticus (Linnaeus, 1758). The diploid number has been estimated as 78 chromosomes with 8 macrochromosomes pairs and 30 microchromosomes pairs, attesting of the stability of chromosome number in avian karyotypes. The description of the karyotype of the Houbara is of crucial importance for the management of the reproduction of this species in captivity. It can be used as a reference in the detection of chromosomal abnormalities, which would be responsible of the early embryonic mortalities.
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Affiliation(s)
- Leila Mahiddine-Aoudjit
- University of Sciences and Technology Houari Boumediene (USTHB), Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneAlgiersAlgeria
- University of M’hamed Bougara of Boumerdes, Faculty of Sciences, Department of Biology, Avenue de l’Indépendance, 35 000 Boumerdès, AlgeriaUniversity of M’hamed Bougara of BoumerdesBoumerdèsAlgeria
| | - Ouahida Boucekkine
- The General Direction of Forests, Ben Aknoun, Algiers, AlgeriaThe General Direction of ForestsAlgiersAlgeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene (USTHB), Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneAlgiersAlgeria
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15
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Bülau SE, Kretschmer R, Gunski RJ, Garnero ADV, O'Brien PCM, Ferguson-Smith MA, Oliveira EHCD, Freitas TROD. Chromosomal polymorphism and comparative chromosome painting in the rufous-collared sparrow (Zonotrichia capensis). Genet Mol Biol 2018; 41:799-805. [PMID: 30534855 PMCID: PMC6415599 DOI: 10.1590/1678-4685-gmb-2017-0367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/21/2018] [Indexed: 01/13/2023] Open
Abstract
Zonotrichia capensis is widely distributed in the Neotropics. Previous cytogenetic studies demonstrated the presence of polymorphisms in two chromosome pairs (ZCA2 and ZCA4). Here, we report results based on comparative chromosome painting, using probes derived from Gallus gallus and Leucopternis albicollis, focused on characterizing the chromosome organization of Z. capensis. Our results demonstrate the conservation of ancestral syntenies as observed previously in other species of passerine. Syntenies were rearranged by a series of inversions in the second chromosome as described in other Passeriformes, but in this species, by using probes derived from L. albicollis we observed an extra inversion in the second chromosome that had not previously been reported. We also report a paracentric inversion in pair 3; this chromosome corresponds to the second chromosome in Zonotrichia albicollis and may indicate the presence of ancestral inversions in the genus. The chromosomal inversions we found might be important for understanding the phenotypic variation that exists throughout the distribution of Z. capensis.
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Affiliation(s)
- Sandra Eloisa Bülau
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas (PPGCB), Universidade Federal do Pampa, São Gabriel, RS, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas (PPGCB), Universidade Federal do Pampa, São Gabriel, RS, Brazil
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Edivaldo Herculano Correa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, Brazil.,Laboratório de Cultura de Tecidos e Citogenética (SAMAM), Instituto Evandro Chagas, Ananindeua, PA, Brazil
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16
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O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 2018; 19:171. [PMID: 30355328 PMCID: PMC6201548 DOI: 10.1186/s13059-018-1550-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/24/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. RESULTS We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. CONCLUSIONS The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
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Affiliation(s)
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Sophie Bennett
- School of Biosciences, University of Kent, Canterbury, UK
| | - Eden A Slack
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Emily Allanson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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Chromosome Painting in Neotropical Long- and Short-Tailed Parrots (Aves, Psittaciformes): Phylogeny and Proposal for a Putative Ancestral Karyotype for Tribe Arini. Genes (Basel) 2018; 9:genes9100491. [PMID: 30309041 PMCID: PMC6210594 DOI: 10.3390/genes9100491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
Most Neotropical Psittacidae have a diploid number of 2n = 70, and a dichotomy in chromosome patterns. Long-tailed species have biarmed macrochromosomes, while short-tailed species have telo/acrocentric macrochromosomes. However, the use of chromosome painting has demonstrated that karyotype evolution in Psittacidae includes a high number of inter/intrachromosomal rearrangements. To determine the phylogeny of long- and short-tailed species, and to propose a putative ancestral karyotype for this group, we constructed homology maps of Pyrrhura frontalis (PFR) and Amazona aestiva (AAE), belonging to the long- and short-tailed groups, respectively. Chromosomes were analyzed by conventional staining and fluorescent in situ hybridization using whole chromosome paints of Gallusgallus and Leucopternis albicollis. Conventional staining showed a karyotype with 2n = 70 in both species, with biarmed macrochromosomes in PFR and telo/acrocentric chromosomes in AAE. Comparison of the results with the putative avian ancestral karyotype (PAK) showed fusions in PFR of PAK1p/PAK4q (PFR1) and PAK6/PAK7 (PFR6) with a paracentric inversion in PFR6. However, in AAE, there was only the fusion between PAK6/7 (AAE7) with a paracentric inversion. Our results indicate that PFR retained a more basal karyotype than long-tailed species previously studied, and AAE a more basal karyotype for Neotropical Psittacidae analyzed so far.
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18
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Ribas TFA, Nagamachi CY, Aleixo A, Pinheiro MLS, O´Brien PCM, Ferguson-Smith MA, Yang F, Suarez P, Pieczarka JC. Chromosome painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes. PLoS One 2018; 13:e0202040. [PMID: 30138388 PMCID: PMC6107148 DOI: 10.1371/journal.pone.0202040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022] Open
Abstract
Glyphorynchus spirurus (GSP), also called the Wedge-billed Woodcreeper (Furnariidae) has an extensive distribution in the Americas, including the Atlantic coast of Brazil. Nevertheless, there is no information about its karyotype or genome organization. To contribute to the knowledge of chromosomal evolution in Passeriformes we analysed the karyotype of Glyphorynchus spirurus by classic and molecular cytogenetics methods. We show that Glyphorynchus spirurus has a 2n = 80 karyotype with a fundamental number (FN) of 84, similar to the avian putative ancestral karyotype (PAK). Glyphorynchus spirurus pair 1 was heteromorphic in the Tapajós population whereby the short arms varied in sizes, possibly due to a pericentric inversion, as described in other Furnariidae birds. FISH with the Histone H5 probe revealed a signal in the pericentromeric region of G. spirurus chromosome 5 and rDNA 18S showed interstitial signal in GSP-1. Chromosome painting with Gallus gallus (GGA) macrochromosomes 1-9 probes showed disruption of chromosome syntenies of GGA-1, 2 and 4 by fission in Glyphorynchus spirurus. Our results confirm that the GGA1 centric fission is a synapomorphic character for the phylogenetic branch composed of Strigiformes, Passeriformes, Columbiformes and Falconiformes. On the other hand, the GGA-2 fission is reported here for the first time in Passeriformes. Chromosome painting with BOE whole chromosome probes confirmed these rearrangements in Glyphorynchus spirurus revealed by Gallus gallus 1-9 probes, in addition to enabling the establishment of genome-wide homology map.
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Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasilia, Brazil
| | - Alexandre Aleixo
- Department of Zoology, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O´Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Pablo Suarez
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Puerto Iguazú, Misiones, Argentina
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasilia, Brazil
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Comparative chromosome painting in Columbidae (Columbiformes) reinforces divergence in Passerea and Columbea. Chromosome Res 2018; 26:211-223. [PMID: 29882066 DOI: 10.1007/s10577-018-9580-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
Abstract
Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the karyotype evolution within Columbiformes remains unclear. To delineate the synteny-conserved segments and karyotypic differences among four Columbidae species, we used chromosome painting from Gallus gallus (GGA, 2n = 78) and Leucopternis albicollis (LAL, 2n = 68). Besides that, a set of painting probes for the eared dove, Zenaida auriculata (ZAU, 2n = 76), was generated from flow-sorted chromosomes. Chromosome painting with GGA and ZAU probes showed conservation of the first ten ancestral pairs in Z. auriculata, Columba livia, and Columbina picui, while in Leptotila verreauxi, fusion of the ancestral chromosomes 6 and 7 was observed. However, LAL probes revealed a complex reorganization of ancestral chromosome 1, involving paracentric and pericentric inversions. Because of the presence of similar intrachromosomal rearrangements in the chromosomes corresponding to GGA1q in the Columbidae and Passeriformes species but without a common origin, these results are consistent with the recent proposal of divergence within Neoaves (Passerea and Columbea). In addition, inversions in chromosome 2 were identified in C. picui and L. verreauxi. Thus, in four species of distinct genera of the Columbidae family, unique chromosomal rearrangements have occurred during karyotype evolution, confirming that despite conservation of the ancestral syntenic groups, these chromosomes have been modified by the occurrence of intrachromosomal rearrangements.
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Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting. Genes (Basel) 2018; 9:genes9040181. [PMID: 29584697 PMCID: PMC5924523 DOI: 10.3390/genes9040181] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/08/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.
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Kretschmer R, de Lima VLC, de Souza MS, Costa AL, O’Brien PCM, Ferguson-Smith MA, de Oliveira EHC, Gunski RJ, Garnero ADV. Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions. COMPARATIVE CYTOGENETICS 2018; 12:97-110. [PMID: 29675139 PMCID: PMC5904361 DOI: 10.3897/compcytogen.v12i1.22344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Vanusa Lilian Camargo de Lima
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Marcelo Santos de Souza
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Alice Lemos Costa
- Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Patricia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
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Zlotina A, Dedukh D, Krasikova A. Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies. Genes (Basel) 2017; 8:genes8110311. [PMID: 29117127 PMCID: PMC5704224 DOI: 10.3390/genes8110311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 01/04/2023] Open
Abstract
Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes. Due to the giant size, peculiarities of organization and enrichment with cytological markers, lampbrush chromosomes can serve as an opportune model for comprehensive high-resolution cytogenetic and cytological investigations. Here, we review the main findings on chromosome evolution in amphibians and birds that were obtained using lampbrush chromosomes. In particular, we discuss the data on evolutionary chromosomal rearrangements, accumulation of polymorphisms, evolution of sex chromosomes as well as chromosomal changes during clonal reproduction of interspecies hybrids.
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Affiliation(s)
- Anna Zlotina
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
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Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017; 18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick-billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick-billed murre genome using a homology-based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
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Affiliation(s)
- Anna Tigano
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Vicki L Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
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dos Santos MDS, Kretschmer R, Frankl-Vilches C, Bakker A, Gahr M, O´Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary. PLoS One 2017; 12:e0170997. [PMID: 28129381 PMCID: PMC5271350 DOI: 10.1371/journal.pone.0170997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.
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Affiliation(s)
| | - Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Patricia C. M. O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Belém, Brazil
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Wójcik E, Smalec E. Constitutive heterochromatin in chromosomes of duck hybrids and goose hybrids. Poult Sci 2016; 96:18-26. [PMID: 27664202 DOI: 10.3382/ps/pew318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 07/28/2016] [Indexed: 02/05/2023] Open
Abstract
Constitutive heterochromatin is a highly condensed fraction of chromatin in chromosomes. It is characterized by a high degree of polymorphism. Heterochromatin is located in the centromeric, telomeric, and interstitial parts of chromosomes. We used the CBG ( C: banding using B: arium hydroxide by G: iemsa) staining technique to identify heterochromatin in chromosomes. Analysis of karyotypes of F1 hybrids resulting from intergeneric hybridization of ducks (A. platyrhynchos × C. moschata) and interspecific crosses of geese (A. anser × A. cygnoides) were used to compare the karyotypes of 2 species of duck and 2 species of geese, as well as to compare the hybrids with the parent species. The localization of C-bands and their size were determined. In the duck hybrid, greater amounts of heterochromatin were noted in the homologous chromosomes from the duck A. platyrhynchos than in the chromosomes from the duck C. moschata. In the goose hybrid more heterochromatin was observed in the homologous chromosomes from the goose A. cygnoides than in the chromosomes from the goose A. anser. Comparison of chromosomes from the duck hybrid with chromosomes of the ducks A. platyrhynchos and C. moschata revealed nearly twice as much constitutive heterochromatin in the chromosomes of the hybrid. When chromosomes from the goose hybrid were compared with those of the geese A. anser and A. cygnoides, differences in the average content of heterochromatin were observed on only a few chromosomes.
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Affiliation(s)
- E Wójcik
- Department of Animal Genetics and Horse Breeding, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
| | - E Smalec
- Department of Animal Genetics and Horse Breeding, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
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Maslova A, Zlotina A, Kosyakova N, Sidorova M, Krasikova A. Three-dimensional architecture of tandem repeats in chicken interphase nucleus. Chromosome Res 2016; 23:625-39. [PMID: 26316311 DOI: 10.1007/s10577-015-9485-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tandem repeats belong to a class of genomic repetitive elements that form arrays of head-to-tail monomers. Due to technical difficulties in sequencing and assembly of large tandem repeat arrays, it remains largely unknown by which mechanisms tandem-repeat-containing regions aid in maintenance of ordered radial genome organization during interphase. Here we analyzed spatial distribution of several types of tandem repeats in interphase nuclei of chicken MDCC-MSB1 cells and somatic tissues relative to heterochromatin compartments and nuclear center. We showed that telomere and subtelomere repeats generally localize at the nuclear or chromocenters periphery. A tandem repeat known as CNM, typical for centromere regions of gene-dense microchromosomes, forms interchromosome clusters and occupies DAPI-positive chromocenters that appear predominantly within the nuclear interior. In contrast, centromere-specific tandem repeats of the majority of gene-poor macrochromosomes are embedded into the peripheral layer of heterochromatin. Chicken chromocenters rarely comprise centromere sequences of both macro- and microchromosomes, whose territories localize in different radial nuclear zones. Possible mechanisms of observed tandem repeats positioning and its implication in highly ordered arrangement of chromosome territories in chicken interphase nucleus are discussed.
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Affiliation(s)
- Antonina Maslova
- Saint Petersburg State University, Saint Petersburg, 198504, Russia
| | - Anna Zlotina
- Saint Petersburg State University, Saint Petersburg, 198504, Russia
| | - Nadezhda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marina Sidorova
- Saint Petersburg State University, Saint Petersburg, 198504, Russia
| | - Alla Krasikova
- Saint Petersburg State University, Saint Petersburg, 198504, Russia.
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27
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Furo IDO, Monte AA, dos Santos MDS, Tagliarini MM, O´Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Cytotaxonomy of Eurypyga helias (Gruiformes, Eurypygidae): First Karyotypic Description and Phylogenetic Proximity with Rynochetidae. PLoS One 2015; 10:e0143982. [PMID: 26624624 PMCID: PMC4666659 DOI: 10.1371/journal.pone.0143982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/11/2015] [Indexed: 11/19/2022] Open
Abstract
The sunbittern (Eurypyga helias) is a South American Gruiformes, the only member of Family Eurypigidae. In most phylogenetic proposals, it is placed in a more distant position than other families of the so-called "core Gruiformes". Different studies based on molecular, morphological and biogeographical data suggest that the Eurypigidae is closely related to the kagu (Rhynochetos jubatus), the only species in Rynochetidae, another family not included in the core Gruiformes. Here, the karyotype of the sunbittern is described for the first time, by classical and molecular cytogenetics, using whole chromosome probes derived from Gallus gallus and Leucopternis albicollis. We found a diploid number of 80, with only one pair of biarmed autosomal macrochromosomes, similar to that observed in the kagu. Chromosome painting revealed that most syntenies found in the avian putative ancestral karyotype (PAK) were conserved in the sunbittern. However, PAK1, PAK2, and PAK5 corresponded to two chromosome pairs each. Probes derived from L. albicollis confirm that fissions in PAK1 and PAK2 were centric, whereas in PAK5 the fission is interstitial. In addition, there is fusion of segments homologous to PAK2q and PAK5. From a phylogenetic point of view, comparisons of our results with two other Gruiformes belonging to family Rallidae suggest that the PAK5q fission might be a synapomorphy for Gruiformes. Fissions in PAK1 and PAK2 are found only in Eurypigidae, and might also occur in Rynochetidae, in view of the similar chromosomal morphology between the sunbittern and the kagu. This suggests a close phylogenetic relationship between Eurypigidae and Rynochetidae, whose common ancestor was separated by the Gondwana vicariancy in South America and New Caledonia, respectively.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Campus Universitário do Guamá, Belém-PA-Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Amanda Almeida Monte
- Universidade Federal do Pará, ICB, Faculdade de Biologia, Universidade Federal do Pará, Campus Universitário do Guamá, Belém-PA-Brazil
| | - Michelly da Silva dos Santos
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Campus Universitário do Guamá, Belém-PA-Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Marcella Mergulhão Tagliarini
- Programa de Pós Graduação em Neurociências e Biologia Celular, Universidade Federal do Pará, Campus Universitário do Guamá, Belém-PA-Brazil
| | - Patricia C. M. O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Instiuto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém-PA-Brazil
- * E-mail:
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28
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Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, Gladkikh OL, Lemskaya NA, Interesova EA, Korentovich MA, Vorobieva NV, Graphodatsky AS, Trifonov VA. Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 2015; 8:90. [PMID: 26587056 PMCID: PMC4652396 DOI: 10.1186/s13039-015-0194-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/07/2015] [Indexed: 11/21/2022] Open
Abstract
Background Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied. Results Cell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases. Conclusions The sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Larisa S Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | | | | | - Olga L Gladkikh
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | - Elena A Interesova
- Novosibirsk Branch of the Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Novosibirsk, Russia ; Tomsk State University, Tomsk, Russia
| | - Marina A Korentovich
- Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Tyumen, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
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Nie W, O'Brien PCM, Fu B, Wang J, Su W, He K, Bed'Hom B, Volobouev V, Ferguson-Smith MA, Dobigny G, Yang F. Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes. BMC Evol Biol 2015; 15:205. [PMID: 26409465 PMCID: PMC4583764 DOI: 10.1186/s12862-015-0484-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/14/2015] [Indexed: 12/03/2022] Open
Abstract
Background Previous cross-species painting studies with probes from chicken (Gallus gallus) chromosomes 1–10 and a paint pool of nineteen microchromosomes have revealed that the drastic karyotypic reorganization in Accipitridae is due to extensive synteny disruptions and associations. However, the number of synteny association events and identities of microchromosomes involved in such synteny associations remain undefined, due to the lack of paint probes derived from individual chicken microchromosomes. Moreover, no genome-wide homology map between Accipitridae species and other avian species with atypical karyotype organization has been reported till now, and the karyotype evolution within Accipitriformes remains unclear. Results To delineate the synteny-conserved segments in Accipitridae, a set of painting probes for the griffon vulture, Gyps fulvus (2n = 66) was generated from flow-sorted chromosomes. Together with previous generated probes from the stone curlew, Burhinus oedicnemus (2n = 42), a Charadriiformes species with atypical karyotype organization, we conducted multidirectional chromosome painting, including reciprocal chromosome painting between B. oedicnemus and G. fulvus and cross-species chromosome painting between B. oedicnemus and two accipitrid species (the Himalayan griffon, G. himalayensis 2n = 66, and the common buzzard, Buteo buteo, 2n = 68). In doing so, genome-wide homology maps between B. oedicnemus and three Accipitridae species were established. From there, a cladistic analysis using chromosomal characters and mapping of chromosomal changes on a consensus molecular phylogeny were conducted in order to search for cytogenetic signatures for different lineages within Accipitriformes. Conclusion Our study confirmed that the genomes of the diurnal birds of prey, especially the genomes of species in Accipitriformes excluding Cathartidae, have been extensively reshuffled when compared to other bird lineages. The chromosomal rearrangements involved include both fusions and fissions. Our chromosome painting data indicated that the Palearctic common buzzard (BBU) shared several common chromosomal rearrangements with some Old World vultures, and was found to be more closely related to other Accipitridae than to Neotropical buteonine raptors from the karyotypic perspective. Using both a chromosome-based cladistic analysis as well as by mapping of chromosomal differences onto a molecular-based phylogenetic tree, we revealed a number of potential cytogenetic signatures that support the clade of Pandionidae (PHA) + Accipitridae. In addition, our cladistic analysis using chromosomal characters appears to support the placement of osprey (PHA) in Accipitridae. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0484-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Jinghuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Weiting Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Bertrand Bed'Hom
- INRA, AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert-Bâtiment 320, 78352, Jouy-en-Josas Cedex, France.
| | - Vitaly Volobouev
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205 Origine, Structure et Evolution de la Biodiversité, 75005, Paris, France.
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France.
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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30
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dos Santos MDS, Kretschmer R, Silva FAO, Ledesma MA, O'Brien PCM, Ferguson-Smith MA, Del Valle Garnero A, de Oliveira EHC, Gunski RJ. Intrachromosomal rearrangements in two representatives of the genus Saltator (Thraupidae, Passeriformes) and the occurrence of heteromorphic Z chromosomes. Genetica 2015; 143:535-43. [PMID: 26092368 DOI: 10.1007/s10709-015-9851-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
Abstract
Saltator is a genus within family Thraupidae, the second largest family of Passeriformes, with more than 370 species found exclusively in the New World. Despite this, only a few species have had their karyotypes analyzed, most of them only with conventional staining. The diploid number is close to 80, and chromosome morphology is similar to the usual avian karyotype. Recent studies using cross-species chromosome painting have shown that, although the chromosomal morphology and number are similar to many species of birds, Passeriformes exhibit a complex pattern of paracentric and pericentric inversions in the chromosome homologous to GGA1q in two different suborders, Oscines and Suboscines. Hence, considering the importance and species richness of Thraupidae, this study aims to analyze two species of genus Saltator, the golden-billed saltator (S. aurantiirostris) and the green-winged saltator (S. similis) by means of classical cytogenetics and cross-species chromosome painting using Gallus gallus and Leucopternis albicollis probes, and also 5S and 18S rDNA and telomeric sequences. The results show that the karyotypes of these species are similar to other species of Passeriformes. Interestingly, the Z chromosome appears heteromorphic in S. similis, varying in morphology from acrocentric to metacentric. 5S and 18S probes hybridize to one pair of microchromosomes each, and telomeric sequences produce signals only in the terminal regions of chromosomes. FISH results are very similar to the Passeriformes already analyzed by means of molecular cytogenetics (Turdus species and Elaenia spectabilis). However, the paracentric and pericentric inversions observed in Saltator are different from those detected in these species, an observation that helps to explain the probable sequence of rearrangements. As these rearrangements are found in both suborders of Passeriformes (Oscines and Suboscines), we propose that the fission of GGA1 and inversions in GGA1q have occurred very early after the radiation of this order.
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Affiliation(s)
- Michelly da Silva dos Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, Pará, Brazil
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de Oliveira Furo I, Kretschmer R, O’Brien PC, Ferguson-Smith MA, de Oliveira EHC. Chromosomal Diversity and Karyotype Evolution in South American Macaws (Psittaciformes, Psittacidae). PLoS One 2015; 10:e0130157. [PMID: 26087053 PMCID: PMC4472783 DOI: 10.1371/journal.pone.0130157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/18/2015] [Indexed: 11/18/2022] Open
Abstract
Most species of macaws, which represent the largest species of Neotropical Psittacidae, characterized by their long tails and exuberant colours, are endangered, mainly because of hunting, illegal trade and habitat destruction. Long tailed species seem to represent a monophyletic group within Psittacidae, supported by cytogenetic data. Hence, these species show karyotypes with predominance of biarmed macrochromosomes, in contrast to short tailed species, with a predominance of acro/telocentric macrochromosomes. Because of their similar karyotypes, it has been proposed that inversions and translocations may be the main types of rearrangements occurring during the evolution of this group. However, only one species of macaw, Ara macao, that has had its genome sequenced was analyzed by means of molecular cytogenetics. Hence, in order to verify the rearrangements, we analyzed the karyotype of two species of macaws, Ara chloropterus and Anodorhynchus hyacinthinus, using cross-species chromosome painting with two different sets of probes from chicken and white hawk. Both intra- and interchromosomal rearrangements were observed. Chicken probes revealed the occurrence of fusions, fissions and inversions in both species, while the probes from white hawk determined the correct breakpoints or chromosome segments involved in the rearrangements. Some of these rearrangements were common for both species of macaws (fission of GGA1 and fusions of GGA1p/GGA4q, GGA6/GGA7 and GGA8/GGA9), while the fissions of GGA 2 and 4p were found only in A. chloropterus. These results confirm that despite apparent chromosomal similarity, macaws have very diverse karyotypes, which differ from each other not only by inversions and translocations as postulated before, but also by fissions and fusions.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Programa de Pós Graduação em Genética e Biologia Molecular, Instituto de Ciências Biológicas Universidade Federal do Pará, Belém, PA, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Rafael Kretschmer
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Patrícia C. O’Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA-Brazil
- * E-mail:
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Kretschmer R, de Oliveira EHC, Dos Santos MS, Furo IDO, O'Brien PCM, Ferguson-Smith MA, Garnero ADV, Gunski RJ. Chromosome mapping of the large elaenia (Elaenia spectabilis): evidence for a cytogenetic signature for passeriform birds? Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12504] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rafael Kretschmer
- Programa de Pós graduação em Ciências Biológicas; PPGCB; Universidade Federal do Pampa; São Gabriel 97300-000 Rio Grande do Sul RS Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua PA Brazil
- Instituto de Ciências Exatas e Naturais; Universidade Federal do Pará; Campus Universitário do Guamá 66075-110 Belém PA Brazil
| | - Michelly S. Dos Santos
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua PA Brazil
- Programa de Pós-Graduação de Genética e Biologia Molecular; PPGBM; Universidade Federal do Pará; Campus Universitário do Guamá 66075-110 Belém PA Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua PA Brazil
- Programa de Pós-Graduação de Genética e Biologia Molecular; PPGBM; Universidade Federal do Pará; Campus Universitário do Guamá 66075-110 Belém PA Brazil
| | - Patricia C. M. O'Brien
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Analía del Valle Garnero
- Programa de Pós graduação em Ciências Biológicas; PPGCB; Universidade Federal do Pampa; São Gabriel 97300-000 Rio Grande do Sul RS Brazil
| | - Ricardo José Gunski
- Programa de Pós graduação em Ciências Biológicas; PPGCB; Universidade Federal do Pampa; São Gabriel 97300-000 Rio Grande do Sul RS Brazil
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Del Priore L, Pigozzi MI. Sex-specific recombination maps for individual macrochromosomes in the Japanese quail (Coturnix japonica). Chromosome Res 2015; 23:199-210. [PMID: 25596820 DOI: 10.1007/s10577-014-9448-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Abstract
Meiotic recombination in the Japanese quail was directly studied by immunolocalization of mutL homolog 1 (MLH1), a mismatch repair protein of mature recombination nodules. In total, 15,862 crossovers were scored along the autosomal synaptonemal complexes in 308 meiotic nuclei from males and females. Crossover frequencies calculated from MLH1 foci show wide similitude between males and females with slightly higher number of foci in females. From this analysis, we predict that the sex-averaged map length of the Japanese quail is 2580 cM, with a genome-wide recombination rate of 1.9 cM/Mb. MLH1 focus mapping along the six largest bivalents showed few intersex differences in the distribution of crossovers along with variant patterns in metacentric and acrocentric macrobivalents. These results provide valuable information to complement linkage map analysis in the species while providing insight into our understanding of the mechanisms of crossover distribution along chromosome arms.
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Affiliation(s)
- Lucía Del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10, C1121ABG, Buenos Aires, Argentina
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Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014; 15:1060. [PMID: 25496766 PMCID: PMC4362836 DOI: 10.1186/1471-2164-15-1060] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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Affiliation(s)
| | - Marta Farré
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Pamela E Lithgow
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Katie E Fowler
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
- />School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU UK
| | - Benjamin M Skinner
- />Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Rebecca O’Connor
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Gothami Fonseka
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Niclas Backström
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Yoichi Matsuda
- />Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 Japan
| | - Peter Houde
- />Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA
| | - Erich D Jarvis
- />Department of Neurobiology, Duke University Medical Center, Box 3209, Durham, NC 27710 USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9PS UK
| | - Denis M Larkin
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Darren K Griffin
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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Braasch I, Schartl M. Evolution of endothelin receptors in vertebrates. Gen Comp Endocrinol 2014; 209:21-34. [PMID: 25010382 DOI: 10.1016/j.ygcen.2014.06.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/07/2014] [Accepted: 06/26/2014] [Indexed: 02/03/2023]
Abstract
Endothelin receptors are G protein coupled receptors (GPCRs) of the β-group of rhodopsin receptors that bind to endothelin ligands, which are 21 amino acid long peptides derived from longer prepro-endothelin precursors. The most basal Ednr-like GPCR is found outside vertebrates in the cephalochordate amphioxus, but endothelin ligands are only present among vertebrates, including the lineages of jawless vertebrates (lampreys and hagfishes), cartilaginous vertebrates (sharks, rays, and chimaeras), and bony vertebrates (ray-finned fishes and lobe-finned vertebrates including tetrapods). A bona fide endothelin system is thus a vertebrate-specific innovation with important roles for regulating the cardiovascular system, renal and pulmonary processes, as well as for the development of the vertebrate-specific neural crest cell population and its derivatives. Expectedly, dysregulation of endothelin receptors and the endothelin system leads to a multitude of human diseases. Despite the importance of different types of endothelin receptors for vertebrate development and physiology, current knowledge on endothelin ligand-receptor interactions, on the expression of endothelin receptors and their ligands, and on the functional roles of the endothelin system for embryonic development and in adult vertebrates is very much biased towards amniote vertebrates. Recent analyses from a variety of vertebrate lineages, however, have shown that the endothelin system in lineages such as teleost fish and lampreys is more diverse and is divergent from the mammalian endothelin system. This diversity is mainly based on differential evolution of numerous endothelin system components among vertebrate lineages generated by two rounds of whole genome duplication (three in teleosts) during vertebrate evolution. Here we review current understanding of the evolutionary history of the endothelin receptor family in vertebrates supplemented with surveys on the endothelin receptor gene complement of newly available genome assemblies from phylogenetically informative taxa. Our assessment further highlights the diversity of the vertebrate endothelin system and calls for detailed functional and pharmacological analyses of the endothelin system beyond tetrapods.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97080 Würzburg, Germany.
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Kretschmer R, Gunski RJ, Garnero ADV, Furo IDO, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Molecular cytogenetic characterization of multiple intrachromosomal rearrangements in two representatives of the genus Turdus (Turdidae, Passeriformes). PLoS One 2014; 9:e103338. [PMID: 25058578 PMCID: PMC4110018 DOI: 10.1371/journal.pone.0103338] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/27/2014] [Indexed: 01/16/2023] Open
Abstract
Turdus rufiventris and Turdus albicollis, two songbirds belonging to the family Turdidae (Aves, Passeriformes) were studied by C-banding, 18S rDNA, as well as the use of whole chromosome probes derived from Gallus gallus (GGA) and Leucopternis albicollis (LAL). They showed very similar karyotypes, with 2n = 78 and the same pattern of distribution of heterochromatic blocks and hybridization patterns. However, the analysis of 18/28S rDNA has shown differences in the number of NOR-bearing chromosomes and ribosomal clusters. The hybridization pattern of GGA macrochromosomes was similar to the one found in songbirds studied by Fluorescent in situ hybridization, with fission of GGA 1 and GGA 4 chromosomes. In contrast, LAL chromosome paintings revealed a complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) on chromosome 2, which corresponds to GGA1q. The first inversion changed the chromosomal morphology and the second and third inversions changed the order of chromosome segments. Karyotype analysis in Turdus revealed that this genus has derived characteristics in relation to the putative avian ancestral karyotype, highlighting the importance of using new tools for analysis of chromosomal evolution in birds, such as the probes derived from L. albicollis, which make it possible to identify intrachromosomal rearrangements not visible with the use of GGA chromosome painting solely.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil; Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil; Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil; Instiuto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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Schmid M, Steinlein C, Feichtinger W, Bogart JP. Chromosome banding in Amphibia. XXXI. The neotropical anuran families Centrolenidae and Allophrynidae. Cytogenet Genome Res 2014; 142:268-85. [PMID: 24776617 DOI: 10.1159/000362216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
The mitotic chromosomes of 11 species from the anuran families Centrolenidae and Allophrynidae were analyzed by means of conventional staining, banding techniques, and in situ hybridization. The amount, location, and fluorochrome affinities of constitutive heterochromatin, the number and positions of nucleolus organizer regions, and the patterns of telomeric DNA sequences were determined for most of the species. The karyotypes were found to be highly conserved with a low diploid chromosome number of 2n = 20 and morphologically similar chromosomes. The sister group relationship between the Centrolenidae and Allophrynidae (unranked taxon Allocentroleniae) is clearly corroborated by the cytogenetic data. The existence of heteromorphic XY♂/XX♀ sex chromosomes in an initial stage of morphological differentiation was confirmed in Vitreorana antisthenesi. The genome sizes of 4 centrolenid species were determined using flow cytometry. For completeness and for comparative purposes, all previously published cytogenetic data on centrolenids are included.
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Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol 2014; 15:549. [PMID: 25496599 PMCID: PMC4290106 DOI: 10.1186/s13059-014-0549-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/19/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.
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Affiliation(s)
- Claudia C Weber
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Bastien Boussau
- />Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558 Villeurbanne, France
| | | | - Erich D Jarvis
- />Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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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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40
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Rodrigues BS, de Assis MDFL, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Chromosomal studies onCoscoroba coscoroba(Aves: Anseriformes) reinforce theCoscoroba-Cereopsisclade. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benilson S. Rodrigues
- Programa de Pós Graduação em Genética e Biologia Molecular; ICB; Universidade Federal do Pará, Campus Universitário do Guamá; 66075-110 Belém-PA, Brazil
| | - Maria De Fatima L. de Assis
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua-PA, Brazil
| | - Patricia C. M. O'Brien
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua-PA, Brazil
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
- Faculdade de Ciências Naturais; ICEN; Universidade Federal do Pará, Campus Universitário do Guamá; 66075-110 Belém-PA, Brazil
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Nishida C, Ishijima J, Ishishita S, Yamada K, Griffin DK, Yamazaki T, Matsuda Y. Karyotype reorganization with conserved genomic compartmentalization in dot-shaped microchromosomes in the Japanese mountain hawk-eagle (Nisaetus nipalensis orientalis, Accipitridae). Cytogenet Genome Res 2013; 141:284-94. [PMID: 23838459 DOI: 10.1159/000352067] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
The karyotype of the Japanese mountain hawk-eagle (Nisaetus nipalensis orientalis) (2n = 66) consists of a large number of medium-sized and small chromosomes but only 4 pairs of dot-shaped microchromosomes, in contrast to the typical avian karyotype with a small number of macrochromosomes and many indistinguishable microchromosomes. To investigate the drastic karyotype reorganization in this species, we performed a molecular cytogenetic characterization employing chromosome in situ hybridization and molecular cloning of centromeric heterochromatin. Cross-species chromosome painting with chicken chromosome-specific probes 1-9 and Z and a paint pool of 20 microchromosome pairs revealed that the N. n. orientalis karyotype differs from chicken by at least 13 fissions of macrochromosomes and 15 fusions between microchromosomes and between micro- and macrochromosomes. A novel family of satellite DNA sequences (NNO-ApaI) was isolated, consisting of a GC-rich 173-bp repeated sequence element. The NNO-ApaI sequence was localized to the C-positive centromeric heterochromatin of 4 pairs of microchromosomes, which evolved concertedly by homogenization between the microchromosomes. These results suggest that the 4 pairs of dot-shaped microchromosomes have retained their genomic compartmentalization from other middle-sized and small chromosomes.
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Affiliation(s)
- C Nishida
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions. Chromosome Res 2012; 20:1017-32. [DOI: 10.1007/s10577-012-9319-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wójcik E, Andraszek K, Gryzinska M, Witkowski A, Palyszka M, Smalec E. Sister chromatid exchange in Greenleg Partridge and Polbar hens covered by the gene-pool protection program for farm animals in Poland. Poult Sci 2012; 91:2424-30. [PMID: 22991523 DOI: 10.3382/ps.2012-02327] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A basic assay that detects genotoxic DNA damage disrupting DNA replication and repair mechanisms is the sister chromatid exchange test. The frequency of sister chromatid exchanges was analyzed in chromosomes of the following hen breeds: Greenleg Partridge and Polbar. Chromosome preparations were obtained from our in vitro culture of peripheral blood lymphocytes stained using the fluorescence plus Giemsa (FPG) technique. The sister chromatid exchange (SCE)/cell mean of the hens under analysis was 7.83 ± 1.76 (7.22 ± 1.70 in the Greenleg Partridge and 8.43 ± 1.61 in the Polbar population). Statistically significant differences were identified between the hen breeds. A higher mean number of SCE/cell was observed in the group of hens producing fewer eggs (8.55 ± 1.51) compared with the group with a better egg yield (7.10 ± 1.65). The differences were statistically significant. Additionally, SCE frequency in the first, second, and third chromosome was analyzed in detail. The highest number of SCE was observed in the first and the lowest in the third chromosome. The SCE distribution in the particular regions of the analyzed chromosomes was also studied. The most numerous exchanges were observed in the proximal region, followed by the interstitial and distal areas.
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Affiliation(s)
- E Wójcik
- Department of Animal Genetics and Horse Breeding, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland.
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Rao M, Morisson M, Faraut T, Bardes S, Fève K, Labarthe E, Fillon V, Huang Y, Li N, Vignal A. A duck RH panel and its potential for assisting NGS genome assembly. BMC Genomics 2012; 13:513. [PMID: 23020625 PMCID: PMC3496577 DOI: 10.1186/1471-2164-13-513] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 08/29/2012] [Indexed: 11/13/2022] Open
Abstract
Background Owing to the low cost of the high throughput Next Generation Sequencing (NGS) technology, more and more species have been and will be sequenced. However, de novo assemblies of large eukaryotic genomes thus produced are composed of a large number of contigs and scaffolds of medium to small size, having no chromosomal assignment. Radiation hybrid (RH) mapping is a powerful tool for building whole genome maps and has been used for several animal species, to help assign sequence scaffolds to chromosomes and determining their order. Results We report here a duck whole genome RH panel obtained by fusing female duck embryonic fibroblasts irradiated at a dose of 6,000 rads, with HPRT-deficient Wg3hCl2 hamster cells. The ninety best hybrids, having an average retention of 23.6% of the duck genome, were selected for the final panel. To allow the genotyping of large numbers of markers, as required for whole genome mapping, without having to cultivate the hybrid clones on a large scale, three different methods involving Whole Genome Amplification (WGA) and/or scaling down PCR volumes by using the Fluidigm BioMarkTM Integrated Fluidic Circuits (IFC) Dynamic ArrayTM for genotyping were tested. RH maps of APL12 and APL22 were built, allowing the detection of intrachromosomal rearrangements when compared to chicken. Finally, the panel proved useful for checking the assembly of sequence scaffolds and for mapping EST located on one of the smallest microchromosomes. Conclusion The Fluidigm BioMarkTM Integrated Fluidic Circuits (IFC) Dynamic ArrayTM genotyping by quantitative PCR provides a rapid and cost-effective method for building RH linkage groups. Although the vast majority of genotyped markers exhibited a picture coherent with their associated scaffolds, a few of them were discordant, pinpointing potential assembly errors. Comparative mapping with chicken chromosomes GGA21 and GGA11 allowed the detection of the first chromosome rearrangements on microchromosomes between duck and chicken. As in chicken, the smallest duck microchromosomes appear missing in the assembly and more EST data will be needed for mapping them. Altogether, this underlines the added value of RH mapping to improve genome assemblies.
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Affiliation(s)
- Man Rao
- UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan 31326, France
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Mácha J, Teichmanová R, Sater AK, Wells DE, Tlapáková T, Zimmerman LB, Krylov V. Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis. BMC Genomics 2012; 13:315. [PMID: 22800176 PMCID: PMC3472169 DOI: 10.1186/1471-2164-13-315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/25/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The X and Y sex chromosomes are conspicuous features of placental mammal genomes. Mammalian sex chromosomes arose from an ordinary pair of autosomes after the proto-Y acquired a male-determining gene and degenerated due to suppression of X-Y recombination. Analysis of earlier steps in X chromosome evolution has been hampered by the long interval between the origins of teleost and amniote lineages as well as scarcity of X chromosome orthologs in incomplete avian genome assemblies. RESULTS This study clarifies the genesis and remodelling of the Eutherian X chromosome by using a combination of sequence analysis, meiotic map information, and cytogenetic localization to compare amniote genome organization with that of the amphibian Xenopus tropicalis. Nearly all orthologs of human X genes localize to X. tropicalis chromosomes 2 and 8, consistent with an ancestral X-conserved region and a single X-added region precursor. This finding contradicts a previous hypothesis of three evolutionary strata in this region. Homologies between human, opossum, chicken and frog chromosomes suggest a single X-added region predecessor in therian mammals, corresponding to opossum chromosomes 4 and 7. A more ancient X-added ancestral region, currently extant as a major part of chicken chromosome 1, is likely to have been present in the progenitor of synapsids and sauropsids. Analysis of X chromosome gene content emphasizes conservation of single protein coding genes and the role of tandem arrays in formation of novel genes. CONCLUSIONS Chromosomal regions orthologous to Therian X chromosomes have been located in the genome of the frog X. tropicalis. These X chromosome ancestral components experienced a series of fusion and breakage events to give rise to avian autosomes and mammalian sex chromosomes. The early branching tetrapod X. tropicalis' simple diploid genome and robust synteny to amniotes greatly enhances studies of vertebrate chromosome evolution.
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Affiliation(s)
- Jaroslav Mácha
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Radka Teichmanová
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Amy K Sater
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Dan E Wells
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Tereza Tlapáková
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Lyle B Zimmerman
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
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Skinner BM, Griffin DK. Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints. Heredity (Edinb) 2011; 108:37-41. [PMID: 22045382 DOI: 10.1038/hdy.2011.99] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intrachromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intrachromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250 kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one-third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.
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Affiliation(s)
- B M Skinner
- School of Biosciences, University of Kent, Canterbury, UK
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Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Basa S, Walker JA, Smith JJ. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 2011; 21:1306-12. [PMID: 21482624 DOI: 10.1101/gr.116491.110] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12-17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution.
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Affiliation(s)
- Stephen R Voss
- Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA.
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Avian Z-specific microsatellites map to pseudoautosomal or autosomal chromosomes in the Siberian jay (Perisoreus infaustus): insights into avian genome evolution from cross-species amplification tests. J Genet 2011; 89:223-8. [PMID: 20861574 DOI: 10.1007/s12041-010-0029-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Aslam ML, Bastiaansen JWM, Crooijmans RPMA, Vereijken A, Megens HJ, Groenen MAM. A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the turkey and chicken genomes. BMC Genomics 2010; 11:647. [PMID: 21092123 PMCID: PMC3091770 DOI: 10.1186/1471-2164-11-647] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 11/20/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions. RESULTS Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species. CONCLUSION Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - John WM Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Richard PMA Crooijmans
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Addie Vereijken
- Hendrix Genetics, Research & Technology Centre, 5830 AC, Boxmeer, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
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Daks AA, Deryusheva SE, Krasikova AV, Zlotina AM, Gaginskaya ER, Galkina SA. Lampbrush chromosomes of the Japanese quail (Coturnix coturnix japonica): A new version of cytogenetic maps. RUSS J GENET+ 2010. [DOI: 10.1134/s102279541010008x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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