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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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de Sousa RPC, Campos PSB, dos Santos MDS, O’Brien PC, Ferguson-Smith MA, de Oliveira EHC. Cytotaxonomy and Molecular Analyses of Mycteria americana (Ciconiidae: Ciconiiformes): Insights on Stork Phylogeny. Genes (Basel) 2023; 14:genes14040816. [PMID: 37107574 PMCID: PMC10138051 DOI: 10.3390/genes14040816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Although molecular information for the wood stork (Mycteria americana) has been well described, data concerning their karyotypical organization and phylogenetic relationships with other storks are still scarce. Thus, we aimed to analyze the chromosomal organization and diversification of M. americana, and provide evolutionary insights based on phylogenetic data of Ciconiidae. For this, we applied both classical and molecular cytogenetic techniques to define the pattern of distribution of heterochromatic blocks and their chromosomal homology with Gallus gallus (GGA). Maximum likelihood analyses and Bayesian inferences (680 bp COI and 1007 bp Cytb genes) were used to determine their phylogenetic relationship with other storks. The results confirmed 2n = 72, and the heterochromatin distribution pattern was restricted to centromeric regions of the chromosomes. FISH experiments identified fusion and fission events involving chromosomes homologous to GGA macrochromosome pairs, some of which were previously found in other species of Ciconiidae, possibly corresponding to synapomorphies for the group. Phylogenetic analyses resulted in a tree that recovered only Ciconinii as a monophyletic group, while Mycteriini and Leptoptlini tribes were configured as paraphyletic clades. In addition, the association between phylogenetic and cytogenetic data corroborates the hypothesis of a reduction in the diploid number throughout the evolution of Ciconiidae.
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Affiliation(s)
| | - Paula Sabrina Bronze Campos
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Michelly da Silva dos Santos
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, Brazil
| | | | | | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Instituto Evandro Chagas, Seção de Meio Ambiente, Ananindeua 67030-000, Brazil
- Correspondence: ; Tel.: +55-91-998314113
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Carvalho CA, Furo IO, O’Brien PCM, Pereira J, O’Connor RE, Griffin D, Ferguson-Smith M, de Oliveira EHC. Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes. PLoS One 2021; 16:e0259905. [PMID: 34793511 PMCID: PMC8601422 DOI: 10.1371/journal.pone.0259905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022] Open
Abstract
Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype, based on homology with GGA. Fissions occurred mainly in syntenic groups homologous to GGA1-GGA5. On the other hand, the majority of the microchromosomes were found fused to other chromosomal elements in STY, indicating these rearrangements played an important role in the reduction of the 2n to 68. Comparison with hybridization pattern of the Japanese-Mountain-Eagle (Nisaetus nipalensis orientalis), the only Aquilinae analyzed by comparative chromosome painting previously, did not reveal any synapomorphy that could represent a chromosome signature to this subfamily. Therefore, conclusions about karyotype evolution in Aquilinae require additional painting studies.
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Affiliation(s)
- Carlos A. Carvalho
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Ivanete O. Furo
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Universidade Federal Rural da Amazônia (UFRA) Laboratório de Reprodução Animal (LABRAC), Parauapebas, Pará, Brazil
| | | | - Jorge Pereira
- Animal and Veterinary Research Center, Universidade de Trá-os-Montes e Alto douro, Vila Real, Portugal
| | | | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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Kretschmer R, Franz I, de Souza MS, Garnero ADV, Gunski RJ, de Oliveira EHC, O’Connor RE, Griffin DK, de Freitas TRO. Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes). Cells 2021; 10:2650. [PMID: 34685630 PMCID: PMC8534115 DOI: 10.3390/cells10102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Ismael Franz
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (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, PA, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
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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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Furo IDO, Kretschmer R, O'Brien PCM, Pereira JCDC, Gunski RJ, Garnero ADV, O'Connor RE, Griffin DK, Ferguson-Smith MA, Oliveira EHCD. Cytotaxonomy of Gallinula melanops (Gruiformes, Rallidae): Karyotype evolution and phylogenetic inference. Genet Mol Biol 2021; 44:e20200241. [PMID: 33821875 PMCID: PMC8022357 DOI: 10.1590/1678-4685-gmb-2020-0241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Universidade Federal Rural da Amazônia (UFRA) Laboratório de Reprodução Animal (LABRAC), Parauapebas, PA, Brazil
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, RS, Brazil
- University of Kent, School of Biosciences, Canterbury, United Kingdom
| | - Patricia C M O'Brien
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Jorge Claudio da Costa Pereira
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
- University of Trás-os-Montes and Alto Douro (UTAD), Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - 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
| | | | | | - Malcolm A Ferguson-Smith
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto Evandro Chagas, Laboratório de Cultura de Tecidos e Citogenética (SAMAM), Ananindeua, PA, Brazil
- Universidade Federal do Pará, Instituto de Ciências Exatas e Naturais, Belém, PA, Brazil
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Degrandi TM, Furo IDO, Oliveira EHCD, Costa AL, Ferguson-Smith MA, O'Brien PCM, Pereira JC, Garnero ADV, Gunski RJ, Artoni RF. Comparative chromosome painting in hummingbirds (Trochilidae). Genet Mol Biol 2020; 43:e20200162. [PMID: 33410454 PMCID: PMC7821849 DOI: 10.1590/1678-4685-gmb-2020-0162] [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: 06/15/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022] Open
Abstract
Hummingbirds (Trochilidae) are one of the most enigmatic avian groups, and also
among the most diverse, with approximately 360 recognized species in 106 genera,
of which 43 are monotypic. This fact has generated considerable interest in the
evolutionary biology of the hummingbirds, which is reflected in a number of
DNA-based studies. However, only a few of them explored chromosomal data. Given
this, the present study provides an analysis of the karyotypes of three species
of Neotropical hummingbirds, Anthracothorax nigricollis (ANI),
Campylopterus largipennis (CLA), and Hylocharis
chrysura (HCH), in order to analyze the chromosomal processes
associated with the evolution of the Trochilidae. The diploid number of ANI is
2n=80 chromosomes, while CLA and HCH have identical karyotypes, with 2n=78.
Chromosome painting with Gallus gallus probes (GGA1-12) shows
that the hummingbirds have a karyotype close to the proposed ancestral bird
karyotype. Despite this, an informative rearrangement was detected: an in-tandem
fusion between GGA7 and GGA9 found in CLA and HCH, but absent in ANI. A
comparative analysis with the tree of life of the hummingbirds indicated that
this fusion must have arisen following the divergence of a number of hummingbird
species.
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Affiliation(s)
- Tiago Marafiga Degrandi
- Universidade Estadual de Ponta Grossa (UEPG), Programa de Pós-Graduação em Biologia Evolutiva, Ponta Grossa, PR, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, PA, Brazil.,University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, Cambridge, UK
| | - Edivaldo Herculano Correia de Oliveira
- Universidade Federal do Pará (UFPA), Programa de Pós-Graduação em Genética e Biologia Molecular, Belém, PA, Brazil.,Instituto Evandro Chagas (IEC), Ananindeua, PA, Brazil
| | - Alice Lemos Costa
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
| | - Malcolm A Ferguson-Smith
- University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, Cambridge, UK
| | - Patrícia C M O'Brien
- University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, Cambridge, UK
| | - Jorge C Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Analía Del Valle Garnero
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa (UNIPAMPA), Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, RS, Brazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa (UEPG), Programa de Pós-Graduação em Biologia Evolutiva, Ponta Grossa, PR, Brazil
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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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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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10
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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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11
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dos Santos MDS, Kretschmer R, Furo IDO, Gunski RJ, del Valle Garnero A, Valeri MP, O’Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Chromosomal evolution and phylogenetic considerations in cuckoos (Aves, Cuculiformes, Cuculidae). PLoS One 2020; 15:e0232509. [PMID: 32469879 PMCID: PMC7259548 DOI: 10.1371/journal.pone.0232509] [Citation(s) in RCA: 3] [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: 03/11/2020] [Accepted: 04/16/2020] [Indexed: 11/21/2022] Open
Abstract
The Cuckoos have a long history of difficult classification. The species of this order have been the subject of several studies based on osteology, behavior, ecology, morphology and molecular data. Despite this, the relationship between Cuculiformes and species of other orders remains controversial. In this work, two species of Cuculidae, Guira guira (Gmelin, 1788) and Piaya cayana (Linnaeus, 1766), were analyzed by means of comparative chromosome painting in order to study the chromosome evolution of this group and to undertake the first chromosome mapping of these species. Our results demonstrate high chromosomal diversity, with 2n = 76 in G. guira, with fission and fusion events involving ancestral syntenies, while P. cayana presented only fissions, which were responsible for the high diploid number of 2n = 90. Interestingly, there were no chromosomal rearrangements in common between these species. Our results, based on Giemsa staining, were compared with previous data for other cuckoos and also with taxa proposed as sister-groups of Cuculiformes (Otidiformes, Musophagiformes and Opisthocomiformes). Cytogenetic comparisons demonstrated that cuckoo species can be divided into at least three major groups. In addition, we found no evidence to place Cuculiformes close to the groups proposed previously as sister-groups.
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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
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - 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, Rio Grande do Sul, Brazil
| | - Ivanete de Oliveira Furo
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Rio Grande do Sul, Brazil
| | - Analía del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Rio Grande do Sul, Brazil
| | - Mirela Pelizaro Valeri
- Departamento de Genética, Ecologia e Evolução, Laboratório de Citogenômica Evolutiva, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patricia C. M. O’Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Edivaldo Herculano Corrêa de Oliveira
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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12
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Degrandi TM, Barcellos SA, Costa AL, Garnero ADV, Hass I, Gunski RJ. Introducing the Bird Chromosome Database: An Overview of Cytogenetic Studies in Birds. Cytogenet Genome Res 2020; 160:199-205. [PMID: 32369809 DOI: 10.1159/000507768] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022] Open
Abstract
Bird chromosomes, which have been investigated scientifically for more than a century, present a number of unique features. In general, bird karyotypes have a high diploid number (2n) of typically around 80 chromosomes that are divided into macro- and microchromosomes. In recent decades, FISH studies using whole chromosome painting probes have shown that the macrochromosomes evolved through both inter- and intrachromosomal rearrangements. However, chromosome painting data are available for only a few bird species, which hinders a more systematic approach to the understanding of the evolutionary history of the enigmatic bird karyotype. Thus, we decided to create an innovative database through compilation of the cytogenetic data available for birds, including chromosome numbers and the results of chromosome painting with chicken (Gallus gallus) probes. The data were obtained through an extensive literature review, which focused on cytogenetic studies published up to 2019. In the first version of the "Bird Chromosome Database (BCD)" (https://sites.unipampa.edu.br/birdchromosomedatabase) we have compiled data on the chromosome numbers of 1,067 bird species and chromosome painting data on 96 species. We found considerable variation in the diploid numbers, which ranged from 40 to 142, although most (around 50%) of the species studied up to now have between 78 and 82 chromosomes. Despite its importance for cytogenetic research, chromosome painting has been applied to less than 1% of all bird species. The BCD will enable researchers to identify the main knowledge gaps in bird cytogenetics, including the most under-sampled groups, and make inferences on chromosomal homologies in phylogenetic studies.
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13
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Degrandi TM, Gunski RJ, Garnero ADV, Oliveira EHCD, Kretschmer R, Souza MSD, Barcellos SA, Hass I. The distribution of 45S rDNA sites in bird chromosomes suggests multiple evolutionary histories. Genet Mol Biol 2020; 43:e20180331. [PMID: 32251493 PMCID: PMC7197993 DOI: 10.1590/1678-4685-gmb-2018-0331] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/08/2019] [Indexed: 03/08/2023] Open
Abstract
The distribution of 45S rDNA cluster in avian karyotypes varies in different
aspects, such as position, number of bearer chromosomes, and bearers being
macro- or microchromosomes. The present study investigated the patterns of
variation in the 45S rDNA-bearer chromosomes of birds in order to understand the
evolutionary dynamics of the cluster configuration and its contribution to the
evolution of bird karyotypes. A total of 73 bird species were analyzed,
including both published data and species for which rDNA-FISH was conducted for
the first time. In most birds, the 45S rDNA clusters were located in a single
pair of microchromosomes. Hence, the location of 45S rDNA in macrochromosomes,
observed only in Neognathae species, seems to be a derived state, probably the
result of chromosomal fusion between microchromosomes and distinct
macrochromosomes. Additionally, the 45S rDNA was observed in multiple
microchromosomes in different branches of the bird phylogeny, suggesting
recurrence of dispersion processeses, such as duplications and translocations.
Overall, this study indicated that the redistribution of the 45S rDNA sites in
bird chromosomes followed different evolutionary trajectories with respect to
each lineage of the class Aves.
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Affiliation(s)
| | | | | | | | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Biociências, Porto Alegre, RS, Brazil
| | | | | | - Iris Hass
- Universidade Federal do Paraná (UFPR), Departamento de Genética, Curitiba, PR, Brazil
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14
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Furo IDO, Kretschmer R, O’Brien PCM, Pereira JC, Ferguson-Smith MA, de Oliveira EHC. Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: Aramides cajaneus and Psophia viridis. Genes (Basel) 2020; 11:E307. [PMID: 32183220 PMCID: PMC7140812 DOI: 10.3390/genes11030307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022] Open
Abstract
Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Post-Graduation Program in Genetics and Molecular Biology, Federal University of Pará, Belém, Pará 66075-110, Brazil;
- Laboratory of Tissue Culture and Cytogenetics, SAMAM, Evandro Chagas Institute, Ananindeua, Pará 67030-000, Brazil
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Rafael Kretschmer
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
- Pos-Graduation Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 91509-900, Brazil
| | - Patrícia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Jorge C. Pereira
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratory of Tissue Culture and Cytogenetics, SAMAM, Evandro Chagas Institute, Ananindeua, Pará 67030-000, Brazil
- Faculty of Natural Sciences, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará 66075-110, Brazil
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15
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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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16
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Kretschmer R, Souza MSD, Barcellos SA, Degrandi TM, Pereira JC, O'Brien PCM, Ferguson-Smith MA, Gunski RJ, Garnero ADV, Oliveira EHCD, Freitas TROD. Novel insights into chromosome evolution of Charadriiformes: extensive genomic reshuffling in the wattled jacana (Jacana jacana, Charadriiformes, Jacanidae). Genet Mol Biol 2020; 43:e20190236. [PMID: 32105288 PMCID: PMC7198006 DOI: 10.1590/1678-4685-gmb-2019-0236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/22/2019] [Indexed: 01/01/2023] Open
Abstract
The order Charadriiformes comprises three major clades: Lari and Scolopaci as sister group to Charadrii. Until now, only three Charadriiformes species have been studied by chromosome painting: Larus argentatus (Lari), Burhinus oedicnemus and Vanellus chilensis (Charadrii). Hence, there is a lack of information concerning the third clade, Scolapaci. Based on this, and to gain a better understanding of karyotype evolution in the order Charadriiformes, we applied conventional and molecular cytogenetic approaches in a species belonging to clade Scolopaci - the wattled jacana (Jacana jacana) - using Gallus gallus and Zenaida auriculata chromosome-specific probes. Cross-species evaluation of J. jacana chromosomes shows extensive genomic reshuffling within macrochromosomes during evolution, with multiple fission and fusion events, although the diploid number remains at high level (2n=82). Interestingly, this species does not have the GGA7-8 fusion, which was found in two representatives of Charadrii clade, reinforcing the idea that this fusion may be exclusive to the Charadrii clade. In addition, it is shown that the chromosome evolution in Charadriiformes is complex and resulted in species with typical and atypical karyotypes. The karyotypic features of Scolopaci are very different from those of Charadrii and Lari, indicating that after divergence, each suborder has undergone different chromosome rearrangements.
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Affiliation(s)
- Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Genética e Biologia Molecular - PPGBM, Porto Alegre, Rio Grande do Sul, RS, Brazil.,University of Cambridge, Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Marcelo Santos de Souza
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Suziane Alves Barcellos
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Tiago Marafiga Degrandi
- Universidade Federal do Paraná, Laboratório de Citogenética e Genética da Conservação Animal, Programa de Pós-graduação em Genética, Curitiba, PR, Brazil
| | - Jorge C Pereira
- University of Cambridge, Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Patricia C M O'Brien
- University of Cambridge, Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Malcolm A Ferguson-Smith
- University of Cambridge, Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Ricardo José Gunski
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Analía Del Valle Garnero
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas - PPGCB, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - 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 - SAMAM, Ananindeua, PA, Brazil
| | - Thales Renato Ochotorena de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Genética e Biologia Molecular - PPGBM, Porto Alegre, Rio Grande do Sul, RS, Brazil
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17
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Seligmann ICA, Furo IO, Dos Santos MS, Tagliarini MM, Araujo CCD, O''Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Chromosome Painting in Two Brazilian Stork Species with Different Diploid Numbers. Cytogenet Genome Res 2019; 159:32-38. [PMID: 31542782 DOI: 10.1159/000503019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2019] [Indexed: 11/19/2022] Open
Abstract
Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.
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18
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Dos Santos MS, Furo IO, Tagliarini MM, Kretschmer R, O''Brien PCM, Ferguson-Smith MA, de Oliveira EHC. The Karyotype of the Hoatzin (Opisthocomus hoazin) - A Phylogenetic Enigma of the Neornithes. Cytogenet Genome Res 2018; 156:158-164. [PMID: 30472715 DOI: 10.1159/000494707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 11/19/2022] Open
Abstract
The hoatzin (Opisthocomus hoazin Müller, 1776) is a folivorous bird, endemic to the Amazonian region. It presents some unique characteristics, including wing claws and foregut fermentation, which make its phylogenetic relationship to other birds difficult to determine. There have been various attempts to place it among the Galliformes, Gruiformes, Musophagiformes, Cuculiformes, and Charadriiformes, but phylogenetic analyses always show low supporting values. Nowadays, the hoatzin is included in the monotypic order Opisthocomiformes, but the relationship of this order to other groups of birds is still unclear. Although its karyotype resembles the typical avian model, fissions of the syntenic groups corresponding to chicken chromosomes 1 and 2 and 2 fusions were found. The presence of 18S rDNA clusters in 2 pairs of microchromosomes is another derived character. Hence, different rearrangements were detected in the karyotype of the hoatzin, indicating it has been derived from the putative ancestral karyotype by the occurrence of fissions and fusions. However, as these rearrangements are not exclusive to O. hoazin, they do not clarify the phylogenetic position of this enigmatic species.
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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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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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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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Degrandi TM, de Oliveira JCP, Soares ADA, Ledesma MA, Hass I, Garnero ADV, Gunski RJ. Karyotype description and comparative analysis in Ringed Kingfisher and Green Kingfisher (Coraciiformes, Alcedinidae). COMPARATIVE CYTOGENETICS 2018; 12:163-170. [PMID: 29780444 PMCID: PMC5958172 DOI: 10.3897/compcytogen.v12i2.23883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Kingfishers comprise about 115 species of the family Alcedinidae, and are an interesting group for cytogenetic studies, for they are among birds with most heterogeneous karyotypes. However, cytogenetics knowledge in Kingfishers is extremely limited. Thus, the aim of this study was to describe the karyotype structure of the Ringed Kingfisher (Megaceryle torquata Linnaeus, 1766) and Green Kingfisher (Chloroceryle americana Gmelin, 1788) and also compare them with related species in order to identify chromosomal rearrangements. The Ringed Kingfisher presented 2n = 84 and the Green Kingfisher had 2n = 94. The increase of the chromosome number in the Green Kingfisher possibly originated by centric fissions in macrochromosomes. In addition, karyotype comparisons in Alcedinidae show a heterogeneity in the size and morphology of macrochromosomes, and chromosome numbers ranging from 2n = 76 to 132. Thus, it is possible chromosomal fissions in macrochromosomes resulted in the increase of the diploid number, whereas chromosome fusions have originated the karyotypes with low diploid number.
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Affiliation(s)
- Tiago Marafiga Degrandi
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | | | - Amanda de Araújo Soares
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | | | - Iris Hass
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | - Analía del Valle Garnero
- Universidade Federal do Pampa, Rua Aluízio Barros Macedo, BR 290, km 423 Bairro Piraí, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa, Rua Aluízio Barros Macedo, BR 290, km 423 Bairro Piraí, São Gabriel, Rio Grande do Sul, Brazil
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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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Kretschmer R, de Oliveira TD, de Oliveira Furo I, Oliveira Silva FA, Gunski RJ, Del Valle Garnero A, de Bello Cioffi M, de Oliveira EHC, de Freitas TRO. Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes). Genet Mol Biol 2018; 41:98-106. [PMID: 29473932 PMCID: PMC5901494 DOI: 10.1590/1678-4685-gmb-2017-0048] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/16/2017] [Indexed: 12/02/2022] Open
Abstract
An extensive karyotype variation is found among species belonging to the
Columbidae family of birds (Columbiformes), both in diploid number and
chromosomal morphology. Although clusters of repetitive DNA sequences play an
important role in chromosomal instability, and therefore in chromosomal
rearrangements, little is known about their distribution and amount in avian
genomes. The aim of this study was to analyze the distribution of 11 distinct
microsatellite sequences, as well as clusters of 18S rDNA, in nine different
Columbidae species, correlating their distribution with the occurrence of
chromosomal rearrangements. We found 2n values ranging from 76 to 86 and nine
out of 11 microsatellite sequences showed distinct hybridization signals among
the analyzed species. The accumulation of microsatellite repeats was found
preferentially in the centromeric region of macro and microchromosomes, and in
the W chromosome. Additionally, pair 2 showed the accumulation of several
microsatellites in different combinations and locations in the distinct species,
suggesting the occurrence of intrachromosomal rearrangements, as well as a
possible fission of this pair in Geotrygon species. Therefore,
although birds have a smaller amount of repetitive sequences when compared to
other Tetrapoda, these seem to play an important role in the karyotype evolution
of these species.
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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
| | - Thays Duarte de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Ivanete de Oliveira Furo
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Ricardo José Gunski
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Edivaldo Herculano Corrêa 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
| | - Thales Renato Ochotorena de Freitas
- 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
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Carvalho PC, de Oliveira EA, Bertollo LAC, Yano CF, Oliveira C, Decru E, Jegede OI, Hatanaka T, Liehr T, Al-Rikabi ABH, Cioffi MDB. First Chromosomal Analysis in Hepsetidae (Actinopterygii, Characiformes): Insights into Relationship between African and Neotropical Fish Groups. Front Genet 2017; 8:203. [PMID: 29312435 PMCID: PMC5733008 DOI: 10.3389/fgene.2017.00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/22/2017] [Indexed: 01/27/2023] Open
Abstract
Hepsetidae is a small fish family with only the genus Hepsetus, with six described species distributed throughout the South, Central and Western regions of Africa, showing a close relationship with the Alestidae and some Neotropical fish families. However, no cytogenetic information is available for both Hepsetidae and Alestidae species, thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing new cytogenetic data for Hepsetus odoe, including the standard karyotype, C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH) and whole chromosome painting (WCP), providing chromosomal patterns and subsidies for comparative cytogenetics with other characiform families. Both males and females H. odoe have 2n = 58 chromosomes (10m + 28sm + 20st/a), with most of the C-band positive heterochromatin localized in the centromeric and subtelomeric regions. Only one pair of chromosomes bears proximal 5S rDNA sites in the short arms, contrasting with the 18S rDNA sequences which are located in the terminal regions of four chromosome pairs. Clear interstitial hybridization signals are evidenced for the U1 and U2 snDNA probes, but in only one and two chromosome pairs, respectively. Microsatellite motifs are widely distributed in the karyotype, with exception for the (CGG)10, (GAA)10 and (GAG)10 probes, which highlight conspicuous interstitial signals on an unique pair of chromosomes. Comparative data from conventional and molecular cytogenetics, including CGH and WCP experiments, indicate that H. odoe and some Erythrinidae species, particularly Erythrinus erythrinus, share similar chromosomal sequences suggesting some relatedness among them, although bearing genomic specificities in view of their divergent evolutionary histories.
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Affiliation(s)
- Pedro C Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso (Seduc-MT), Cuiabá, Brazil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Cassia F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Eva Decru
- Section Vertebrates, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Oladele I Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, Mubi, Nigeria
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Marcelo de B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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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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Seibold-Torres C, Owens E, Chowdhary R, Ferguson-Smith MA, Tizard I, Raudsepp T. Comparative Cytogenetics of the Congo African Grey Parrot (Psittacus erithacus). Cytogenet Genome Res 2016; 147:144-53. [PMID: 26894300 DOI: 10.1159/000444136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 11/19/2022] Open
Abstract
The Congo African grey parrot (Psittacus erithacus, PER) is an endemic species of Central Africa, valued for its intelligence and listed as vulnerable due to poaching and habitat destruction. Improved knowledge about the P. erithacus genome is needed to address key biological questions and conservation of this species. The P. erithacus genome was studied using conventional and molecular cytogenetic approaches including Zoo-FISH. P. erithacus has a 'typical' parrot karyotype with 2n = 62-64 and 8 pairs of macrochromosomes. A distinct feature was a sharp macro-microchromosome boundary. Telomeric sequences were present at all chromosome ends and interstitially in PER2q, the latter coinciding with a C-band. NORs mapped to 4 pairs of microchromosomes which is in contrast to a single NOR in ancestral type avian karyotypes. Zoo-FISH with chicken macrochromosomes GGA1-9 and Z revealed patterns of conserved synteny similar to many other avian groups, though neighboring synteny combinations of GGA6/7, 8/9, and 1/4 were distinctive only to parrots. Overall, P. erithacus shared more Zoo-FISH patterns with neotropical macaws than Australian species such as cockatiel and budgerigar. The observations suggest that Psittaciformes karyotypes have undergone more extensive evolutionary rearrangements compared to the majority of other avian genomes.
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Affiliation(s)
- Cassandra Seibold-Torres
- Department of Veterinary Integrative Biosciences, Schubot Exotic Bird Health Center, CVM, Texas A&M University, College Station, Tex., USA
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29
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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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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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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, Gunski RJ, del Valle Garnero A, O'Brien PCM, Ferguson-Smith MA, Ochotorena de Freitas TR, Correa de Oliveira EH. Chromosome Painting in Vanellus chilensis: Detection of a Fusion Common to Clade Charadrii (Charadriiformes). Cytogenet Genome Res 2015; 146:58-63. [PMID: 26088018 DOI: 10.1159/000431387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
The Southern lapwing (Vanellus chilensis) is endemic to America and is well-known because of the vast expansion of its geographical distribution and its involvement in air accidents. Despite its popularity, there is no information concerning the genomic organization and karyotype of this species. Hence, because other species of the genus Vanellus have variable diploid numbers from 2n = 58 to 76, the aim of this report was to analyze the karyotype of V. chilensis by means of classical and molecular cytogenetics. We found that 2n = 78 and chromosome painting using probes of Gallus gallus (GGA) and Leucopternis albicollis revealed an organization similar to the avian putative ancestral karyotype, except for the fusion of GGA7 and GGA8, also found in Burhinus oedicnemus, the only Charadriiforme species analyzed by FISH so far. This rearrangement may represent a cytogenetic signature for this group and, in addition, must be responsible for the difference between the diploid number found in the avian putative ancestral karyotype (2n = 80) and V. chilensis (2n = 78).
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Affiliation(s)
- Rafael Kretschmer
- Programa de Px00F3;s Graduax00E7;x00E3;o em Genx00E9;tica e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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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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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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Nishida C, Ishishita S, Yamada K, Griffin DK, Matsuda Y. Dynamic chromosome reorganization in the osprey ( Pandion haliaetus , Pandionidae, Falconiformes): relationship between chromosome size and the chromosomal distribution of centromeric repetitive DNA sequences. Cytogenet Genome Res 2014; 142:179-89. [PMID: 24513810 DOI: 10.1159/000358407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2013] [Indexed: 11/19/2022] Open
Abstract
The osprey (Pandion haliaetus) has a diploid number of 74 chromosomes, consisting of a large number of medium-sized macrochromosomes and relatively few microchromosomes; this differs greatly from the typical avian karyotype. Chromosome painting with chicken DNA probes revealed that the karyotype of P. haliaetus differs from the chicken karyotype by at least 14 fission events involving macrochromosomes (chicken chromosomes 1-9 and Z) and at most 15 fusions of microchromosomes, suggesting that considerable karyotype reorganization occurred in P. haliaetus in a similar manner previously reported for Accipitridae. A distinct difference was observed, however, between Accipitridae and Pandionidae with respect to the pattern of chromosome rearrangements that occurred after fissions of macrochromosomes. Metacentric or submetacentric chromosomes 1-5 in P. haliaetus appear to have been formed by centric fusion of chromosome segments derived from macrochromosomal fissions. By contrast, many pairs of bi-armed chromosomes in Accipitridae species seem to result from pericentric inversions that occurred in the fission-derived chromosomes. Two families of repetitive sequences were isolated; the 173-bp PHA-HaeIII sequence occurred on all chromosomes, whereas intense signals from the 742-bp PHA-NsiI sequence were localized to all acrocentric chromosomes, with weak signals on most of the bi-armed chromosomes. Two repetitive sequences cohybridized in the centromeric heterochromatin; however, the sequences differed in unit size, nucleotide sequence and GC content. The results suggest that the 2 sequence families originated from different ancestral sequences and were homogenized independently in centromeres, and that a chromosome size-dependent compartmentalization may have been lost in P. haliaetus.
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Affiliation(s)
- C Nishida
- Department of Natural History Sciences, Hokkaido University, Sapporo, Japan
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Comparison of the Chromosome Structures between the Chicken and Three Anserid Species, the Domestic Duck ( Anas platyrhynchos), Muscovy Duck ( Cairina moschata), and Chinese Goose ( Anser cygnoides), and the Delineation of their Karyotype Evolution by Comparative Chromosome Mapping. J Poult Sci 2014. [DOI: 10.2141/jpsa.0130090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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de Oliveira EHC, Tagliarini MM, dos Santos MS, O'Brien PCM, Ferguson-Smith MA. Chromosome painting in three species of buteoninae: a cytogenetic signature reinforces the monophyly of South American species. PLoS One 2013; 8:e70071. [PMID: 23922908 PMCID: PMC3724671 DOI: 10.1371/journal.pone.0070071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/15/2013] [Indexed: 11/18/2022] Open
Abstract
Buteoninae (Falconiformes, Accipitridae) consist of the widely distributed genus Buteo, and several closely related species in a group called “sub-buteonine hawks”, such as Buteogallus, Parabuteo, Asturina, Leucopternis and Busarellus, with unsolved phylogenetic relationships. Diploid number ranges between 2n = 66 and 2n = 68. Only one species, L. albicollis had its karyotype analyzed by molecular cytogenetics. The aim of this study was to present chromosomal analysis of three species of Buteoninae: Rupornis magnirostris, Asturina nitida and Buteogallus meridionallis using fluorescence in situ hybridization (FISH) experiments with telomeric and rDNA probes, as well as whole chromosome probes derived from Gallus gallus and Leucopternis albicollis. The three species analyzed herein showed similar karyotypes, with 2n = 68. Telomeric probes showed some interstitial telomeric sequences, which could be resulted by fusion processes occurred in the chromosomal evolution of the group, including the one found in the tassociation GGA1p/GGA6. In fact, this association was observed in all the three species analyzed in this paper, and also in L. albicollis, suggesting that it represents a cytogenetic signature which reinforces the monophyly of Neotropical buteoninae species.
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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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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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Tagliarini MM, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Maintenance of syntenic groups between Cathartidae and Gallus gallus indicates symplesiomorphic karyotypes in new world vultures. Genet Mol Biol 2011; 34:80-3. [PMID: 21637548 PMCID: PMC3085379 DOI: 10.1590/s1415-47572010005000117] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 09/29/2010] [Indexed: 11/22/2022] Open
Abstract
Similarities between New World and Old World vultures have been interpreted to reflect a close relationship and to suggest the inclusion of both in Accipitridae (Falconiformes). However, deeper analyses indicated that the placement of the New World vultures (cathartids) in this Order is uncertain. Chromosome analysis has shown that cathartids retained a karyotype similar to the putative avian ancestor. In order to verify the occurrence of intrachromosomal rearrangements in cathartids, we hybridized whole chromosome probes of two species (Gallus gallus and Leucopternis albicollis) onto metaphases of Cathartes aura. The results showed that not only were the syntenic groups conserved between Gallus and C. aura, but probably also the general gene order, suggesting that New World vultures share chromosomal symplesiomorphies with most bird lineages.
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Affiliation(s)
- Marcella M Tagliarini
- Pós-Graduação em Neurociências e Biologia Celular, ICB, Universidade Federal do Pará, Belém, PA, Brazil
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