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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: 0] [Impact Index Per Article: 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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2
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Seligmann ICA, Furo IDO, dos Santos MDS, Gunski RJ, Garnero ADV, Silva FAO, O´Brien P, Ferguson-Smith M, Kretschmer R, de Oliveira EHC. Comparative chromosome painting in three Pelecaniformes species (Aves): Exploring the role of macro and microchromosome fusions in karyotypic evolution. PLoS One 2023; 18:e0294776. [PMID: 38011093 PMCID: PMC10681242 DOI: 10.1371/journal.pone.0294776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
Pelecaniformes is an order of waterbirds that exhibit diverse and distinct morphologies. Ibis, heron, pelican, hammerkop, and shoebill are included within the order. Despite their fascinating features, the phylogenetic relationships among the families within Pelecaniformes remain uncertain and pose challenges due to their complex evolutionary history. Their karyotypic evolution is another little-known aspect. Therefore, to shed light on the chromosomal rearrangements that have occurred during the evolution of Pelecaniformes, we have used whole macrochromosome probes from Gallus gallus (GGA) to show homologies on three species with different diploid numbers, namely Cochlearius cochlearius (2n = 74), Eudocimus ruber (2n = 66), and Syrigma sibilatrix (2n = 62). A fusion between GGA6 and GGA7 was found in C. cochlearius and S. sibilatrix. In S. sibilatrix the GGA8, GGA9 and GGA10 hybridized to the long arms of biarmed macrochromosomes, indicating fusions with microchromosomes. In E. ruber the GGA7 and GGA8 hybridized to the same chromosome pair. After comparing our painting results with previously published data, we show that distinct chromosomal rearrangements have occurred in different Pelecaniformes lineages. Our study provides new insight into the evolutionary history of Pelecaniformes and the chromosomal changes involving their macrochromosomes and microchromosomes that have taken place in different species within this order.
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Affiliation(s)
- Igor Chamon Assumpção Seligmann
- Programa de Pós-graduação em Biodiversidade e Biotecnologia da Rede Bionorte, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, State of Pará, Brazil
| | - Michelly da Silva dos Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, State of Pará, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, State of Rio Grande do Sul, Brazil
| | - Analía del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, State of Rio Grande do Sul, Brazil
| | - Fabio Augusto Oliveira Silva
- Programa de Pós-graduação em Neurociência e Biologia Molecular, Universidade Federal do Pará, Belém, State of Pará, Brazil
| | - Patricia O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas, State of Rio Grande do Sul, Brazil
| | - Edivaldo Herculano C. de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, State of Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SEAMB, Instituto Evandro Chagas, Ananindeua, State of Pará, Brazil
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3
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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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Kretschmer R, de Souza MS, Furo IDO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O’Connor RE, Griffin DK. Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds. Cells 2021; 10:cells10040826. [PMID: 33916942 PMCID: PMC8067558 DOI: 10.3390/cells10040826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/18/2023] Open
Abstract
Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900 Rio Grande do Sul, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, 68515-000 Pará, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, 67030-000 Pará, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, 66075-110 Pará, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Correspondence: ; Tel.: +44-1227-823022
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Ribas TFA, Pieczarka JC, Griffin DK, Kiazim LG, Nagamachi CY, O Brien PCM, Ferguson-Smith MA, Yang F, Aleixo A, O'Connor RE. Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype. BMC Ecol Evol 2021; 21:34. [PMID: 33653261 PMCID: PMC7927240 DOI: 10.1186/s12862-021-01768-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. RESULTS The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. CONCLUSIONS Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.
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Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- School of Biosciences, University of Kent, Canterbury, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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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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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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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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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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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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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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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10040113] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.
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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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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: 48] [Impact Index Per Article: 8.0] [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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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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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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