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Alves Barcellos S, Kretschmer R, Santos de Souza M, Tura V, Pozzobon LC, Ochotorena de Freitas TR, Griffin DK, O'Connor R, Gunski RJ, Del Valle Garnero A. Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis. Genome 2024; 67:223-232. [PMID: 38742652 DOI: 10.1139/gen-2023-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.
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Affiliation(s)
- Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Victoria Tura
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Luciano Cesar Pozzobon
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Thales Renato Ochotorena de Freitas
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
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2
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Kretschmer R, Toma GA, Deon GA, dos Santos N, dos Santos RZ, Utsunomia R, Porto-Foresti F, Gunski RJ, Garnero ADV, Liehr T, de Oliveira EHC, de Freitas TRO, Cioffi MDB. Satellitome Analysis in the Southern Lapwing ( Vanellus chilensis) Genome: Implications for SatDNA Evolution in Charadriiform Birds. Genes (Basel) 2024; 15:258. [PMID: 38397247 PMCID: PMC10887557 DOI: 10.3390/genes15020258] [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: 01/29/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Vanellus (Charadriidae; Charadriiformes) comprises around 20 species commonly referred to as lapwings. In this study, by integrating cytogenetic and genomic approaches, we assessed the satellite DNA (satDNA) composition of one typical species, Vanellus chilensis, with a highly conserved karyotype. We additionally underlined its role in the evolution, structure, and differentiation process of the present ZW sex chromosome system. Seven distinct satellite DNA families were identified within its genome, accumulating on the centromeres, microchromosomes, and the W chromosome. However, these identified satellite DNA families were not found in two other Charadriiformes members, namely Jacana jacana and Calidris canutus. The hybridization of microsatellite sequences revealed the presence of a few repetitive sequences in V. chilensis, with only two out of sixteen displaying positive hybridization signals. Overall, our results contribute to understanding the genomic organization and satDNA evolution in Charadriiform birds.
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Affiliation(s)
- Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Gustavo A. Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
| | - Natalia dos Santos
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Rodrigo Zeni dos Santos
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Fabio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, SP, Brazil; (N.d.S.); (R.Z.d.S.); (R.U.); (F.P.-F.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (R.J.G.); (A.D.V.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (R.J.G.); (A.D.V.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, University Hospital Jena, 07747 Jena, Germany
| | - Edivaldo Herculano Corra de Oliveira
- Laboratório de Citogenô mica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - 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;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (G.A.T.); (G.A.D.); (M.d.B.C.)
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3
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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4
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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: 0] [Impact Index Per Article: 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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van Dijk A, Guabiraba R, Bailleul G, Schouler C, Haagsman HP, Lalmanach AC. Evolutionary diversification of defensins and cathelicidins in birds and primates. Mol Immunol 2023; 157:53-69. [PMID: 36996595 DOI: 10.1016/j.molimm.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Divergent evolution for more than 310 million years has resulted in an avian immune system that is complex and more compact than that of primates, sharing much of its structure and functions. Not surprisingly, well conserved ancient host defense molecules, such as defensins and cathelicidins, have diversified over time. In this review, we describe how evolution influenced the host defense peptides repertoire, its distribution, and the relationship between structure and biological functions. Marked features of primate and avian HDPs are linked to species-specific characteristics, biological requirements, and environmental challenge.
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Tura V, Kretschmer R, Sassi FDMC, de Moraes RLR, Barcellos SA, de Rosso VO, de Souza MS, Cioffi MDB, Gunski RJ, Garnero ADV. Chromosomal Evolution of Suboscines: Karyotype Diversity and Evolutionary Trends in Ovenbirds (Passeriformes, Furnariidae). Cytogenet Genome Res 2023; 162:644-656. [PMID: 36996794 DOI: 10.1159/000530428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/28/2023] [Indexed: 04/01/2023] Open
Abstract
Furnariidae (ovenbirds) is one of the most diversified families in the Passeriformes order and Suboscines suborder. Despite the great diversity of species, cytogenetic research is still in its early stages, restricting our knowledge of their karyotype evolution. We combined traditional and molecular cytogenetic analyses in three representative species, Synallaxis frontalis, Syndactyla rufosuperciliata, and Cranioleuca obsoleta, to examine the chromosomal structure and evolution of ovenbirds. Our findings revealed that all the species studied had the same diploid number (2n = 82). Differences in chromosomal morphology of some macrochromosomes indicate the presence of intrachromosomal rearrangements. Although the three species only had the 18S rDNA on one microchromosome pair, chromosomal mapping of six simple short repeats revealed a varied pattern of chromosome distribution among them, suggesting that each species underwent different repetitive DNA accumulation upon their divergence. The interspecific comparative genomic hybridization experiment revealed that the Furnariidae species investigated carry centromeric regions enriched in similar repetitive sequences, bolstering the Furnariidae family's karyotype conservation. Nonetheless, the outgroup species Turdus rufiventris (Turdidae) demonstrated an advanced stage of sequence divergence with hybridization signals that were almost entirely limited to a few microchromosomes. Overall, the findings imply that Furnariidae species have a high degree of chromosomal conservation, and we could also observe a differentiation of repetitive sequences in both Passeriformes suborders (Suboscines and Oscines).
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Affiliation(s)
- Victoria Tura
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | | | - Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Vitor Oliveira de Rosso
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | | | - Ricardo J Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
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Maslova A, Plotnikov V, Nuriddinov M, Gridina M, Fishman V, Krasikova A. Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line. BMC Genomics 2023; 24:66. [PMID: 36750787 PMCID: PMC9906895 DOI: 10.1186/s12864-023-09158-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line. RESULTS We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH. CONCLUSIONS In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.
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Affiliation(s)
- A. Maslova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - V. Plotnikov
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - M. Nuriddinov
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - M. Gridina
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - V. Fishman
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - A. Krasikova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
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8
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A conserved karyotype? Chromosomal rearrangements in Charadrius collaris detected by BAC-FISH. PLoS One 2023; 18:e0280164. [PMID: 36630423 PMCID: PMC9833595 DOI: 10.1371/journal.pone.0280164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Charadriidae comprise 142 valid species and the most recent checklist for the occurrence of this family in Brazil describes 11 species. There are few chromosomal studies in Charadriidae, most of them using a conventional approach. In Charadrius, only five species had their karyotypes described by classical cytogenetics, of which four have 2n = 76 (C. hiaticula, C. dubius, C. vociferou and C. collaris) and one 2n = 78 (C. alexandrinus alexandrinus). Among these species, only Charadrius collaris had the karyotype studied by chromosome painting, which allowed the identification of chromosomal homeologies with the karyotypes of Gallus gallus (GGA) and Burhinus oedicnemus (BOE). According to the literature, studies performed with BAC-FISH using probes from Gallus gallus and Taeniopygia guttata (TGU) libraries have shown interactions between macro and microchromosomes and micro inversions in chromosomes previously considered conserved. Other studies have shown the fusion of several microchromosomes, forming new macrochromosomes, leading to a decrease in the 2n of some species. The present study aims to deepen the chromosomal information in Charadrius collaris through the application of BAC-FISH with probes from the GGA and TGU libraries, in order to investigate possible rearrangements within the apparently conserved karyotype of this species, and thus better clarify the evolutionary history of the species. Charadrius collaris presented 2n = 76 and fundamental number (FN) equal to 94. Comparative mapping of BAC probes from GGA and TGU in Charadrius collaris revealed hybridization signals from 26 macrochromosome probes. Probes from microchromosomes 9 to 28 of GGA were also used and revealed 31 hybridization signals. The karyotype is well conserved, but it contains a paracentric and a pericentric inversion on the CCO1 chromosome, a paracentric and a pericentric inversion on the CCO4 and the separation of GGA4 into CCO4 and CCO8, demonstrating that the BAC-FISH approach allows for greater data resolution. More studies are needed to improve the understanding of chromosomal evolution within the order Charadriiformes and thus clarify whether these characteristics demonstrated here are specific traits for Charadrius collaris or if other species share these characteristics.
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9
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de Souza MS, Barcellos SA, dos Santos MDS, Gunski RJ, Garnero ADV, de Oliveira EHC, O’Connor RE, Griffin DK, Kretschmer R. Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species. Animals (Basel) 2022; 12:ani12213052. [PMID: 36359176 PMCID: PMC9655014 DOI: 10.3390/ani12213052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds-Calidris canutus, Jacana jacana, and Vanellus chilensis-combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10-28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in C. canutus, we found two microchromosomes involved in chromosome fusions, they were present as single pairs in V. chilensis. We also described a new chromosome number for C. canutus (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species.
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Affiliation(s)
- Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Michelly da Silva dos Santos
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | | | | | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
- Correspondence:
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10
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Stuart KC, Edwards RJ, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA. Transcript- and annotation-guided genome assembly of the European starling. Mol Ecol Resour 2022; 22:3141-3160. [PMID: 35763352 PMCID: PMC9796300 DOI: 10.1111/1755-0998.13679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/10/2022] [Indexed: 01/01/2023]
Abstract
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
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Affiliation(s)
- Katarina C. Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Yuanyuan Cheng
- School of Life and Environmental SciencesThe University of Sydney, SydneyNew South WalesAustralia
| | - Wesley C. Warren
- Department of Animal Sciences, Institute for Data Science and InformaticsThe University of MissouriColumbiaMissouriUSA
| | - David W. Burt
- Office of the Deputy Vice‐Chancellor (Research and Innovation)The University of QueenslandBrisbaneAustralia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Natalie R. Hofmeister
- Department of Ecology and Evolutionary BiologyCornell UniversityNew YorkUSA,Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyNew YorkUSA
| | - Scott J. Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | | | - Melissa Bateson
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPennsylvaniaUSA
| | - Katherine L. Buchanan
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology LabUniversity of AdelaideAdelaideAustralia
| | - David F. Clayton
- Department of Genetics & BiochemistryClemson UniversitySouth CarolinaUSA
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Simone L. Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia,School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
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11
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Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes. Chromosoma 2022; 131:207-223. [PMID: 36031655 DOI: 10.1007/s00412-022-00780-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]
Abstract
In diplotene oocyte nuclei of all vertebrate species, except mammals, chromosomes lack interchromosomal contacts and chromatin is linearly compartmentalized into distinct chromomere-loop complexes forming lampbrush chromosomes. However, the mechanisms underlying the formation of chromomere-loop complexes remain unexplored. Here we aimed to compare somatic topologically associating domains (TADs), recently identified in chicken embryonic fibroblasts, with chromomere-loop complexes in lampbrush meiotic chromosomes. By measuring 3D-distances and colocalization between linear equidistantly located genomic loci, positioned within one TAD or separated by a TAD border, we confirmed the presence of predicted TADs in chicken embryonic fibroblast nuclei. Using three-colored FISH with BAC probes, we mapped equidistant genomic regions included in several sequential somatic TADs on isolated chicken lampbrush chromosomes. Eight genomic regions, each comprising two or three somatic TADs, were mapped to non-overlapping neighboring lampbrush chromatin domains - lateral loops, chromomeres, or chromomere-loop complexes. Genomic loci from the neighboring somatic TADs could localize in one lampbrush chromomere-loop complex, while genomic loci belonging to the same somatic TAD could be localized in neighboring lampbrush chromomere-loop domains. In addition, FISH-mapping of BAC probes to the nascent transcripts on the lateral loops indicates transcription of at least 17 protein-coding genes and 2 non-coding RNA genes during the lampbrush stage of chicken oogenesis, including genes involved in oocyte maturation and early embryo development.
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12
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Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O´Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Chromosomal painting in Charadrius collaris Vieillot, 1818 and Vanellus chilensis Molina, 1782 and an analysis of chromosomal signatures in Charadriiformes. PLoS One 2022; 17:e0272836. [PMID: 35947613 PMCID: PMC9365183 DOI: 10.1371/journal.pone.0272836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/27/2022] [Indexed: 11/19/2022] Open
Abstract
Charadriiformes represent one of the largest orders of birds; members of this order are diverse in morphology, behavior and reproduction, making them an excellent model for studying evolution. It is accepted that the avian putative ancestral karyotype, with 2n = 80, remains conserved for about 100 million years. So far, only a few species of Charadriiformes have been studied using molecular cytogenetics. Here, we performed chromosome painting on metphase chromosomes of two species of Charadriidae, Charadrius collaris and Vanellus chilensis, with whole chromosome paint probes from Burhinus oedicnemus. Charadrius collaris has a diploid number of 76, with both sex chromosomes being submetacentric. In V. chilensi a diploid number of 78 was identified, and the Z chromosome is submetacentric. Chromosome painting suggests that chromosome conservation is a characteristic common to the family Charadriidae. The results allowed a comparative analysis between the three suborders of Charadriiformes and the order Gruiformes using chromosome rearrangements to understand phylogenetic relationships between species and karyotypic evolution. However, the comparative analysis between the Charadriiformes suborders so far has not revealed any shared rearrangements, indicating that each suborder follows an independent evolutionary path, as previously proposed. Likewise, although the orders Charadriiformes and Gruiformes are placed on sister branches, they do not share any signature chromosomal rearrangements.
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Affiliation(s)
- Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal do Pará, Campus de Bragança, Bragança, Pará, Brazil
| | - Patricia Caroline Mary O´Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
- * E-mail:
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13
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Sotelo-Muñoz M, Poignet M, Albrecht T, Kauzál O, Dedukh D, Schlebusch SA, Janko K, Reifová R. Germline-restricted chromosome shows remarkable variation in size among closely related passerine species. Chromosoma 2022; 131:77-86. [PMID: 35389062 DOI: 10.1007/s00412-022-00771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
Passerine birds have a supernumerary chromosome in their germ cells called the germline-restricted chromosome (GRC). The GRC was first discovered more than two decades ago in zebra finch but recent studies have suggested that it is likely present in all passerines, the most species rich avian order, encompassing more than half of all modern bird species. Despite its wide taxonomic distribution, studies on this chromosome are still scarce and limited to a few species. Here, we cytogenetically analyzed the GRC in five closely related estrildid finch species of the genus Lonchura. We show that the GRC varies enormously in size, ranging from a tiny micro-chromosome to one of the largest macro-chromosomes in the cell, not only among recently diverged species but also within species and sometimes even between germ cells of a single individual. In Lonchura atricapilla, we also observed variation in GRC copy number among male germ cells of a single individual. Finally, our analysis of hybrids between two Lonchura species with noticeably different GRC size directly supported maternal inheritance of the GRC. Our results reveal the extraordinarily dynamic nature of the GRC, which might be caused by frequent gains and losses of sequences on this chromosome leading to substantial differences in genetic composition of the GRC between and even within species. Such differences might theoretically contribute to reproductive isolation between species and thus accelerate the speciation rate of passerine birds compared to other bird lineages.
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Affiliation(s)
- Manuelita Sotelo-Muñoz
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.
| | - Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic
| | - Ondřej Kauzál
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
| | - Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.
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14
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Wang J, Su W, Hu Y, Li S, O'Brien PCM, Ferguson-Smith MA, Yang F, Nie W. Comparative chromosome maps between the stone curlew and three ciconiiform species (the grey heron, little egret and crested ibis). BMC Ecol Evol 2022; 22:23. [PMID: 35240987 PMCID: PMC8892796 DOI: 10.1186/s12862-022-01979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Previous cytogenetic studies show that the karyotypes of species in Ciconiiformes vary considerably, from 2n = 52 to 78. Their karyotypes include different numbers of small to minute bi-armed chromosomes that have evolved probably by fusions of two ancestral microchromosomes, besides macrochromosomes and dot-like microchromosomes. However, it is impossible to define the inter-species homologies of such small-sized bi-armed chromosomes based on chromosome morphology and banding characteristics. Although painting probes from the chicken (Gallus gallus, GGA) chromosomes 1–9 and Z have been widely used to investigate avian chromosome homologies, GGA microchromosome probes are rarely used in these studies because most GGA microchromosome probes generated by flow sorting often contain multiple GGA microchromosomes. In contrast, the stone curlew (Burhinus oedicnemus, BOE, Charadriiformes) has an atypical low diploid chromosome number (42) karyotype and only 4 pairs of dot-like microchromosomes; a set of chromosome-specific painting probes that cover all BOE chromosomes has been generated. To get a genome-wide view of evolutionary chromosomal rearrangements in different lineages of Ciconiiformes, we used BOE painting probes instead of GGA painting probes to analyze the karyotypes of three ciconiiform species belonging to two different families: the eastern grey heron (Ardea cinerea, ACI, 2n = 64, Ardeidae), the little egret (Egretta garzetta, EGA, 2n = 64, Ardeidae) and the crested ibis (Nipponia nippon, NNI, 2n = 68, Threskiornithidae). Results BOE painting probes display the same hybridization pattern on chromosomes of ACI and EGA, while a different hybridization pattern is observed on chromosomes of NNI. BOE autosome probes detected 21 conserved homologous segments and 5 fusions on the sixteen pairs of recognizable chromosomes of ACI and EGA, while 16 conserved homologous segments and 4 fusions were found on the twelve pairs of recognizable chromosomes of NNI. Only a portion of smaller bi-armed chromosomes in the karyotypes of the ciconiiform species could have evolved from fusions of ancestral microchromosomes. In particular BOE 5, which is the result of a fusion between two segments homologous to GGA 7 and 8 respectively, was retained also as either a single chromosome in ACI (ACI 5) and EGA (EGA 5) or had fused with a part of the BOE 10 equivalent in NNI (NNI 5). Conclusion Our painting results indicate that different chromosome rearrangements occur in different ciconiiform lineages. Some of the small-sized bi-armed chromosomes in ACI, EGA and NNI are derived from the fusions of two microchromosomes, indicating that microchromosome fusions play an important role in ciconiiform chromosome evolution. The fusion segment homologous to GGA 7 and 8 is a potential cytogenetic signature that unites Ardeidae and Threskiornithidae.
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Affiliation(s)
- Jinhuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Weiting Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Yi Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China
| | - Shengbin Li
- Key Laboratory of Forensic Sciences, Ministry of Health, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, Shandong, People's Republic of China.
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, People's Republic of China.
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15
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Poignet M, Johnson Pokorná M, Altmanová M, Majtánová Z, Dedukh D, Albrecht T, Reif J, Osiejuk TS, Reifová R. Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats. Front Genet 2021; 12:768987. [PMID: 34938317 PMCID: PMC8687609 DOI: 10.3389/fgene.2021.768987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.
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Affiliation(s)
- Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Johnson Pokorná
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Zuzana Majtánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Dmitry Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Tomasz S. Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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16
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Waters PD, Patel HR, Ruiz-Herrera A, Álvarez-González L, Lister NC, Simakov O, Ezaz T, Kaur P, Frere C, Grützner F, Georges A, Graves JAM. Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proc Natl Acad Sci U S A 2021; 118:e2112494118. [PMID: 34725164 PMCID: PMC8609325 DOI: 10.1073/pnas.2112494118] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly, de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early-branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently, multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus, microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles and birds, that are atypical.
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Affiliation(s)
- Paul D Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Hardip R Patel
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, 1010 Vienna, Austria
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
| | - Celine Frere
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3068, Australia
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17
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Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features. Int J Mol Sci 2021; 22:ijms222111403. [PMID: 34768834 PMCID: PMC8584138 DOI: 10.3390/ijms222111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists.
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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: 2] [Impact Index Per Article: 0.7] [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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19
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Rovatsos M, Gamble T, Nielsen SV, Georges A, Ezaz T, Kratochvíl L. Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200102. [PMID: 34304587 PMCID: PMC8310713 DOI: 10.1098/rstb.2020.0102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 Ma, one species in particular, Burton's legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Stuart V. Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
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20
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Kratochvíl L, Gamble T, Rovatsos M. Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random? Philos Trans R Soc Lond B Biol Sci 2021; 376:20200108. [PMID: 34304592 PMCID: PMC8310715 DOI: 10.1098/rstb.2020.0108] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
- Milwaukee Public Museum, Milwaukee, WI, USA
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
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21
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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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22
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Keinath MC, Davidian A, Timoshevskiy V, Timoshevskaya N, Gall JG. Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining. Exp Cell Res 2021; 401:112523. [PMID: 33675804 PMCID: PMC8123938 DOI: 10.1016/j.yexcr.2021.112523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 10/25/2022]
Abstract
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Measurements of relative LBC arm lengths and polymerase III localization patterns enabled us to identify all LBCs. This study presents a relatively simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences (from the axolotl genome assembly) to the physical LBCs by immunostaining and fluorescence in situ hybridization. Our data will facilitate a more detailed transcription analysis of individual LBC loops.
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Affiliation(s)
| | - Asya Davidian
- Carnegie Institution for Science, Baltimore, MD, USA; Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, MD, USA.
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23
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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: 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: 03/22/2021] [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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24
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Lamb TD. Analysis of Paralogons, Origin of the Vertebrate Karyotype, and Ancient Chromosomes Retained in Extant Species. Genome Biol Evol 2021; 13:6159445. [PMID: 33751101 PMCID: PMC8040251 DOI: 10.1093/gbe/evab044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 01/06/2023] Open
Abstract
A manually curated set of ohnolog families has been assembled, for seven species of bony vertebrates, that includes 255 four-member families and 631 three-member families, encompassing over 2,900 ohnologs. Across species, the patterns of chromosomes upon which the ohnologs reside fall into 17 distinct categories. These 17 paralogons reflect the 17 ancestral chromosomes that existed in our chordate ancestor immediately prior to the two rounds of whole-genome duplication (2R-WGD) that occurred around 600 Ma. Within each paralogon, it has now been possible to assign those pairs of ohnologs that diverged from each other at the first round of duplication, through analysis of the molecular phylogeny of four-member families. Comparison with another recent analysis has identified four apparently incorrect assignments of pairings following 2R, along with several omissions, in that study. By comparison of the patterns between paralogons, it has also been possible to identify nine chromosomal fusions that occurred between 1R and 2R, and three chromosomal fusions that occurred after 2R, that generated an ancestral bony-vertebrate karyotype comprising 47 chromosomes. At least 27 of those ancestral bony-vertebrate chromosomes can, in some extant species, be shown not to have undergone any fusion or fission events. Such chromosomes are here termed “archeochromosomes,” and have each survived essentially unchanged in their content of genes for some 400 Myr. Their utility lies in their potential for tracking the various fusion and fission events that have occurred in different lineages throughout the expansion of bony vertebrates.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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25
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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: 4] [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: 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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Liu J, Wang Z, Li J, Xu L, Liu J, Feng S, Guo C, Chen S, Ren Z, Rao J, Wei K, Chen Y, Jarvis ED, Zhang G, Zhou Q. A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Res 2021; 31:497-511. [PMID: 33408157 PMCID: PMC7919449 DOI: 10.1101/gr.271569.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023]
Abstract
Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo 315100, China
| | - Jing Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Jiaqi Liu
- Wuhan Gooalgene Technology Company, Wuhan 430070, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Chunxue Guo
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Shengchan Chen
- Longteng Ecological Culture Company, Limited, Zhashui 711400, China
| | - Zhanjun Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jinpeng Rao
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Kai Wei
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Yuezhou Chen
- Jianzhou Poultry Industry Company, Limited, Yong'an 366000, China
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, New York 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes). BMC Ecol Evol 2021; 21:8. [PMID: 33514318 PMCID: PMC7853317 DOI: 10.1186/s12862-020-01737-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/14/2020] [Indexed: 11/12/2022] Open
Abstract
Background The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes. Conclusion Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.
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Affiliation(s)
- Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil
| | - Cristovam Guerreiro Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal do Pará, Campus de Bragança, Avenida dos Bragançanos s/nº, Bragança, Pará, 68600-000, Brazil
| | - Patricia Caroline Mary O Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridgeshire, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, PCT-Guamá, Terreno 11, Belém, Pará, 66075-750, Brazil.
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Li J, Zhang J, Liu J, Zhou Y, Cai C, Xu L, Dai X, Feng S, Guo C, Rao J, Wei K, Jarvis ED, Jiang Y, Zhou Z, Zhang G, Zhou Q. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. Gigascience 2021; 10:giaa142. [PMID: 33406261 PMCID: PMC7787181 DOI: 10.1093/gigascience/giaa142] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/31/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. RESULTS A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. CONCLUSIONS Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.
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Affiliation(s)
- Jing Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 5 Nobels väg, Stockholm 17177, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
| | - Yang Zhou
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Cheng Cai
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Luohao Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China
| | - Shaohong Feng
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Chunxue Guo
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Jinpeng Rao
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
| | - Kai Wei
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Ave, NY 10065, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, 12 Zhong Guan Cun Da Jie, Beijing, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 10 Nørregade, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming 650223, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
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30
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Chromosomal Analysis in Crotophaga ani (Aves, Cuculiformes) Reveals Extensive Genomic Reorganization and an Unusual Z-Autosome Robertsonian Translocation. Cells 2020; 10:cells10010004. [PMID: 33375072 PMCID: PMC7822047 DOI: 10.3390/cells10010004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023] Open
Abstract
Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.
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31
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He C, Zhao L, Xiao L, Xu K, Ding J, Zhou H, Zheng Y, Han C, Akinyemi F, Luo H, Yang L, Luo L, Yuan H, Lu X, Meng H. Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant. Mol Ecol Resour 2020; 21:897-911. [PMID: 33188724 DOI: 10.1111/1755-0998.13296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 12/30/2022]
Abstract
The common pheasant Phasianus colchicus, belonging to the order Galliformes and family Phasianidae, is the most widespread species. Despite a long history of captivity, the domestication of this bird is still at a preliminary stage. Recently, the demand for accelerating its transformation to poultry for meat and egg production has been increasing. In this study, we assembled high quality, chromosome scale genome of the common pheasant by using PacBio long reads, next-generation short reads, and Hi-C technology. The primary assembly has contig N50 size of 1.33 Mb and scaffold N50 size of 59.46 Mb, with a total size of 0.99 Gb, resolving most macrochromosomes into single scaffolds. A total of 23,058 genes and 10.71 Mb interspersed repeats were identified, constituting 30.31% and 10.71% of the common pheasant genome, respectively. Our phylogenetic analysis revealed that the common pheasant shared common ancestors with turkey about 24.7-34.5 million years ago (Ma). Rapidly evolved gene families, as well as branch-specific positively selected genes, indicate that calcium-related genes are potentially related to the adaptive and evolutionary change of the common pheasant. Interestingly, we found that the common pheasant has a unique major histocompatibility complex B locus (MHC-B) structure: three major inversions occurred in the sequence compared with chicken MHC-B. Furthermore, we detected signals of selection in five breeds of domestic common pheasant, several of which are production-oriented.
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Affiliation(s)
- Chuan He
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lele Zhao
- Shanghai Animal Disease Control Center, Shanghai, China
| | - Lu Xiao
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Xu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jinmei Ding
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Zhou
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuming Zheng
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chengxiao Han
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Fisayo Akinyemi
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Huaixi Luo
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingyu Yang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxiao Luo
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyan Yuan
- Shanghai Xinhao Rare Poultry Breeding Co. Ltd., Shanghai, China
| | - Xuelin Lu
- Shanghai Animal Disease Control Center, Shanghai, China
| | - He Meng
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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32
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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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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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34
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del Priore L, Pigozzi MI. MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds. PLoS One 2020; 15:e0240245. [PMID: 33017431 PMCID: PMC7535058 DOI: 10.1371/journal.pone.0240245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/22/2020] [Indexed: 11/21/2022] Open
Abstract
Crossover rates and localization are not homogeneous throughout the genomes. Along the chromosomes of almost all species, domains with high crossover rates alternate with domains where crossover rates are significantly lower than the genome-wide average. The distribution of crossovers along chromosomes constitutes the recombination landscape of a given species and can be analyzed at broadscale using immunostaining of the MLH1 protein, a component of mature recombination nodules found on synaptonemal complexes during pachytene. We scored the MLH1 foci in oocytes of the chicken and the guinea fowl and compared their frequencies in the largest bivalents. The average autosomal number of foci is 62 in the chicken and 44 in the guinea fowl. The lower number in the guinea fowl responds to the occurrence of fewer crossovers in the six largest bivalents, where most MLH1 foci occur within one-fifth of the chromosome length with high polarization towards opposite ends. The skewed distribution of foci in the guinea fowl contrast with the more uniform distribution of numerous foci in the chicken, especially in the four largest bivalents. The crossover distribution observed in the guinea fowl is unusual among Galloanserae and also differs from other, more distantly related birds. We discussed the current evidence showing that the shift towards crossover localization, as observed in the guinea fowl, was not a unique event but also occurred at different moments of bird evolution. A comparative analysis of genome-wide average recombination rates in birds shows variations within narrower limits compared to mammals and the absence of a phylogenetic trend.
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Affiliation(s)
- Lucía del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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35
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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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Ma S, Liu H, Sun W, Mustafa A, Xi Y, Pu F, Li Y, Han C, Bai L, Hua H. Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds. BMC Evol Biol 2020; 20:85. [PMID: 32664916 PMCID: PMC7362505 DOI: 10.1186/s12862-020-01654-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Background ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds. Results We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution. Conclusions We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.
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Affiliation(s)
- Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China.
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Fajun Pu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - He Hua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
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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: 9] [Impact Index Per Article: 2.3] [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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38
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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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39
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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: 30] [Impact Index Per Article: 7.5] [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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40
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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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41
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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: 0] [Impact Index Per Article: 0] [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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42
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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: 5] [Impact Index Per Article: 1.3] [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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43
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Zlotina A, Maslova A, Pavlova O, Kosyakova N, Al-Rikabi A, Liehr T, Krasikova A. New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing. Front Genet 2020; 11:57. [PMID: 32127797 PMCID: PMC7038795 DOI: 10.3389/fgene.2020.00057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
Giant lampbrush chromosomes (LBCs) typical for growing oocytes of various animal species are characterized by a specific chromomere-loop appearance and massive transcription. Chromomeres represent universal units of chromatin packaging at LBC stage. While quite good progress has been made in investigation of LBCs structure and function, chromomere organization still remains poorly understood. To extend our knowledge on chromomere organization, we applied microdissection to chicken LBCs. In particular, 31 and 5 individual chromomeres were dissected one by one along the macrochromosome 4 and one microchromosome, respectively. The data on genomic context of individual chromomeres was obtained by high-throughput sequencing of the corresponding chromomere DNA. Alignment of adjacent chromomeres to chicken genome assembly provided information on chromomeres size and genomic boarders, indicating that prominent marker chromomeres are about 4–5 Mb in size, while common chromomeres of 1.5–3.5 Mb. Analysis of genomic features showed that the majority of chromomere-loop complexes combine gene-dense and gene-poor regions, while massive loopless DAPI-positive chromomeres lack genes and are remarkably enriched with different repetitive elements. Finally, dissected LBC chromomeres were compared with chromatin domains (topologically associated domains [TADs] and A/B-compartments), earlier identified by Hi-C technique in interphase nucleus of chicken embryonic fibroblasts. Generally, the results obtained suggest that chromomeres of LBCs do not correspond unambiguously to any type of well-established spatial domains of interphase nucleus in chicken somatic cells.
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Affiliation(s)
- Anna Zlotina
- Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Olga Pavlova
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Alla Krasikova
- Saint Petersburg State University, Saint Petersburg, Russia
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44
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Hagen IJ, Lien S, Billing AM, Elgvin TO, Trier C, Niskanen AK, Tarka M, Slate J, Sætre G, Jensen H. A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. Mol Ecol Resour 2020; 20:544-559. [DOI: 10.1111/1755-0998.13134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 12/10/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Ingerid J. Hagen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - Anna M. Billing
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Tore O. Elgvin
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Cassandra Trier
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Maja Tarka
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Department of Biology Lund University Lund Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences University of Sheffield Western Bank Sheffield UK
| | - Glenn‐Peter Sætre
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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Maugars G, Nourizadeh-Lillabadi R, Weltzien FA. New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts. Front Endocrinol (Lausanne) 2020; 11:538196. [PMID: 33071966 PMCID: PMC7541902 DOI: 10.3389/fendo.2020.538196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
In order to improve our understanding of melatonin signaling, we have reviewed and revised the evolutionary history of melatonin receptor genes (mtnr) in vertebrates. All gnathostome mtnr genes have a conserved gene organization with two exons, except for mtnr1b paralogs of some teleosts that show intron gains. Phylogeny and synteny analyses demonstrate the presence of four mtnr subtypes, MTNR1A, MTNR1B, MTNR1C, MTNR1D that arose from duplication of an ancestral mtnr during the vertebrate tetraploidizations (1R and 2R). In tetrapods, mtnr1d was lost, independently, in mammals, in archosaurs and in caecilian amphibians. All four mtnr subtypes were found in two non-teleost actinopterygian species, the spotted gar and the reedfish. As a result of teleost tetraploidization (3R), up to seven functional mtnr genes could be identified in teleosts. Conservation of the mtnr 3R-duplicated paralogs differs among the teleost lineages. Synteny analysis showed that the mtnr1d was conserved as a singleton in all teleosts resulting from an early loss after tetraploidization of one of the teleost 3R and salmonid 4R paralogs. Several teleosts including the eels and the piranha have conserved both 3R-paralogs of mtnr1a, mtnr1b, and mtnr1c. Loss of one of the 3R-paralogs depends on the lineage: mtnr1ca was lost in euteleosts whereas mtnr1cb was lost in osteoglossomorphs and several ostariophysians including the zebrafish. We investigated the tissue distribution of mtnr expression in a large range of tissues in medaka. The medaka has conserved the four vertebrate paralogs, and these are expressed in brain and retina, and, differentially, in peripheral tissues. Photoperiod affects mtnr expression levels in a gene-specific and tissue-specific manner. This study provides new insights into the repertoire diversification and functional evolution of the mtnr gene family in vertebrates.
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Malinovskaya LP, Tishakova KV, Volkova NA, Torgasheva AA, Tsepilov YA, Borodin PM. Interbreed variation in meiotic recombination rate and distribution in the domestic chicken Gallus gallus. Arch Anim Breed 2019; 62:403-411. [PMID: 31807651 PMCID: PMC6859913 DOI: 10.5194/aab-62-403-2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/21/2019] [Indexed: 11/11/2022] Open
Abstract
The efficiency of natural and artificial selection is critically dependent on the recombination rate. However, interbreed and individual variation in recombination rate in poultry remains unknown. Conventional methods of analysis of recombination such as genetic linkage analysis, sperm genotyping and chiasma count at lampbrush chromosomes are expensive and time-consuming. In this study, we analyzed the number and distribution of recombination nodules in spermatocytes of the roosters of six chicken breeds using immunolocalization of key proteins involved in chromosome pairing and recombination. We revealed significant effects of breed ( R 2 = 0.17 ; p < 0.001 ) and individual ( R 2 = 0.28 ; p < 0.001 ) on variation in the number of recombination nodules. Both interbreed and individual variations in recombination rate were almost entirely determined by variation in recombination density on macrochromosomes, because almost all microchromosomes in each breed had one recombination nodule. Despite interbreed differences in the density of recombination nodules, the patterns of their distribution along homologous chromosomes were similar. The breeds examined in this study showed a correspondence between the age of the breed and its recombination rate. Those with high recombination rates (Pervomai, Russian White and Brahma) are relatively young breeds created by crossing several local breeds. The breeds displaying low recombination rate are ancient local breeds: Cochin (Indo-China), Brown Leghorn (Tuscany, Italy) and Russian Crested (the European part of Russia).
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Affiliation(s)
- Lyubov P Malinovskaya
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Katerina V Tishakova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Anna A Torgasheva
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yakov A Tsepilov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Pavel M Borodin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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48
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Gunski RJ, Kretschmer R, Santos de Souza M, de Oliveira Furo I, Barcellos SA, Costa AL, Cioffi MB, de Oliveira EHC, Del Valle Garnero A. Evolution of Bird Sex Chromosomes Narrated by Repetitive Sequences: Unusual W Chromosome Enlargement in Gallinula melanops (Aves: Gruiformes: Rallidae). Cytogenet Genome Res 2019; 158:152-159. [PMID: 31272100 DOI: 10.1159/000501381] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Among birds, species with the ZZ/ZW sex determination system generally show significant differences in morphology and size between the Z and W chromosomes (with the W usually being smaller than the Z). In the present study, we report for the first time the karyotype of the spot-flanked gallinule (Gallinula melanops) by means of classical and molecular cytogenetics. The spot-flanked gallinule has 2n = 80 (11 pairs of macrochromosomes and 29 pairs of microchromosomes) with an unusual W chromosome that is larger than the Z. Besides being totally heterochromatic, it has a secondary constriction in its long arm corresponding to the nucleolar organizer region, as confirmed by both silver staining and mapping of 18S rDNA probes. This is an unprecedented fact among birds. Additionally, 18S rDNA sites were also observed in 6 microchromosomes, while 5S rDNA was found in just 1 microchromosomal pair. Seven out of the 11 used microsatellite sequences were found to be accumulated in microchromosomes, and 6 microsatellite sequences were found in the W chromosome. In addition to the involvement of heterochromatin and repetitive DNAs in the differentiation of the large W chromosome, the results also show an alternative scenario that highlights the plasticity that shapes the evolutionary history of bird sex chromosomes.
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Mahiddine-Aoudjit L, Boucekkine O, Ladjali-Mohammedi K. Banding cytogenetics of the vulnerable species Houbara bustard (Otidiformes) and comparative analysis with the Domestic fowl. COMPARATIVE CYTOGENETICS 2019; 13:1-17. [PMID: 30701036 PMCID: PMC6351704 DOI: 10.3897/compcytogen.v13i1.30660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
The Houbara bustard Chlamydotisundulata (Jacquin, 1784) is an emblematic and endangered bird of steppes and desert spaces of North Africa. This species belonging to Otidiformes is recognized as vulnerable by the International Union for Nature Conservation. The critical situation of this species and the revision of its classification on the tree of birds encouraged the authors to start accumulating chromosome data. For that, we propose the GTG- and RBG-banded karyotypes of the Houbara bustard prepared from primary fibroblast cell cultures. The first eight autosomal pairs and sex chromosomes have been described and compared to those of the domestic fowl Gallusdomesticus (Linnaeus, 1758). The diploid number has been estimated as 78 chromosomes with 8 macrochromosomes pairs and 30 microchromosomes pairs, attesting of the stability of chromosome number in avian karyotypes. The description of the karyotype of the Houbara is of crucial importance for the management of the reproduction of this species in captivity. It can be used as a reference in the detection of chromosomal abnormalities, which would be responsible of the early embryonic mortalities.
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Affiliation(s)
- Leila Mahiddine-Aoudjit
- University of Sciences and Technology Houari Boumediene (USTHB), Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneAlgiersAlgeria
- University of M’hamed Bougara of Boumerdes, Faculty of Sciences, Department of Biology, Avenue de l’Indépendance, 35 000 Boumerdès, AlgeriaUniversity of M’hamed Bougara of BoumerdesBoumerdèsAlgeria
| | - Ouahida Boucekkine
- The General Direction of Forests, Ben Aknoun, Algiers, AlgeriaThe General Direction of ForestsAlgiersAlgeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene (USTHB), Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneAlgiersAlgeria
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50
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Corcoran P, Gossmann TI, Barton HJ, Slate J, Zeng K. Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species. Genome Biol Evol 2018; 9:2987-3007. [PMID: 29045655 PMCID: PMC5714183 DOI: 10.1093/gbe/evx213] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 02/06/2023] Open
Abstract
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.
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Affiliation(s)
- Pádraic Corcoran
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | | | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
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