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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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Clemente L, Mazzoleni S, Pensabene Bellavia E, Augstenová B, Auer M, Praschag P, Protiva T, Velenský P, Wagner P, Fritz U, Kratochvíl L, Rovatsos M. Interstitial Telomeric Repeats Are Rare in Turtles. Genes (Basel) 2020; 11:genes11060657. [PMID: 32560114 PMCID: PMC7348932 DOI: 10.3390/genes11060657] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/18/2023] Open
Abstract
Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.
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Affiliation(s)
- Lorenzo Clemente
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Eleonora Pensabene Bellavia
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Markus Auer
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | | | | | - Petr Velenský
- Prague Zoological Garden, 17100 Prague, Czech Republic;
| | | | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
- Correspondence:
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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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Furo IDO, Kretschmer R, O’Brien PCM, Pereira JC, Ferguson-Smith MA, de Oliveira EHC. Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: Aramides cajaneus and Psophia viridis. Genes (Basel) 2020; 11:E307. [PMID: 32183220 PMCID: PMC7140812 DOI: 10.3390/genes11030307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022] Open
Abstract
Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Post-Graduation Program in Genetics and Molecular Biology, Federal University of Pará, Belém, Pará 66075-110, Brazil;
- Laboratory of Tissue Culture and Cytogenetics, SAMAM, Evandro Chagas Institute, Ananindeua, Pará 67030-000, Brazil
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Rafael Kretschmer
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
- Pos-Graduation Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 91509-900, Brazil
| | - Patrícia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Jorge C. Pereira
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Cambridge CB3 0ES, UK; (R.K.); (P.C.M.O.); (J.C.P.); (M.A.F.-S.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratory of Tissue Culture and Cytogenetics, SAMAM, Evandro Chagas Institute, Ananindeua, Pará 67030-000, Brazil
- Faculty of Natural Sciences, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará 66075-110, Brazil
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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10040113] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.
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Chromosome Painting in Neotropical Long- and Short-Tailed Parrots (Aves, Psittaciformes): Phylogeny and Proposal for a Putative Ancestral Karyotype for Tribe Arini. Genes (Basel) 2018; 9:genes9100491. [PMID: 30309041 PMCID: PMC6210594 DOI: 10.3390/genes9100491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
Most Neotropical Psittacidae have a diploid number of 2n = 70, and a dichotomy in chromosome patterns. Long-tailed species have biarmed macrochromosomes, while short-tailed species have telo/acrocentric macrochromosomes. However, the use of chromosome painting has demonstrated that karyotype evolution in Psittacidae includes a high number of inter/intrachromosomal rearrangements. To determine the phylogeny of long- and short-tailed species, and to propose a putative ancestral karyotype for this group, we constructed homology maps of Pyrrhura frontalis (PFR) and Amazona aestiva (AAE), belonging to the long- and short-tailed groups, respectively. Chromosomes were analyzed by conventional staining and fluorescent in situ hybridization using whole chromosome paints of Gallusgallus and Leucopternis albicollis. Conventional staining showed a karyotype with 2n = 70 in both species, with biarmed macrochromosomes in PFR and telo/acrocentric chromosomes in AAE. Comparison of the results with the putative avian ancestral karyotype (PAK) showed fusions in PFR of PAK1p/PAK4q (PFR1) and PAK6/PAK7 (PFR6) with a paracentric inversion in PFR6. However, in AAE, there was only the fusion between PAK6/7 (AAE7) with a paracentric inversion. Our results indicate that PFR retained a more basal karyotype than long-tailed species previously studied, and AAE a more basal karyotype for Neotropical Psittacidae analyzed so far.
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Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting. Genes (Basel) 2018; 9:genes9040181. [PMID: 29584697 PMCID: PMC5924523 DOI: 10.3390/genes9040181] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/08/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.
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