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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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Human Achilles tendon mechanical behavior is more strongly related to collagen disorganization than advanced glycation end-products content. Sci Rep 2021; 11:24147. [PMID: 34921194 PMCID: PMC8683434 DOI: 10.1038/s41598-021-03574-4] [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: 05/10/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
Diabetes is associated with impaired tendon homeostasis and subsequent tendon dysfunction, but the mechanisms underlying these associations is unclear. Advanced glycation end-products (AGEs) accumulate with diabetes and have been suggested to alter tendon function. In vivo imaging in humans has suggested collagen disorganization is more frequent in individuals with diabetes, which could also impair tendon mechanical function. The purpose of this study was to examine relationships between tendon tensile mechanics in human Achilles tendon with accumulation of advanced glycation end-products and collagen disorganization. Achilles tendon specimens (n = 16) were collected from individuals undergoing lower extremity amputation or from autopsy. Tendons were tensile tested with simultaneous quantitative polarized light imaging to assess collagen organization, after which AGEs content was assessed using a fluorescence assay. Moderate to strong relationships were observed between measures of collagen organization and tendon tensile mechanics (range of correlation coefficients: 0.570-0.727), whereas no statistically significant relationships were observed between AGEs content and mechanical parameters (range of correlation coefficients: 0.020-0.210). Results suggest that the relationship between AGEs content and tendon tensile mechanics may be masked by multifactorial collagen disorganization at larger length scales (i.e., the fascicle level).
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Carvalho CA, Furo IO, O’Brien PCM, Pereira J, O’Connor RE, Griffin D, Ferguson-Smith M, de Oliveira EHC. Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes. PLoS One 2021; 16:e0259905. [PMID: 34793511 PMCID: PMC8601422 DOI: 10.1371/journal.pone.0259905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022] Open
Abstract
Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype, based on homology with GGA. Fissions occurred mainly in syntenic groups homologous to GGA1-GGA5. On the other hand, the majority of the microchromosomes were found fused to other chromosomal elements in STY, indicating these rearrangements played an important role in the reduction of the 2n to 68. Comparison with hybridization pattern of the Japanese-Mountain-Eagle (Nisaetus nipalensis orientalis), the only Aquilinae analyzed by comparative chromosome painting previously, did not reveal any synapomorphy that could represent a chromosome signature to this subfamily. Therefore, conclusions about karyotype evolution in Aquilinae require additional painting studies.
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Affiliation(s)
- Carlos A. Carvalho
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Ivanete O. Furo
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Universidade Federal Rural da Amazônia (UFRA) Laboratório de Reprodução Animal (LABRAC), Parauapebas, Pará, Brazil
| | | | - Jorge Pereira
- Animal and Veterinary Research Center, Universidade de Trá-os-Montes e Alto douro, Vila Real, Portugal
| | | | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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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, 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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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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Hyperglycemia compromises Rat Cortical Bone by Increasing Osteocyte Lacunar Density and Decreasing Vascular Canal Volume. Commun Biol 2020; 3:20. [PMID: 31925331 PMCID: PMC6952406 DOI: 10.1038/s42003-019-0747-1] [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: 08/06/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
Uncontrolled diabetes is associated with increased risk of bony fractures. However, the mechanisms have yet to be understood. Using high-resolution synchrotron micro-CT, we calculated the changes in the microstructure of femoral cortices of streptozotocin-induced hyperglycemic (STZ) Wistar Albino rats and tested the mechanical properties of the mineralized matrix by nanoindentation. Total lacunar volume of femoral cortices increased in STZ group due to a 9% increase in lacunar density. However, total vascular canal volume decreased in STZ group due to a remarkable decrease in vascular canal diameter (7 ± 0.3 vs. 8.5 ± 0.4 µm). Osteocytic territorial matrix volume was less in the STZ group (14,908 ± 689 µm3) compared with healthy controls (16,367 ± 391 µm3). In conclusion, hyperglycemia increased cellularity and lacunar density, decreased osteocyte territorial matrix, and reduced vascular girth, in addition to decreasing matrix mechanical properties in the STZ group when compared with euglycemic controls. Birol Ay et al. use high-resolution synchrotron radiation micro-CT to calculate the changes in the microstructure of femoral cortices in STZ-induced hyperglycemic rats. They show that hyperglycemia increases lacunar density due to a reduction in osteocytic territorial matrix volume but decreases total vascular canal volume due to a decrease in canal diameter.
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Seligmann ICA, Furo IO, Dos Santos MS, Tagliarini MM, Araujo CCD, O''Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Chromosome Painting in Two Brazilian Stork Species with Different Diploid Numbers. Cytogenet Genome Res 2019; 159:32-38. [PMID: 31542782 DOI: 10.1159/000503019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2019] [Indexed: 11/19/2022] Open
Abstract
Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.
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Gerbault-Seureau M, Fuchs J, Dutrillaux B. High BrdU Sensitivity of Passeriformes Chromosomes: Conservation of BrdU-Sensitive Fragile Sites on Their Z Chromosomes during Evolution. Cytogenet Genome Res 2019; 157:158-165. [PMID: 30974432 DOI: 10.1159/000499590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2018] [Indexed: 12/29/2022] Open
Abstract
Amongst 15 bird species, representative of 7 orders, recurrent breakages evocating the presence of fragile sites were detected in the chromosomes of the 5 species belonging to Passeriformes. These breaks appeared when 5-bromodeoxyuridine (BrdU) was added to the cell culture medium at a dose inefficient for inducing chromosome structure alterations in other birds and mammals. They involved, similarly in male and female, 3 loci on the Z chromosome of 3 Turdus species (Turdidae). Labeling by BrdU antibody confirmed the correlation between BrdU incorporation into DNA and breakage, especially around and in the sites of breakage. Thus, 3 BrdU-sensitive fragile sites were present in the Z chromosomes of these birds. Three fragile sites were also detected at different locations in the Z chromosomes of the European robin (Erithacus rubecula, Muscicapidae), suggesting that a structural rearrangement occurred during the evolution of Turdidae and Muscicapidae. Chromosome banding confirmed this interpretation. Finally, in the more distantly related species Parus major (Paridae), the almost acrocentric Z chromosome displayed a single BrdU-sensitive fragile site in its short arm, and the W appeared to be pulverized by BrdU incorporation. Although it cannot be excluded that the BrdU-sensitive fragile sites may be involved in rearrangements, their conservation in many species, and possibly all Passeriformes, provides evidence that they do not constitute a pejorative character during evolution.
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Dos Santos MS, Furo IO, Tagliarini MM, Kretschmer R, O''Brien PCM, Ferguson-Smith MA, de Oliveira EHC. The Karyotype of the Hoatzin (Opisthocomus hoazin) - A Phylogenetic Enigma of the Neornithes. Cytogenet Genome Res 2018; 156:158-164. [PMID: 30472715 DOI: 10.1159/000494707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 11/19/2022] Open
Abstract
The hoatzin (Opisthocomus hoazin Müller, 1776) is a folivorous bird, endemic to the Amazonian region. It presents some unique characteristics, including wing claws and foregut fermentation, which make its phylogenetic relationship to other birds difficult to determine. There have been various attempts to place it among the Galliformes, Gruiformes, Musophagiformes, Cuculiformes, and Charadriiformes, but phylogenetic analyses always show low supporting values. Nowadays, the hoatzin is included in the monotypic order Opisthocomiformes, but the relationship of this order to other groups of birds is still unclear. Although its karyotype resembles the typical avian model, fissions of the syntenic groups corresponding to chicken chromosomes 1 and 2 and 2 fusions were found. The presence of 18S rDNA clusters in 2 pairs of microchromosomes is another derived character. Hence, different rearrangements were detected in the karyotype of the hoatzin, indicating it has been derived from the putative ancestral karyotype by the occurrence of fissions and fusions. However, as these rearrangements are not exclusive to O. hoazin, they do not clarify the phylogenetic position of this enigmatic species.
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Chromosome 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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Degrandi TM, de Oliveira JCP, Soares ADA, Ledesma MA, Hass I, Garnero ADV, Gunski RJ. Karyotype description and comparative analysis in Ringed Kingfisher and Green Kingfisher (Coraciiformes, Alcedinidae). COMPARATIVE CYTOGENETICS 2018; 12:163-170. [PMID: 29780444 PMCID: PMC5958172 DOI: 10.3897/compcytogen.v12i2.23883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Kingfishers comprise about 115 species of the family Alcedinidae, and are an interesting group for cytogenetic studies, for they are among birds with most heterogeneous karyotypes. However, cytogenetics knowledge in Kingfishers is extremely limited. Thus, the aim of this study was to describe the karyotype structure of the Ringed Kingfisher (Megaceryle torquata Linnaeus, 1766) and Green Kingfisher (Chloroceryle americana Gmelin, 1788) and also compare them with related species in order to identify chromosomal rearrangements. The Ringed Kingfisher presented 2n = 84 and the Green Kingfisher had 2n = 94. The increase of the chromosome number in the Green Kingfisher possibly originated by centric fissions in macrochromosomes. In addition, karyotype comparisons in Alcedinidae show a heterogeneity in the size and morphology of macrochromosomes, and chromosome numbers ranging from 2n = 76 to 132. Thus, it is possible chromosomal fissions in macrochromosomes resulted in the increase of the diploid number, whereas chromosome fusions have originated the karyotypes with low diploid number.
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Affiliation(s)
- Tiago Marafiga Degrandi
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | | | - Amanda de Araújo Soares
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | | | - Iris Hass
- Universidade Federal do Paraná, Av. Coronel Francisco Heráclito dos Santos, s/n, Curitiba, Paraná, Brazil
| | - Analía del Valle Garnero
- Universidade Federal do Pampa, Rua Aluízio Barros Macedo, BR 290, km 423 Bairro Piraí, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Universidade Federal do Pampa, Rua Aluízio Barros Macedo, BR 290, km 423 Bairro Piraí, São Gabriel, Rio Grande do Sul, Brazil
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13
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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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dos Santos MDS, Kretschmer R, Frankl-Vilches C, Bakker A, Gahr M, O´Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary. PLoS One 2017; 12:e0170997. [PMID: 28129381 PMCID: PMC5271350 DOI: 10.1371/journal.pone.0170997] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.
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Affiliation(s)
| | - Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Patricia C. M. O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Belém, Brazil
- * E-mail:
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Abstract
Myo-inositol and phosphatidylinositol(s) play a pivotal function in many metabolic pathways that, if impaired, impact unfavorably on human health. This review analyzes several experimental and clinical investigations regarding the involvement of this class of molecules in physiological and pathological situations, with a major focus on thyroid. Central issues are the relationship between phosphatidylinositol and thyrotropin (TSH) signaling on one hand, and phosphatydylinositol and autoimmunity on the other hand. Other issues are the consequences of malfunction of some receptors, such as those ones for TSH (TSHR), insulin (IR) and insulin-like growth factor-1 (IGF-1R), or the connection between serum TSH concentrations and insulin resistance. Also covered are insulin resistance, metabolic syndrome and their allied disorders (diabetes, polycystic ovary syndrome [PCOS]), autoimmunity and certain malignancies, with their reciprocal links. Myoinositol has promising therapeutic potential. Appreciation of the inositol pathways involved in certain disorders, as mentioned in this review, may stimulate researchers to envisage additional therapeutic applications.
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Affiliation(s)
- Salvatore Benvenga
- Department of Clinical and Experimental Medicine, University of Messina School of Medicine, via Consolare Valeria, 1, 98125, Messina, Italy.
- Master Program of Childhood, Adolescence and Women's Endocrine Health, University of Messina School of Medicine, via Consolare Valeria, 1, 98125, Messina, Italy.
- Interdepartmental Program of Molecular & Clinical Endocrinology, and Women's Endocrine Health, University hospital, Padiglione H, 4 piano, Policlinico G. Martino, 98125, Messina, Italy.
| | - Alessandro Antonelli
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
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Nie W, O'Brien PCM, Fu B, Wang J, Su W, He K, Bed'Hom B, Volobouev V, Ferguson-Smith MA, Dobigny G, Yang F. Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes. BMC Evol Biol 2015; 15:205. [PMID: 26409465 PMCID: PMC4583764 DOI: 10.1186/s12862-015-0484-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/14/2015] [Indexed: 12/03/2022] Open
Abstract
Background Previous cross-species painting studies with probes from chicken (Gallus gallus) chromosomes 1–10 and a paint pool of nineteen microchromosomes have revealed that the drastic karyotypic reorganization in Accipitridae is due to extensive synteny disruptions and associations. However, the number of synteny association events and identities of microchromosomes involved in such synteny associations remain undefined, due to the lack of paint probes derived from individual chicken microchromosomes. Moreover, no genome-wide homology map between Accipitridae species and other avian species with atypical karyotype organization has been reported till now, and the karyotype evolution within Accipitriformes remains unclear. Results To delineate the synteny-conserved segments in Accipitridae, a set of painting probes for the griffon vulture, Gyps fulvus (2n = 66) was generated from flow-sorted chromosomes. Together with previous generated probes from the stone curlew, Burhinus oedicnemus (2n = 42), a Charadriiformes species with atypical karyotype organization, we conducted multidirectional chromosome painting, including reciprocal chromosome painting between B. oedicnemus and G. fulvus and cross-species chromosome painting between B. oedicnemus and two accipitrid species (the Himalayan griffon, G. himalayensis 2n = 66, and the common buzzard, Buteo buteo, 2n = 68). In doing so, genome-wide homology maps between B. oedicnemus and three Accipitridae species were established. From there, a cladistic analysis using chromosomal characters and mapping of chromosomal changes on a consensus molecular phylogeny were conducted in order to search for cytogenetic signatures for different lineages within Accipitriformes. Conclusion Our study confirmed that the genomes of the diurnal birds of prey, especially the genomes of species in Accipitriformes excluding Cathartidae, have been extensively reshuffled when compared to other bird lineages. The chromosomal rearrangements involved include both fusions and fissions. Our chromosome painting data indicated that the Palearctic common buzzard (BBU) shared several common chromosomal rearrangements with some Old World vultures, and was found to be more closely related to other Accipitridae than to Neotropical buteonine raptors from the karyotypic perspective. Using both a chromosome-based cladistic analysis as well as by mapping of chromosomal differences onto a molecular-based phylogenetic tree, we revealed a number of potential cytogenetic signatures that support the clade of Pandionidae (PHA) + Accipitridae. In addition, our cladistic analysis using chromosomal characters appears to support the placement of osprey (PHA) in Accipitridae. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0484-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Jinghuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Weiting Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, P R China.
| | - Bertrand Bed'Hom
- INRA, AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert-Bâtiment 320, 78352, Jouy-en-Josas Cedex, France.
| | - Vitaly Volobouev
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205 Origine, Structure et Evolution de la Biodiversité, 75005, Paris, France.
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France.
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Kretschmer R, Gunski RJ, Garnero ADV, Furo IDO, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Molecular cytogenetic characterization of multiple intrachromosomal rearrangements in two representatives of the genus Turdus (Turdidae, Passeriformes). PLoS One 2014; 9:e103338. [PMID: 25058578 PMCID: PMC4110018 DOI: 10.1371/journal.pone.0103338] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/27/2014] [Indexed: 01/16/2023] Open
Abstract
Turdus rufiventris and Turdus albicollis, two songbirds belonging to the family Turdidae (Aves, Passeriformes) were studied by C-banding, 18S rDNA, as well as the use of whole chromosome probes derived from Gallus gallus (GGA) and Leucopternis albicollis (LAL). They showed very similar karyotypes, with 2n = 78 and the same pattern of distribution of heterochromatic blocks and hybridization patterns. However, the analysis of 18/28S rDNA has shown differences in the number of NOR-bearing chromosomes and ribosomal clusters. The hybridization pattern of GGA macrochromosomes was similar to the one found in songbirds studied by Fluorescent in situ hybridization, with fission of GGA 1 and GGA 4 chromosomes. In contrast, LAL chromosome paintings revealed a complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) on chromosome 2, which corresponds to GGA1q. The first inversion changed the chromosomal morphology and the second and third inversions changed the order of chromosome segments. Karyotype analysis in Turdus revealed that this genus has derived characteristics in relation to the putative avian ancestral karyotype, highlighting the importance of using new tools for analysis of chromosomal evolution in birds, such as the probes derived from L. albicollis, which make it possible to identify intrachromosomal rearrangements not visible with the use of GGA chromosome painting solely.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Ivanete de Oliveira Furo
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil; Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil; Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil; Instiuto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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