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Naveira H, Rojo V, Gómez-Seoane I, Ferguson-Smith MA, Pereira JC, Martínez-Lage A. Chromosome evolution in Iberolacerta, a genus that deviates from the standard karyotype formula of Lacertidae. Genetica 2023; 151:267-279. [PMID: 37656321 PMCID: PMC10654178 DOI: 10.1007/s10709-023-00194-w] [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: 05/10/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
This paper describes the preparation of flow-sorted chromosome paints from the Iberian Rock lizard Iberolacerta monticola, exemplifying their subsequent use in cross-species comparisons of chromosome painting. We carried out comparative analyses of chromosome evolution in the congeneric species I. galani and I. bonnali, as well as in two other species of Lacertini (Lacerta schreiberi and Timon lepidus) whose sex chromosomes were also studied through comparative genomic hybridization. Most species of Lacertini possess a diplod number of 2n = 38, with 36 acrocentric macrochromosomes and 2 microchromosomes. However, the nine species included in the genus Iberolacerta do not possess microchromosomes. Furthermore, very conspicuous differences from the standard Lacertini karyotype were observed in the three Pyrenean species of this genus, which included several biarmed metacentrics and a Z1Z2W multiple sex-chromosome system. With the possible exception of L. schreiberi, all the species of the family Lacertidae described to date appear to share homologous Z chromosomes, which date back to the last common ancestor of the whole group. We provide conclusive evidence that L. schreiberi should no longer be considered an exception to this rule, and demonstrate that the loss of microchromosomes in Iberolacerta was produced by their fusion to a middle-sized chromosome. Furthermore, we show that the multiple sex-chromosome system of the Pyrenean species of Iberolacerta originated from the fusion of the ancestral W chromosome with one of the shortest autosomes, and provide additional evidence of the fast evolution of DNA sequences linked to the W chromosome in Lacertini.
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Affiliation(s)
- Horacio Naveira
- Grupo de Investigación en Bioloxía Evolutiva, Departamento de Bioloxía, Facultade de Ciencias, CICA, Universidade da Coruña, A Coruña, Spain.
| | | | - Iván Gómez-Seoane
- Grupo de Investigación en Terapia Celular y Medicina Regenerativa, INIBIC, Universidade da Coruña, A Coruña, Spain
| | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, UK
| | - Jorge C Pereira
- Animal and Veterinary Research Centre (CECAV), UTAD, AL 4AnimalS, Vila Real, Vila Real, Portugal
| | - Andrés Martínez-Lage
- Grupo de Investigación en Bioloxía Evolutiva, Departamento de Bioloxía, Facultade de Ciencias, CICA, Universidade da Coruña, A Coruña, Spain
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da Silva MJ, de Araújo Vieira AP, Galvão Cipriano FM, Dos Santos Cândido MR, de Oliveira EHC, Gimenez Pinheiro T, da Silva EL. The Karyotype of Salvator merianae (Squamata, Teiidae): Analyses by Classical and Molecular Cytogenetic Techniques. Cytogenet Genome Res 2020; 160:94-99. [PMID: 32062647 DOI: 10.1159/000506140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2020] [Indexed: 12/28/2022] Open
Abstract
In this study, we analyzed the karyotype of Salvator merianae (Teiidae) from the Brazilian semiarid region using different cytogenetic markers. Chromosomes were examined by classical (Giemsa and AgNOR staining) and molecular (FISH with ribosomal, telomeric, and microsatellite probes) cytogenetic approaches. S. merianae showed a diploid chromosome number of 2n = 38 (10 biarmed macrochromosomes + 28 microchromosomes). No sex-linked chromosome heteromorphisms were observed. Clusters of 18S/28S rDNA were localized in the terminal region of the long arm of pair 2. In addition to the typical telomeric signals, (TTAGGG)n repeats were detected in the pericentromeric region of some macrochromosome pairs, which might indicate the occurrence of chromosomal rearrangements via chromosome fusions. Hybridization signals of the microsatellite probes (GA)n, (GAA)n, and (GAG)n were uniformly distributed across all chromosomes, while (CA)n, (CAA)n, and (CAC)n produced brighter signals in the telomeric and pericentromeric regions of specific chromosome pairs. The comparison with previous studies demonstrates that, despite the wide distribution of S. merianae, the macrostructure organization of the karyotype remained unchanged, showing stability in diploid number and chromosome morphology.
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Little evidence for switches to environmental sex determination and turnover of sex chromosomes in lacertid lizards. Sci Rep 2019; 9:7832. [PMID: 31127134 PMCID: PMC6534595 DOI: 10.1038/s41598-019-44192-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022] Open
Abstract
Amniotes possess variability in sex determination, from environmental sex determination (ESD), where no sex chromosomes are present, to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Some evolutionary scenarios postulate high stability of differentiated sex chromosomes and rare transitions from GSD to ESD. However, sex chromosome turnovers and two independent transitions from highly differentiated ZZ/ZW sex chromosomes to ESD were previously reported in the lacertid lizards. Here, we examined the homology of sex chromosomes in the wide phylogenetic spectrum of lacertids and their outgroups by comparing gene copy numbers between sexes in genes previously found to be Z-specific in some lacertids. Our current sampling covers 45 species from 26 genera including lineages supposed to possess a derived sex determining systems. We found that all tested lacertids share homologous differentiated ZZ/ZW sex chromosomes, which were present already in their common ancestor living around 85 million years ago. These differentiated sex chromosomes are not present in amphisbaenians and teiid lizards, the close relatives of lacertids. Our study demonstrates how inaccuracies in data can influence the outcome of phylogenetic reconstructions of evolution of sex determination, in this case they overestimated the number of shifts from GSD to ESD and the rate in turnovers of sex chromosomes.
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Giovannotti M, Nisi Cerioni P, Rojo V, Olmo E, Slimani T, Splendiani A, Caputo Barucchi V. Characterization of a satellite DNA in the genera Lacerta andTimon(Reptilia, Lacertidae) and its role in the differentiation of the W chromosome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:83-95. [DOI: 10.1002/jez.b.22790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 12/04/2017] [Accepted: 01/09/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Verónica Rojo
- AllGenetics & Biology SL; Edificio CICA; Campus de Elviña s/n, A Coruña Spain
- Department of Molecular and Cell Biology; Evolutionary Biology Group (GIBE); Universidade da Coruña; A Fraga 10, A Coruña Spain
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Tahar Slimani
- Cadi Ayyad University; Faculty of Sciences Semlalia; Laboratory Biodiversity and Ecosystem Dynamics; Marrakech Morocco
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
- Consiglio Nazionale delle Ricerche; Istituto di Scienze Marine Sezione Pesca Marittima; Largo Fiera della Pesca; Ancona Italy
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Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits. Chromosome Res 2016; 23:441-61. [PMID: 26384818 DOI: 10.1007/s10577-015-9489-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberolacerta. These families showed different chromosomal locations, abundances, and evolutionary rates. Here, we extend the study of both satellite DNAs (satDNAs) to the remaining Iberolacerta species, with the aim to investigate the patterns of variability and factors influencing the evolution of these repetitive sequences. Our results revealed disparate patterns but also common traits in the evolutionary histories of these satellite families: (i) each satellite DNA is made up of a library of monomer variants or subfamilies shared by related species; (ii) species-specific profiles of satellite repeats are shaped by expansions and/or contractions of different variants from the library; (iii) different turnover rates, even among closely related species, result in great differences in overall sequence homogeneity and in concerted or non-concerted evolution patterns, which may not reflect the phylogenetic relationships among taxa. Contrasting turnover rates are possibly related to genomic constraints such as karyotype architecture and the interspersed organization of diverging repeat variants in satellite arrays. Moreover, rapid changes in copy number, especially in the centromeric HindIII satDNA, may have been associated with chromosomal rearrangements and even contributed to speciation within Iberolacerta.
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Altmanová M, Rovatsos M, Kratochvíl L, Johnson Pokorná M. Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12751 10.1080/11250000409356641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marie Altmanová
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Michail Rovatsos
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Lukáš Kratochvíl
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Martina Johnson Pokorná
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Rumburská 89 Liběchov Czech Republic
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Rovatsos M, Vukić J, Altmanová M, Johnson Pokorná M, Moravec J, Kratochvíl L. Conservation of sex chromosomes in lacertid lizards. Mol Ecol 2016; 25:3120-6. [DOI: 10.1111/mec.13635] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Jasna Vukić
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Jiří Moravec
- Department of Zoology; National Museum; Václavské nám. 68 115 79 Prague Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
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Carvalho NDM, Pinheiro VSS, Carmo EJ, Goll LG, Schneider CH, Gross MC. The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae. Cytogenet Genome Res 2016; 147:161-8. [PMID: 26867142 DOI: 10.1159/000443714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2015] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.
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Affiliation(s)
- Natalia D M Carvalho
- Laboratx00F3;rio de Citogenx00F4;mica Animal, Instituto de Cix00EA;ncias Biolx00F3;gicas, Universidade Federal do Amazonas, Manaus, Brazil
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Altmanová M, Rovatsos M, Kratochvíl L, Johnson Pokorná M. Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12751] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Marie Altmanová
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Michail Rovatsos
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Lukáš Kratochvíl
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
| | - Martina Johnson Pokorná
- Faculty of Science; Department of Ecology; Charles University in Prague; Viničná 7 Praha 2 Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Rumburská 89 Liběchov Czech Republic
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Female heterogamety in Madagascar chameleons (Squamata: Chamaeleonidae: Furcifer): differentiation of sex and neo-sex chromosomes. Sci Rep 2015; 5:13196. [PMID: 26286647 PMCID: PMC4541320 DOI: 10.1038/srep13196] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/14/2015] [Indexed: 12/26/2022] Open
Abstract
Amniotes possess variability in sex determining mechanisms, however, this diversity is still only partially known throughout the clade and sex determining systems still remain unknown even in such a popular and distinctive lineage as chameleons (Squamata: Acrodonta: Chamaeleonidae). Here, we present evidence for female heterogamety in this group. The Malagasy giant chameleon (Furcifer oustaleti) (chromosome number 2n = 22) possesses heteromorphic Z and W sex chromosomes with heterochromatic W. The panther chameleon (Furcifer pardalis) (2n = 22 in males, 21 in females), the second most popular chameleon species in the world pet trade, exhibits a rather rare Z1Z1Z2Z2/Z1Z2W system of multiple sex chromosomes, which most likely evolved from W-autosome fusion. Notably, its neo-W chromosome is partially heterochromatic and its female-specific genetic content has expanded into the previously autosomal region. Showing clear evidence for genotypic sex determination in the panther chameleon, we resolve the long-standing question of whether or not environmental sex determination exists in this species. Together with recent findings in other reptile lineages, our work demonstrates that female heterogamety is widespread among amniotes, adding another important piece to the mosaic of knowledge on sex determination in amniotes needed to understand the evolution of this important trait.
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Interstitial Telomeric Motifs in Squamate Reptiles: When the Exceptions Outnumber the Rule. PLoS One 2015; 10:e0134985. [PMID: 26252002 PMCID: PMC4529230 DOI: 10.1371/journal.pone.0134985] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/15/2015] [Indexed: 12/19/2022] Open
Abstract
Telomeres are nucleoprotein complexes protecting the physical ends of linear eukaryotic chromosomes and therefore helping to ensure their stability and integrity. Additionally, telomeric sequences can be localized in non-terminal regions of chromosomes, forming so-called interstitial telomeric sequences (ITSs). ITSs are traditionally considered to be relics of chromosomal rearrangements and thus very informative in the reconstruction of the evolutionary history of karyotype formation. We examined the distribution of the telomeric motifs (TTAGGG)n using fluorescence in situ hybridization (FISH) in 30 species, representing 17 families of squamate reptiles, and compared them with the collected data from another 38 species from literature. Out of the 68 squamate species analyzed, 35 possess ITSs in pericentromeric regions, centromeric regions and/or within chromosome arms. We conclude that the occurrence of ITSs is rather common in squamates, despite their generally conserved karyotypes, suggesting frequent and independent cryptic chromosomal rearrangements in this vertebrate group.
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Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, Valenzuela N. Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation. Genome Biol Evol 2015; 7:2038-50. [PMID: 26108489 PMCID: PMC4524486 DOI: 10.1093/gbe/evv119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 01/04/2023] Open
Abstract
Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.
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Affiliation(s)
- Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | | | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | | | | | - Yingjia Shen
- The Genome Institute at Washington University, St Louis
| | - Patrick Minx
- The Genome Institute at Washington University, St Louis
| | - Daniel E Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Department of Organismic and Evolutionary Biology, Harvard University
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
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