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Mezzasalma M, Odierna G, Macirella R, Brunelli E. Comparative Cytogenetics of the Malagasy Ground Geckos of the Paroedura bastardi and Paroedura picta Species Groups. Animals (Basel) 2024; 14:1708. [PMID: 38891755 PMCID: PMC11171197 DOI: 10.3390/ani14111708] [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: 05/08/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
We present a comparative chromosome study of several taxa of the Malagasy ground geckos of the Paroedura bastardi and P. picta species groups. We employed a preliminary molecular analysis using a trait of the mitochondrial 16S rRNA gene (of about 570 bp) to assess the taxonomic status of the samples studied and a cytogenetic analysis with standard karyotyping (5% Giemsa solution), silver staining (Ag-NOR staining) and sequential C-banding (C-banding + Giemsa and + fluorochromes). Our results show that all the taxa studied of the P. bastardi group (P. ibityensis, P. rennerae and P. cf. guibeae) have a similar karyotype composed of 2n = 34 chromosomes, with two metacentric pairs (1 and 3) and all other pairs being acrocentric. Chromosome diversification in the P. bastardi group was mainly linked to the diversification of heteromorphic sex chromosome systems (ZZ/ZW) in P. ibityensis and P. rennerae, while no heteromorphic sex chromosome pair was found in P. cf. guibeae. The two taxa investigated of the P. picta species group (here named P. picta and P. cf. picta based on molecular data) showed the same chromosome number of 2n = 36, mostly acrocentric elements, but differed in the number of metacentric elements, probably as a result of an inversion at chromosome pair 2. We highlight that the genus Paroedura is characterized by the independent diversification of heterogametic sex chromosomes in different evolutionary lineages and, similarly to other phylogenetically related gecko genera, by a progressive formation of a biarmed element by means of tandem fusions and inversions of distinct pairs.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Gaetano Odierna
- Independent Researcher, Via Michelangelo 123, 81031 Aversa, Italy
| | - Rachele Macirella
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
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Uno Y, Matsubara K. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:230-241. [PMID: 38155517 DOI: 10.1002/jez.2776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
Sex determination systems have greatly diversified between amphibians and reptiles, with such as the different sex chromosome compositions within a single species and transition between temperature-dependent sex determination (TSD) and genetic sex determination (GSD). In most sex chromosome studies on amphibians and reptiles, the whole-genome sequence of Xenopous tropicalis and chicken have been used as references to compare the chromosome homology of sex chromosomes among each of these taxonomic groups, respectively. In the present study, we reviewed existing reports on sex chromosomes, including karyotypes, in amphibians and reptiles. Furthermore, we compared the identified genetic linkages of sex chromosomes in amphibians and reptiles with the chicken genome as a reference, which is believed to resemble the ancestral tetrapod karyotype. Our findings revealed that sex chromosomes in amphibians are derived from genetic linkages homologous to various chicken chromosomes, even among several frogs within single families, such as Ranidae and Pipidae. In contrast, sex chromosomes in reptiles exhibit conserved genetic linkages with chicken chromosomes, not only across most species within a single family, but also within closely related families. The diversity of sex chromosomes in amphibians and reptiles may be attributed to the flexibility of their sex determination systems, including the ease of sex reversal in these animals.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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Mezzasalma M, Macirella R, Odierna G, Brunelli E. Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles. Genes (Basel) 2024; 15:371. [PMID: 38540430 PMCID: PMC10970613 DOI: 10.3390/genes15030371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Rachele Macirella
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Gaetano Odierna
- Independent Researcher, Via Michelangelo 123, 81031 Aversa, Italy;
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
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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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Mezzasalma M. First Cytogenetic Analysis of Hemidactylus mercatorius Gray, 1842 Provides Insights on Interspecific Chromosomal Diversification in the Genus Hemidactylus (Squamata: Gekkonidae). Life (Basel) 2024; 14:181. [PMID: 38398689 PMCID: PMC10890220 DOI: 10.3390/life14020181] [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: 12/13/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
This contribution provides the first karyotype description of Hemidactylus mercatorius and discusses the interspecific chromosome diversification in the genus. Chromosomal analysis was performed on samples from different Malagasy populations using standard karyotyping, Ag-NOR staining, and banding methods (sequential C-banding + Giemsa, + Chromomycin A3, +4',6-diamidino-2-phenylindole). Irrespective of sex or sampling locality, H. mercatorius shows a karyotype of 2n = 42 with metacentric (1, 18-21), submetacentric (4), subtelocentric (5, 11), and acrocentric pairs (all the remaining pairs). There was no heteromorphic chromosome pair and no clear distinction between macro- and microchromosomes. NORs were localised close to the centromeres of a medium acrocentric pair (14). Heterochromatic blocks were identified on the telomeric and centromeric regions of most chromosome pairs. A comparison with the karyotype of H. mabouia highlights that the different morphology of several chromosome pairs clearly distinguishes the two species, contrasting the previously proposed synonymy. The differences between the karyotypes of H. mercatorius and H. mabouia concern the number of biarmed and acrocentric elements, suggesting the occurrence of several chromosome inversions. Considering all the available karyotype data on Hemidactylus and its sister genus Cyrtodactylus, it is possible to advance an evolutionary hypothesis on their chromosomal evolution, starting from a common ancestor with 2n = 48 and all acrocentric elements. From this ancestral condition, the karyotype diversification in the two genera has been prevalently characterised by a progressive accumulation of fusions and inversions which have reduced the total chromosome count and increased the number of biarmed chromosomes.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
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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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Mezzasalma M, Streicher JW, Guarino FM, Jones MEH, Loader SP, Odierna G, Cooper N. Microchromosome fusions underpin convergent evolution of chameleon karyotypes. Evolution 2023; 77:1930-1944. [PMID: 37288542 DOI: 10.1093/evolut/qpad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/26/2022] [Accepted: 04/17/2023] [Indexed: 06/09/2023]
Abstract
Evolutionary shifts in chromosome compositions (karyotypes) are major drivers of lineage and genomic diversification. Fusion of ancestral chromosomes is one hypothesized mechanism for the evolutionary reduction of the total chromosome number, a frequently implied karyotypic shift. Empirical tests of this hypothesis require model systems with variable karyotypes, known chromosome features, and a robust phylogeny. Here we used chameleons, diverse lizards with exceptionally variable karyotypes ($2n=20\text{-}62$), to test whether chromosomal fusions explain the repeated evolution of karyotypes with fewer chromosomes than ancestral karyotypes. Using a multidisciplinary approach including cytogenetic analyses and phylogenetic comparative methods, we found that a model of constant loss through time best explained chromosome evolution across the chameleon phylogeny. Next, we tested whether fusions of microchromosomes into macrochromosomes explained these evolutionary losses using generalized linear models. Multiple comparisons supported microchromosome fusions as the predominant agent of evolutionary loss. We further compared our results to various natural history traits and found no correlations. As such, we infer that the tendency of microchromosomes to fuse was a quality of the ancestral chameleon genome and that the genomic predisposition of ancestors is a more substantive predictor of chromosome change than the ecological, physiological, and biogeographical factors involved in their diversification.
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Affiliation(s)
- Marcello Mezzasalma
- Science Group, Natural History Museum, Cromwell Road, London, United Kingdom
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Jeffrey W Streicher
- Science Group, Natural History Museum, Cromwell Road, London, United Kingdom
| | - Fabio M Guarino
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Marc E H Jones
- Science Group, Natural History Museum, Cromwell Road, London, United Kingdom
- Research Department of Cell and Developmental Biology, University College London, London, United Kingdom
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Simon P Loader
- Science Group, Natural History Museum, Cromwell Road, London, United Kingdom
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Natalie Cooper
- Science Group, Natural History Museum, Cromwell Road, London, United Kingdom
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Comparative cytogenetics of Hemorrhois hippocrepis and Malpolon monspessulanus highlights divergent karyotypes in Colubridae and Psammophiidae (Squamata: Serpentes). THE EUROPEAN ZOOLOGICAL JOURNAL 2023. [DOI: 10.1080/24750263.2023.2180547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
- M. Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - E. Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - G. Odierna
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - F. M. Guarino
- Department of Biology, University of Naples Federico II, Naples, Italy
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Chromosome Diversity and Evolution of the Endemic Malagasy Velvet Geckos of the Genus Blaesodactylus (Reptilia, Gekkonidae). Animals (Basel) 2023; 13:2068. [PMID: 37443866 DOI: 10.3390/ani13132068] [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: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
We performed a molecular and phylogenetic analysis and a comparative cytogenetic study with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, + fluorochromes on several Blaesodactylus samples. The phylogenetic inference retrieved two main clades, the first comprises B. victori, B. microtuberculatus and B. boivini, while the second includes B. sakalava, B. antongilensis and B. ambonihazo. The available samples of B. sakalava form two different clades (here named B. sakalava clade A and clade B), which probably deserve a taxonomic re-evaluation. We found a karyological variability in Blaesodactylus in terms of chromosome number (2n = 40-42), morphology, location of NORs, and heterochromatin distribution pattern. Blaesodactylus antongilensis and B. sakalava clade A and B showed a karyotype of 2n = 40 mostly telocentric chromosomes. Pairs 1 and 6 were metacentric in B. sakalava clade A and B, while pair 1 was composed of subtelocentric/submetacentric elements in B. antongilensis. In contrast, B. boivini displayed a karyotype with 2n = 42 only telocentric chromosomes. NORs were on the first chromosome pair in B. boivini, and on the second pair in B. antongilensis. Adding our data to those available from the literature on evolutionarily related species, we highlight that the chromosome diversification in the genus probably proceeded towards a progressive reduction in the chromosome number and the formation of metacentric elements.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
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Olmo E. Reptile Evolution and Genetics: An Overview. Animals (Basel) 2023; 13:1924. [PMID: 37370434 PMCID: PMC10295626 DOI: 10.3390/ani13121924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The study of evolution has been indissolubly linked to the study of heredity since its inception [1]. [...].
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Affiliation(s)
- Ettore Olmo
- Department of Life and Environmental Sciences, Università Politecnica delle Marche via Brecce Bianche Ancona, 60121 Ancona, Italy
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Romanenko SA, Prokopov DY, Proskuryakova AA, Davletshina GI, Tupikin AE, Kasai F, Ferguson-Smith MA, Trifonov VA. The Cytogenetic Map of the Nile Crocodile ( Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs. Int J Mol Sci 2022; 23:13063. [PMID: 36361851 PMCID: PMC9656864 DOI: 10.3390/ijms232113063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 01/16/2024] Open
Abstract
Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S-28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.
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Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Anastasia A. Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Guzel I. Davletshina
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, The National Institute of Biomedical Innovation, Health and Nutrition, Saito-Asagi, Ibaraki 567-0085, Osaka, Japan
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | | | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia
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First Insights on the Karyotype Diversification of the Endemic Malagasy Leaf-Toed Geckos (Squamata: Gekkonidae: Uroplatus). Animals (Basel) 2022; 12:ani12162054. [PMID: 36009644 PMCID: PMC9404452 DOI: 10.3390/ani12162054] [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: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The geckos of the genus Uroplatus include peculiar endemic species to Madagascar. Even though they have been the subject of several morphological and molecular studies, karyological analyses have been performed only on U. phantasticus, leaving the chromosomal diversity of the genus completely unexplored. In this study, we performed a preliminary molecular analysis and a comparative cytogenetic study providing the first karyotype description of eight species of Uroplatus and an assessment of their karyological variability. We found chromosome diversity in the species studied in terms of total chromosome number (2n = 34–38), localization of loci of Nucleolar Organizer Regions (NORs) (alternatively on the 2nd, 6th, 10th or 16th pair), heterochromatin composition and occurrence of heteromorphic sex chromosome pairs. Adding our newly generated data to those available from the literature, we show that in the genus Uroplatus, as well as in a larger group of phylogenetically related gecko genera, chromosome diversification mainly occurred toward a reduction in the chromosome number by means of chromosome fusions and translocation of NOR-bearing chromosomes. We also hypothesize that the diversification of sex chromosome systems occurred independently in different genera. Abstract We provide here the first karyotype description of eight Uroplatus species and a characterization of their chromosomal diversity. We performed a molecular taxonomic assessment of several Uroplatus samples using the mitochondrial 12S marker and a comparative cytogenetic analysis with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, +Chromomycin A3 (CMA3), +4′,6-diamidino-2-phenylindole (DAPI). We found chromosomal variability in terms of chromosome number (2n = 34–38), heterochromatin composition and number and localization of loci or Nucleolar Organizer Regions (NORs) (alternatively on the 2nd, 6th, 10th or 16th pair). Chromosome morphology is almost constant, with karyotypes composed of acrocentric chromosomes, gradually decreasing in length. C-banding evidenced a general low content of heterochromatin, mostly localized on pericentromeric and telomeric regions. Centromeric bands varied among the species studied, resulting in CMA3 positive and DAPI negative or positive to both fluorochromes. We also provide evidence of a first putative heteromorphic sex chromosome system in the genus. In fact, in U. alluaudi the 10th pair was highly heteromorphic, with a metacentric, largely heterochromatic W chromosome, which was much bigger than the Z. We propose an evolutionary scenario of chromosome reduction from 2n = 38 to 2n = 34, by means of translocations of microchromosomes on larger chromosomes (often involving the NOR-bearing microchromosomes). Adding our data to those available from the literature, we show that similar processes characterized the evolutionary radiation of a larger gecko clade. Finally, we hypothesize that sex chromosome diversification occurred independently in different genera.
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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: 64] [Impact Index Per Article: 21.3] [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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14
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Singchat W, Panthum T, Ahmad SF, Baicharoen S, Muangmai N, Duengkae P, Griffin DK, Srikulnath K. Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome. Cells 2021; 10:cells10112969. [PMID: 34831192 PMCID: PMC8616239 DOI: 10.3390/cells10112969] [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: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/18/2022] Open
Abstract
Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages-the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- 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; (W.S.); (T.P.); (S.F.A.)
- 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;
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- 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;
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand;
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- 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;
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence:
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15
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Westfall AK, Telemeco RS, Grizante MB, Waits DS, Clark AD, Simpson DY, Klabacka RL, Sullivan AP, Perry GH, Sears MW, Cox CL, Cox RM, Gifford ME, John-Alder HB, Langkilde T, Angilletta MJ, Leaché AD, Tollis M, Kusumi K, Schwartz TS. A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology. Gigascience 2021; 10:6380105. [PMID: 34599334 PMCID: PMC8486681 DOI: 10.1093/gigascience/giab066] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 04/16/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.
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Affiliation(s)
- Aundrea K Westfall
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rory S Telemeco
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Biology, California State University Fresno, Fresno, CA 93740, USA
| | | | - Damien S Waits
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Amanda D Clark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Dasia Y Simpson
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Randy L Klabacka
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael W Sears
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Christian L Cox
- Department of Biology, Georgia Southern University, Statesboro, GA 30460, USA.,Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Robert M Cox
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Matthew E Gifford
- Department of Biology, University of Central Arkansas, Conway, AR 72035, USA
| | - Henry B John-Alder
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Tracy Langkilde
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA.,Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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16
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Mezzasalma M, Guarino FM, Odierna G. Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data? Genes (Basel) 2021; 12:1341. [PMID: 34573323 PMCID: PMC8468487 DOI: 10.3390/genes12091341] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/19/2023] Open
Abstract
Lizards represent unique model organisms in the study of sex determination and sex chromosome evolution. Among tetrapods, they are characterized by an unparalleled diversity of sex determination systems, including temperature-dependent sex determination (TSD) and genetic sex determination (GSD) under either male or female heterogamety. Sex chromosome systems are also extremely variable in lizards. They include simple (XY and ZW) and multiple (X1X2Y and Z1Z2W) sex chromosome systems and encompass all the different hypothesized stages of diversification of heterogametic chromosomes, from homomorphic to heteromorphic and completely heterochromatic sex chromosomes. The co-occurrence of TSD, GSD and different sex chromosome systems also characterizes different lizard taxa, which represent ideal models to study the emergence and the evolutionary drivers of sex reversal and sex chromosome turnover. In this review, we present a synthesis of general genome and karyotype features of non-snakes squamates and discuss the main theories and evidences on the evolution and diversification of their different sex determination and sex chromosome systems. We here provide a systematic assessment of the available data on lizard sex chromosome systems and an overview of the main cytogenetic and molecular methods used for their identification, using a qualitative and quantitative approach.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairaõ, Portugal
| | - Fabio M. Guarino
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
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17
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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: 24] [Impact Index Per Article: 8.0] [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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18
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Oliveira VCS, Altmanová M, Viana PF, Ezaz T, Bertollo LAC, Ráb P, Liehr T, Al-Rikabi A, Feldberg E, Hatanaka T, Scholz S, Meurer A, de Bello Cioffi M. Revisiting the Karyotypes of Alligators and Caimans (Crocodylia, Alligatoridae) after a Half-Century Delay: Bridging the Gap in the Chromosomal Evolution of Reptiles. Cells 2021; 10:cells10061397. [PMID: 34198806 PMCID: PMC8228166 DOI: 10.3390/cells10061397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Although crocodilians have attracted enormous attention in other research fields, from the cytogenetic point of view, this group remains understudied. Here, we analyzed the karyotypes of eight species formally described from the Alligatoridae family using differential staining, fluorescence in situ hybridization with rDNA and repetitive motifs as a probe, whole chromosome painting (WCP), and comparative genome hybridization. All Caimaninae species have a diploid chromosome number (2n) 42 and karyotypes dominated by acrocentric chromosomes, in contrast to both species of Alligatorinae, which have 2n = 32 and karyotypes that are predominantly metacentric, suggesting fusion/fission rearrangements. Our WCP results supported this scenario by revealing the homeology of the largest metacentric pair present in both Alligator spp. with two smaller pairs of acrocentrics in Caimaninae species. The clusters of 18S rDNA were found on one chromosome pair in all species, except for Paleosuchus spp., which possessed three chromosome pairs bearing these sites. Similarly, comparative genomic hybridization demonstrated an advanced stage of sequence divergence among the caiman genomes, with Paleosuchus standing out as the most divergent. Thus, although Alligatoridae exhibited rather low species diversity and some level of karyotype stasis, their genomic content indicates that they are not as conserved as previously thought. These new data deepen the discussion of cytotaxonomy in this family.
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Affiliation(s)
- Vanessa C. S. Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Patrik F. Viana
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69083-000, Brazil; (P.F.V.); (E.F.)
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Correspondence: ; Tel.: +49-36-41-939-68-50; Fax: +49-3641-93-96-852
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69083-000, Brazil; (P.F.V.); (E.F.)
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
| | | | | | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil; (V.C.S.O.); (L.A.C.B.); (T.H.); (M.d.B.C.)
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19
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Machado CRD, Domit C, Pucci MB, Gazolla CB, Glugoski L, Nogaroto V, Vicari MR. Heterochromatin and microsatellites detection in karyotypes of four sea turtle species: Interspecific chromosomal differences. Genet Mol Biol 2020; 43:e20200213. [PMID: 33270075 PMCID: PMC7734918 DOI: 10.1590/1678-4685-gmb-2020-0213] [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: 06/24/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
The wide variation in size and content of eukaryotic genomes is mainly attributed to the accumulation of repetitive DNA sequences, like microsatellites, which are tandemly repeated DNA sequences. Sea turtles share a diploid number (2n) of 56, however recent molecular cytogenetic data have shown that karyotype conservatism is not a rule in the group. In this study, the heterochromatin distribution and the chromosomal location of microsatellites (CA)n, (GA)n, (CAG)n, (GATA)n, (GAA)n, (CGC)n and (GACA)n in Chelonia mydas, Caretta caretta, Eretmochelys imbricata and Lepidochelys olivacea were comparatively investigated. The obtained data showed that just the (CA)n, (GA)n, (CAG)n and (GATA)n microsatellites were located on sea turtle chromosomes, preferentially in heterochromatic regions of the microchromosomes (mc). Variations in the location of heterochromatin and microsatellites sites, especially in some pericentromeric regions of macrochromosomes, corroborate to proposal of centromere repositioning occurrence in Cheloniidae species. Furthermore, the results obtained with the location of microsatellites corroborate with the temperature sex determination mechanism proposal and the absence of heteromorphic sex chromosomes in sea turtles. The findings are useful for understanding part of the karyotypic diversification observed in sea turtles, especially those that explain the diversification of Carettini from Chelonini species.
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Affiliation(s)
- Caroline Regina Dias Machado
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Camila Domit
- Universidade Federal do Paraná, Laboratório de Ecologia e
Conservação, Pontal do Paraná, PR, Brazil
| | | | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Programa de Pós-Graduação em
Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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20
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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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21
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Dissanayake DSB, Holleley CE, Hill LK, O'Meally D, Deakin JE, Georges A. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 2020; 21:667. [PMID: 32993477 PMCID: PMC7526180 DOI: 10.1186/s12864-020-07071-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
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Affiliation(s)
- Duminda Sampath Bandara Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Clare Ellen Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Laura Kate Hill
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present Address: Centre for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Janine Eileen Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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22
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Singchat W, Ahmad SF, Sillapaprayoon S, Muangmai N, Duengkae P, Peyachoknagul S, O’Connor RE, Griffin DK, Srikulnath K. Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes. Front Genet 2020; 11:948. [PMID: 33014016 PMCID: PMC7461878 DOI: 10.3389/fgene.2020.00948] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell's viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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23
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Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. Genes (Basel) 2020; 11:E827. [PMID: 32708239 PMCID: PMC7397244 DOI: 10.3390/genes11070827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the "repeatome", remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Integrative Genomics Lab-LGI, Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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24
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Molecular Cytogenetic Characterization of the Sicilian Endemic Pond Turtle Emys trinacris and the Yellow-Bellied Slider Trachemys scripta scripta (Testudines, Emydidae). Genes (Basel) 2020; 11:genes11060702. [PMID: 32630506 PMCID: PMC7348936 DOI: 10.3390/genes11060702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/15/2023] Open
Abstract
Turtles, a speciose group consisting of more than 300 species, demonstrate karyotypes with diploid chromosome numbers ranging from 2n = 26 to 2n = 68. However, cytogenetic analyses have been conducted only to 1/3rd of the turtle species, often limited to conventional staining methods. In order to expand our knowledge of the karyotype evolution in turtles, we examined the topology of the (TTAGGG)n telomeric repeats and the rDNA loci by fluorescence in situ hybridization (FISH) on the karyotypes of two emydids: the Sicilian pond turtle, Emys trinacris, and the yellow-bellied slider, Trachemys scripta scripta (family Emydidae). Furthermore, AT-rich and GC-rich chromosome regions were detected by DAPI and CMA3 stains, respectively. The cytogenetic analysis revealed that telomeric sequences are restricted to the terminal ends of all chromosomes and the rDNA loci are localized in one pair of microchromosomes in both species. The karyotype of the Sicilian endemic E. trinacris with diploid number 2n = 50, consisting of 13 pairs of macrochromosomes and 12 pairs of microchromosomes, is presented here for first time. Our comparative examination revealed similar cytogenetic features in Emys trinacris and the closely related E. orbicularis, as well as to other previously studied emydid species, demonstrating a low rate of karyotype evolution, as chromosomal rearrangements are rather infrequent in this group of turtles.
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25
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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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26
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Machado CR, Glugoski L, Domit C, Pucci MB, Goldberg DW, Marinho LA, da Costa GW, Nogaroto V, Vicari MR. Comparative Cytogenetics of Four Sea Turtle Species (Cheloniidae): G-Banding Pattern and in situ Localization of Repetitive DNA Units. Cytogenet Genome Res 2020; 160:531-538. [DOI: 10.1159/000511118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/19/2020] [Indexed: 02/04/2023] Open
Abstract
Sea turtles are considered flagship species for marine biodiversity conservation and are considered to be at varying risk of extinction globally. Cases of hybridism have been reported in sea turtles, but chromosomal analyses are limited to classical karyotype descriptions and a few molecular cytogenetic studies. In order to compare karyotypes and understand evolutive mechanisms related to chromosome differentiation in this group, <i>Chelonia mydas</i>, <i>Caretta caretta</i>, <i>Eretmochelys imbricata</i>, and <i>Lepidochelys olivacea</i> were cytogenetically characterized in the present study. When the obtained cytogenetic data were compared with the putative ancestral Cryptodira karyotype, the studied species showed the same diploid number (2n) of 56 chromosomes, with some variations in chromosomal morphology (karyotypic formula) and minor changes in longitudinal band locations. In situ localization using a 18S ribosomal DNA probe indicated a homeologous microchromosome pair bearing a 45S ribosomal DNA locus and size heteromorphism in all 4 species. Interstitial telomeric sites were identified in a microchromosome pair in <i>C. mydas</i> and <i>C. caretta</i>. The data showed that interspecific variations occurred in chromosomal sets among the Cheloniidae species, in addition to other Cryptodira karyotypes. These variations generated lineage-specific karyotypic diversification in sea turtles, which will have considerable implications for hybrid recognition and for the study, the biology, ecology, and evolutionary history of regional and global populations. Furthermore, we demonstrated that some chromosome rearrangements occurred in sea turtle species, which is in conflict with the hypothesis of conserved karyotypes in this group.
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Distribution and amplification of interstitial telomeric sequences (ITSs) in Australian dragon lizards support frequent chromosome fusions in Iguania. PLoS One 2019; 14:e0212683. [PMID: 30794668 PMCID: PMC6386254 DOI: 10.1371/journal.pone.0212683] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/07/2019] [Indexed: 11/19/2022] Open
Abstract
Telomeric sequences are generally located at the ends of chromosomes; however, they can also be found in non-terminal chromosomal regions when they are known as interstitial telomeric sequences (ITSs). Distribution of ITSs across closely related and divergent species elucidates karyotype evolution and speciation as ITSs provide evolutionary evidence for chromosome fusion. In this study, we performed physical mapping of telomeric repeats by fluorescence in situ hybridisation (FISH) in seven Australian dragon lizards thought to represent derived karyotypes of squamate reptiles and a gecko lizard with considerably different karyotypic feature. Telomeric repeats were present at both ends of all chromosomes in all species, while varying numbers of ITSs were also found on microchromosomes and in pericentromeric or centromeric regions on macrochromosomes in five lizard species examined. This suggests that chromosomal rearrangements from ancestral squamate reptiles to Iguania occurred mainly by fusion between ancestral types of acrocentric chromosomes and/or between microchromosomes, leading to appearance of bi-armed macrochromosomes, and in the reduction of microchromosome numbers. These results support the previously proposed hypothesis of karyotype evolution in squamate reptiles. In addition, we observed the presence of telomeric sequences in the similar regions to heterochromatin of the W microchromosome in Pogona barbata and Doporiphora nobbi, while sex chromosomes for the two species contained part of the nucleolar organiser regions (NORs). This likely implies that these ITSs are a part of the satellite DNA and not relics of chromosome fusions. Amplification of telomeric repeats may have involved heterochromatinisation of sex-specific W chromosomes and play a role in the organisation of the nucleolus.
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28
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Menezes RST, Gazoni T, Costa MA. Cytogenetics of warrior wasps (Vespidae:Synoeca) reveals intense evolutionary dynamics of ribosomal DNA clusters and an unprecedented number of microchromosomes in Hymenoptera. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras – Universidade de São Paulo (FFCLRP/USP), Ribeirão Preto, SP, Brazil
| | - Thiago Gazoni
- Departamento de Biologia – Universidade Estadual Paulista (UNESP), Instituto de Biociências, Rio Claro, SP, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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29
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Iannucci A, Svartman M, Bellavita M, Chelazzi G, Stanyon R, Ciofi C. Insights into Emydid Turtle Cytogenetics: The European Pond Turtle as a Model Species. Cytogenet Genome Res 2019; 157:166-171. [PMID: 30630162 DOI: 10.1159/000495833] [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: 07/31/2018] [Indexed: 12/22/2022] Open
Abstract
Our knowledge of Testudines evolution is limited by the lack of modern cytogenetic data. Compared to other reptiles, there is little information even on chromosome banding, let alone molecular cytogenetic data. Here, we provide detailed information on the karyotype of the European pond turtle Emys orbicularis, a model Emydidae, employing both chromosome banding and molecular cytogenetics. We provide a high-resolution G-banded karyotype and a map of rDNA genes and telomeric sequences using fluorescence in situ hybridization. We test hypotheses of sex-determining mechanisms in Emys by comparative genomic hybridization to determine if Emys has a cryptic sex-specific region. Our results provide valuable data to guide future efforts on genome sequencing and anchoring in Emydidae and for understanding karyotype evolution in Testudines.
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30
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Zlotina A, Dedukh D, Krasikova A. Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies. Genes (Basel) 2017; 8:genes8110311. [PMID: 29117127 PMCID: PMC5704224 DOI: 10.3390/genes8110311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 01/04/2023] Open
Abstract
Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes. Due to the giant size, peculiarities of organization and enrichment with cytological markers, lampbrush chromosomes can serve as an opportune model for comprehensive high-resolution cytogenetic and cytological investigations. Here, we review the main findings on chromosome evolution in amphibians and birds that were obtained using lampbrush chromosomes. In particular, we discuss the data on evolutionary chromosomal rearrangements, accumulation of polymorphisms, evolution of sex chromosomes as well as chromosomal changes during clonal reproduction of interspecies hybrids.
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Affiliation(s)
- Anna Zlotina
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
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Lewandowski D, Dubińska-Magiera M, Posyniak E, Rupik W, Daczewska M. Does the grass snake (Natrix natrix) (Squamata: Serpentes: Natricinae) fit the amniotes-specific model of myogenesis? PROTOPLASMA 2017; 254:1507-1516. [PMID: 27834030 PMCID: PMC5487930 DOI: 10.1007/s00709-016-1040-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
In the grass snake (Natrix natrix), the newly developed somites form vesicles that are located on both sides of the neural tube. The walls of the vesicles are composed of tightly connected epithelial cells surrounding the cavity (the somitocoel). Also, in the newly formed somites, the Pax3 protein can be observed in the somite wall cells. Subsequently, the somite splits into three compartments: the sclerotome, dermomyotome (with the dorsomedial [DM] and the ventrolateral [VL] lips) and the myotome. At this stage, the Pax3 protein is detected in both the DM and VL lips of the dermomyotome and in the mononucleated cells of the myotome, whereas the Pax7 protein is observed in the medial part of the dermomyotome and in some of the mononucleated cells of the myotome. The mononucleated cells then become elongated and form myotubes. As myogenesis proceeds, the myotome is filled with multinucleated myotubes accompanied by mononucleated, Pax7-positive cells (satellite cells) that are involved in muscle growth. The Pax3-positive progenitor muscle cells are no longer observed. Moreover, we have observed unique features in the differentiation of the muscles in these snakes. Specifically, our studies have revealed the presence of two classes of muscles in the myotomes. The first class is characterised by fast muscle fibres, with myofibrils equally distributed throughout the sarcoplasm. In the second class, composed of slow muscle fibres, the sarcoplasm is filled with lipid droplets. We assume that their storage could play a crucial role during hibernation in the adult snakes. We suggest that the model of myotomal myogenesis in reptiles, birds and mammals shows the same morphological and molecular character. We therefore believe that the grass snake, in spite of the unique features of its myogenesis, fits into the amniotes-specific model of trunk muscle development.
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Affiliation(s)
- Damian Lewandowski
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Magda Dubińska-Magiera
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Ewelina Posyniak
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Weronika Rupik
- Department of Animal Histology and Embryology, University of Silesia, Bankowa 9, 40-007, Katowice, Poland
| | - Małgorzata Daczewska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland.
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Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae). COMPARATIVE CYTOGENETICS 2017; 11:129-141. [PMID: 28919954 PMCID: PMC5599703 DOI: 10.3897/compcytogen.v11i1.10916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/16/2017] [Indexed: 05/13/2023]
Abstract
Although the evolutionary importance of meiotic recombination is not disputed, the significance of interspecies differences in the recombination rates and recombination landscapes remains under-appreciated. Recombination rates and distribution of chiasmata have been examined cytologically in many mammalian species, whereas data on other vertebrates are scarce. Immunolocalization of the protein of the synaptonemal complex (SYCP3), centromere proteins and the mismatch-repair protein MLH1 was used, which is associated with the most common type of recombination nodules, to analyze the pattern of meiotic recombination in the male of two species of iguanian lizards, Anolis carolinensis Voigt, 1832 and Deiroptyx coelestinus (Cope, 1862). These species are separated by a relatively long evolutionary history although they retain the ancestral iguanian karyotype. In both species similar and extremely uneven distributions of MLH1 foci along the macrochromosome bivalents were detected: approximately 90% of crossovers were located at the distal 20% of the chromosome arm length. Almost total suppression of recombination in the intermediate and proximal regions of the chromosome arms contradicts the hypothesis that "homogenous recombination" is responsible for the low variation in GC content across the anole genome. It also leads to strong linkage disequilibrium between the genes located in these regions, which may benefit conservation of co-adaptive gene arrays responsible for the ecological adaptations of the anoles.
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Affiliation(s)
- Artem P. Lisachov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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Lisachov AP, Borodin PM. Microchromosome polymorphism in the sand lizard, Lacerta agilis Linnaeus, 1758 (Reptilia, Squamata). COMPARATIVE CYTOGENETICS 2016; 10:387-399. [PMID: 27830048 PMCID: PMC5088351 DOI: 10.3897/compcytogen.v10i3.7655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/28/2016] [Indexed: 06/06/2023]
Abstract
Most true lizards (Lacertidae) share a conservative karyotype, consisting of 18 pairs of macrochromosomes and one microchromosome pair. Homeologues of the microchromosome are present in other squamates and even in chickens. No structural autosomal microchromosome polymorphisms have been described previously in lizards. We found homozygous and heterozygous carriers of a microchromosome variant in a Siberian population of the sand lizard, Lacerta agilis Linnaeus, 1758. The variant microchromosome was almost twice as long as the standard one. In heterozygotes at pachytene, the microchromosomes firstly pair in proximal regions and the central part of the longer axial element undergoes foldback synapsis, then its distal region pairs with the distal region of the standard partner. At metaphase-I, the heteromorphic microchromosome bivalents have a proximal chiasma. The content of the additional segment was Ag-NOR, C-like DAPI, CMA3 negative. FISH with telomere PNA probe did not detect interstitial (TTAGGG)n sequences in the heteromorphic and any other bivalents. Both homo- and heterozygous carriers were phenotypically normal. The presence of homozygotes shows that heterozygotes are fertile. Reduction in the number of microchromosomes is a clear trend in squamate evolution, as a result of microchromosomes fusing together or with macrochromosomes. Our findings indicate that gaining additional DNA may lead to a transformation of microchromosomes into small macrochromosomes without fusion.
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Affiliation(s)
- Artem P. Lisachov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia
- Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
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Montiel EE, Badenhorst D, Lee LS, Literman R, Trifonov V, Valenzuela N. Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes. Cytogenet Genome Res 2016; 148:292-304. [DOI: 10.1159/000447478] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.
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Deakin JE, Edwards MJ, Patel H, O'Meally D, Lian J, Stenhouse R, Ryan S, Livernois AM, Azad B, Holleley CE, Li Q, Georges A. Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome. BMC Genomics 2016; 17:447. [PMID: 27286959 PMCID: PMC4902969 DOI: 10.1186/s12864-016-2774-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/25/2016] [Indexed: 12/30/2022] Open
Abstract
Background Squamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it difficult to reconstruct the events that have led to extant squamate karyotypic diversity. The purpose of this study was to anchor the recently sequenced central bearded dragon (Pogona vitticeps) genome to chromosomes to trace the evolution of squamate chromosomes. Assigning sequence to sex chromosomes was of particular interest for identifying candidate sex determining genes. Results By using two different approaches to map conserved blocks of genes, we were able to anchor approximately 42 % of the dragon genome sequence to chromosomes. We constructed detailed comparative maps between dragon, anole and chicken genomes, and where possible, made broader comparisons across Squamata using cytogenetic mapping information for five other species. We show that squamate macrochromosomes are relatively well conserved between species, supporting findings from previous molecular cytogenetic studies. Macrochromosome diversity between members of the Toxicofera clade has been generated by intrachromosomal, and a small number of interchromosomal, rearrangements. We reconstructed the ancestral squamate macrochromosomes by drawing upon comparative cytogenetic mapping data from seven squamate species and propose the events leading to the arrangements observed in representative species. In addition, we assigned over 8 Mbp of sequence containing 219 genes to the Z chromosome, providing a list of genes to begin testing as candidate sex determining genes. Conclusions Anchoring of the dragon genome has provided substantial insight into the evolution of squamate genomes, enabling us to reconstruct ancestral macrochromosome arrangements at key positions in the squamate phylogeny, demonstrating that fusions between macrochromosomes or fusions of macrochromosomes and microchromosomes, have played an important role during the evolution of squamate genomes. Assigning sequence to the sex chromosomes has identified NR5A1 as a promising candidate sex determining gene in the dragon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2774-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.
| | - Melanie J Edwards
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Hardip Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Jinmin Lian
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Rachael Stenhouse
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Sam Ryan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Alexandra M Livernois
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Bhumika Azad
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, 1350, Denmark
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
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Mezzasalma M, Visone V, Petraccioli A, Odierna G, Capriglione T, Guarino FM. Non-random accumulation of LINE1-like sequences on differentiated snake W chromosomes. J Zool (1987) 2016. [DOI: 10.1111/jzo.12355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- M. Mezzasalma
- Department of Biology; University of Naples Federico II; Naples Italy
| | - V. Visone
- Department of Biology; University of Naples Federico II; Naples Italy
| | - A. Petraccioli
- Department of Biology; University of Naples Federico II; Naples Italy
| | - G. Odierna
- Department of Biology; University of Naples Federico II; Naples Italy
| | - T. Capriglione
- Department of Biology; University of Naples Federico II; Naples Italy
| | - F. M. Guarino
- Department of Biology; University of Naples Federico II; Naples Italy
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Discovery of the youngest sex chromosomes reveals first case of convergent co-option of ancestral autosomes in turtles. Chromosoma 2016; 126:105-113. [DOI: 10.1007/s00412-016-0576-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/27/2022]
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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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Mezzasalma M, Andreone F, Branch WR, Glaw F, Guarino FM, Nagy ZT, Odierna G, Aprea G. Chromosome evolution in pseudoxyrhophiine snakes from Madagascar: a wide range of karyotypic variability. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12280] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marcello Mezzasalma
- Department of Biology; University of Naples Federico II; Via Cinthia Naples Italy
| | - Franco Andreone
- Museo Regionale di Scienze Naturali; Via Giolitti, 36 I-10123 Torino Italy
| | - William R. Branch
- Department of Zoology; Nelson Mandela Metropolitan University; PO Box 77000 Port Elizabeth 6031 South Africa
| | - Frank Glaw
- Zoologische Staatssammlung München; Münchhausenstraße 21 81247 München Germany
| | - Fabio M. Guarino
- Department of Biology; University of Naples Federico II; Via Cinthia Naples Italy
| | - Zoltán T. Nagy
- Royal Belgian Institute of Natural Sciences; JEMU Rue Vautier 29 1000 Brussels Belgium
| | - Gaetano Odierna
- Department of Biology; University of Naples Federico II; Via Cinthia Naples Italy
| | - Gennaro Aprea
- Department of Biology; University of Naples Federico II; Via Cinthia Naples Italy
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Deakin JE, Ezaz T. Tracing the evolution of amniote chromosomes. Chromosoma 2014; 123:201-16. [PMID: 24664317 PMCID: PMC4031395 DOI: 10.1007/s00412-014-0456-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 01/09/2023]
Abstract
A great deal of diversity in chromosome number and arrangement is observed across the amniote phylogeny. Understanding how this diversity is generated is important for determining the role of chromosomal rearrangements in generating phenotypic variation and speciation. Gaining this understanding is achieved by reconstructing the ancestral genome arrangement based on comparisons of genome organization of extant species. Ancestral karyotypes for several amniote lineages have been reconstructed, mainly from cross-species chromosome painting data. The availability of anchored whole genome sequences for amniote species has increased the evolutionary depth and confidence of ancestral reconstructions from those made solely from chromosome painting data. Nonetheless, there are still several key lineages where the appropriate data required for ancestral reconstructions is lacking. This review highlights the progress that has been made towards understanding the chromosomal changes that have occurred during amniote evolution and the reconstruction of ancestral karyotypes.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, 2601, Australia,
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41
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Pokorná M, Altmanová M, Kratochvíl L. Multiple sex chromosomes in the light of female meiotic drive in amniote vertebrates. Chromosome Res 2014; 22:35-44. [DOI: 10.1007/s10577-014-9403-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Pinthong K, Tanomtong A, Getlekha N, Sangpadee W, Sangpakdee K, Sanoamuang LO. First Cytogenetic Study of Puff-Faced Water Snake, Homalopsis buccata (Squamata, Colubridae) by Conventional Staining, Ag-NOR Banding and GTG-Banding Techniques. CYTOLOGIA 2013. [DOI: 10.1508/cytologia.78.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Krit Pinthong
- Biology Program, Faculty of Science and Technology, Surindra Rajabhat University
| | - Alongklod Tanomtong
- Applied Taxonomic Research Center (ATRC), Department of Biology, Faculty of Science, Khon Kaen University
| | - Nuntaporn Getlekha
- Applied Taxonomic Research Center (ATRC), Department of Biology, Faculty of Science, Khon Kaen University
| | - Wiwat Sangpadee
- Biology Program, Faculty of Science, Udon-Thani Rajabhat University
| | | | - La-orsri Sanoamuang
- Applied Taxonomic Research Center (ATRC), Department of Biology, Faculty of Science, Khon Kaen University
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Chiari Y, Cahais V, Galtier N, Delsuc F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol 2012; 10:65. [PMID: 22839781 PMCID: PMC3473239 DOI: 10.1186/1741-7007-10-65] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 07/27/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. RESULTS In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. CONCLUSIONS These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.
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Affiliation(s)
- Ylenia Chiari
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Vincent Cahais
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
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44
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Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting. Chromosoma 2012; 121:409-18. [DOI: 10.1007/s00412-012-0371-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 04/05/2012] [Accepted: 04/10/2012] [Indexed: 01/06/2023]
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Strong conservation of the bird Z chromosome in reptilian genomes is revealed by comparative painting despite 275 million years divergence. Chromosoma 2011; 120:455-68. [PMID: 21725690 DOI: 10.1007/s00412-011-0322-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 04/18/2011] [Accepted: 04/25/2011] [Indexed: 01/20/2023]
Abstract
The divergence of lineages leading to extant squamate reptiles (lizards, snakes, and amphisbaenians) and birds occurred about 275 million years ago. Birds, unlike squamates, have karyotypes that are typified by the presence of a number of very small chromosomes. Hence, a number of chromosome rearrangements might be expected between bird and squamate genomes. We used chromosome-specific DNA from flow-sorted chicken (Gallus gallus) Z sex chromosomes as a probe in cross-species hybridization to metaphase spreads of 28 species from 17 families representing most main squamate lineages and single species of crocodiles and turtles. In all but one case, the Z chromosome was conserved intact despite very ancient divergence of sauropsid lineages. Furthermore, the probe painted an autosomal region in seven species from our sample with characterized sex chromosomes, and this provides evidence against an ancestral avian-like system of sex determination in Squamata. The avian Z chromosome synteny is, therefore, conserved albeit it is not a sex chromosome in these squamate species.
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Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Basa S, Walker JA, Smith JJ. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 2011; 21:1306-12. [PMID: 21482624 DOI: 10.1101/gr.116491.110] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12-17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution.
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Affiliation(s)
- Stephen R Voss
- Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA.
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