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Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
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Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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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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Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features. Int J Mol Sci 2021; 22:ijms222111403. [PMID: 34768834 PMCID: PMC8584138 DOI: 10.3390/ijms222111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists.
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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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Oliveira VCS, Viana PF, Gross MC, Feldberg E, Da Silveira R, de Bello Cioffi M, Bertollo LAC, Schneider CH. Looking for genetic effects of polluted anthropized environments on Caiman crocodilus crocodilus (Reptilia, Crocodylia): A comparative genotoxic and chromosomal analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111835. [PMID: 33383344 DOI: 10.1016/j.ecoenv.2020.111835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The Amazon aquatic ecosystems have been modified by the human population growth, going through changes in their water bodies and aquatic biota. The spectacled alligator (Caiman crocodilus crocodilus) has a wide distribution and adaptability to several environments, even those polluted ones. This study aimed to investigate if a Caiman species living in urban streams of Manaus city (Amazonas State, Brazil) is affected by environmental pollution. For that, it was used classical and molecular cytogenetic procedures, in addition to micronucleus and comet assays. Although the karyotype macrostructure remains unaltered (2 n = 42 chromosomes; 24 t + 18 m/sm; NF = 60), the genotoxic analysis and the cytogenetic mapping of repetitive DNA sequences demonstrated that polluted environments alter the genome of the specimens, affecting both the chromosomal organization and the genetic material.
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Affiliation(s)
- Vanessa Cristina Sales Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil; Laboratório de Citogenômica Animal, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Maria Claudia Gross
- Parque Tecnológico Itaipu, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Paraná, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Ronis Da Silveira
- Laboratório de Zoologia Aplicada à Conservação, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carlos Henrique Schneider
- Centro Universitário Dinâmica das Cataratas, Faculdade Anglo Americano, Foz do Iguaçu, Paraná, Brazil
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6
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Viana PF, Ribeiro LB, Lima T, de Carvalho VT, Vogt RC, Gross MC, Feldberg E. An optimized protocol for obtaining mitotic chromosomes from cultured reptilian lymphocytes. THE NUCLEUS 2016. [DOI: 10.1007/s13237-016-0174-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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7
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Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014; 15:1060. [PMID: 25496766 PMCID: PMC4362836 DOI: 10.1186/1471-2164-15-1060] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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Affiliation(s)
| | - Marta Farré
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Pamela E Lithgow
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Katie E Fowler
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
- />School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU UK
| | - Benjamin M Skinner
- />Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Rebecca O’Connor
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Gothami Fonseka
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Niclas Backström
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Yoichi Matsuda
- />Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 Japan
| | - Peter Houde
- />Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA
| | - Erich D Jarvis
- />Department of Neurobiology, Duke University Medical Center, Box 3209, Durham, NC 27710 USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9PS UK
| | - Denis M Larkin
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Darren K Griffin
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012; 13:415. [PMID: 22293439 PMCID: PMC3334581 DOI: 10.1186/gb-2012-13-1-415] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
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Establishment and cryopreservation of liver, heart and muscle cell lines derived from the Chinese alligator (Alligator sinensis). ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4622-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. Methods Mol Biol 2008; 422:91-117. [PMID: 18629663 DOI: 10.1007/978-1-59745-581-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.
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Abstract
Reptiles are a karyologically heterogeneous group, where some orders and suborders exhibit characteristics similar to those of anamniotes and others share similarities with homeotherms. The class also shows different evolutionary trends, for instance in genome and chromosome size and composition. The turtle DNA base composition is similar to that of mammals, whereas that of lizards and snakes is more similar to that of anamniotes. The major karyological differences between turtles and squamates are the size and composition of the genome and the rate at which chromosomes change. Turtles have larger and more variable genome sizes, and a greater amount of middle repetitive DNA that differs even among related species. In lizards and snakes size of the genome are smaller, single-copy DNA is constant within each suborder, and differences in repetitive DNA involve fractions that become increasingly heterogeneous with widening phylogenetic distance. With regard to variation in karyotype morphology, turtles and crocodiles show low variability in chromosome number, morphology, and G-banding pattern. Greater variability is found among squamates, which have a similar degree of karyotypic change-as do some mammals, such as carnivores and bats-and in which there are also differences among congeneric species. An interesting relationship has been highlighted in the entire class Reptilia between rates of change in chromosomes, number of living species, and rate of extinction. However, different situations obtain in turtles and crocodiles on the one hand, and squamates on the other. In the former, the rate of change in chromosomes is lower and the various evolutionary steps do not seem to have entailed marked chromosomal variation, whereas squamates have a higher rate of change in chromosomes clearly related to the number of living species, and chromosomal variation seems to have played an important role in the evolution of several taxa. The different evolutionary trends in chromosomes observed between turtles and crocodiles on the one hand and squamates on the other might depend on their different patterns of G-banding.
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Affiliation(s)
- Ettore Olmo
- Istituto di Biologia e Genetica, Università Politecnica delle Marche and Istituto Nazionale di Biosistemi e Biostrutture, Via Brecce Bianche, 60131 Ancona, Italy
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Isberg SR, Johnston SM, Chen Y, Moran C. First evidence of higher female recombination in a species with temperature-dependent sex determination: the saltwater crocodile. ACTA ACUST UNITED AC 2006; 97:599-602. [PMID: 17114347 DOI: 10.1093/jhered/esl035] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The first evidence of genetic linkage and sex-specific recombination in the order Crocodylia is reported. This study was conducted using a resource pedigree of saltwater crocodiles consisting of 16 known-breeding pairs (32 adults) and 101 juveniles. A total of 21 microsatellite loci were available for analysis. Ten of the 21 loci showed linkage with 4 linkage groups: 3 pairwise (Cj131/Cj127, CUD68/Cj101, and Cj107/Cp10) and 1 four-locus (Cj122, CUD78, Cj16, and Cj104) being found. Linkage analysis on the 21 loci revealed evidence of sex-specific differences in recombination rates. All 5 nonzero interlocus intervals were longer in females than in males, with the 4-loci linkage group 3-fold longer in females than in males (41.63 cM and 14.1 cM, respectively). This is the first report of sex-specific recombination rates in a species that exhibits temperature-dependent sex determination.
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Affiliation(s)
- Sally Robyn Isberg
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, NSW, Australia
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Abstract
Although Reptiles occupy a strategic position among terrestrial vertebrates, studies of the composition and evolution of their genome are scarce. The cytogenetic analysis of nearly 1400 species evidenced different karyotypical evolutionary rates and different G-banding structures in turtles and crocodiles on the one hand and squamates on the other. A similar dichotomy was also identified through the study of the quantitative and compositional characteristics of the genome. The different evolutionary rates of chromosome morphology and genome size and composition and the diversification of coding and non-coding sequences bear an interesting relationship to the number of extant species and the extinction rates of the reptilian orders and suborders studied, suggesting a large role for such different evolutionary rates in the phylogenesis of this class. The different molecular and structural organisation of chromosomes could be an important, though by no means the sole, factor affecting the genome's evolutionary rate.
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Affiliation(s)
- E Olmo
- Istituto di Biologia e Genetica, Facoltà di Scienze, Università di Ancona, Via Brecce Bianche, Ancona, Italy.
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Johnston CM, Barnett M, Sharpe PT. The molecular biology of temperature-dependent sex determination. Philos Trans R Soc Lond B Biol Sci 1995; 350:297-303; discussion 303-4. [PMID: 8570695 DOI: 10.1098/rstb.1995.0165] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Many reptiles do not have heteromorphic sex chromosomes and for these species sex is determined during embryogenesis by the temperature of egg incubation rather than at conception. The phenomenon of temperature-dependent sex determination (TSD) was discovered almost thirty years ago, but few advances have been made towards the elucidation of its mechanism. In the past few years substantial progress has been made in the understanding of the molecular basis of XY chromosomal (genetic) sex determination (GSD) through the discovery of SRY. It is now possible to start comparing TSD with GSD. TSD is found in some evolutionarily ancient vertebrates and has been postulated to be the ancestral process from which GSD has evolved. If this is true then the two mechanisms may share a common molecular basis. This paper details the current knowledge of TSD, our progress on the investigation of the involvement of SRY-type proteins, and finally presents some of the problems that need to be resolved to gain an understanding of the molecular basis of TSD.
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Affiliation(s)
- C M Johnston
- Department of Craniofacial Development, UMDS Guy's Hospital, London, U.K
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15
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Martínez-Lage A, González-Tizón A, Méndez J. Chromosomal markers in three species of the genus Mytilus (Mollusca: Bivalvia). Heredity (Edinb) 1995. [DOI: 10.1038/hdy.1995.55] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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16
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Valleley EM, Harrison CJ, Cook Y, Ferguson MW, Sharpe PT. The karyotype of Alligator mississippiensis, and chromosomal mapping of the ZFY/X homologue, Zfc. Chromosoma 1994; 103:502-7. [PMID: 7720416 DOI: 10.1007/bf00337388] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Comparative mapping studies of X-linked genes in mammals have provided insights into the evolution of the X chromosome. Many reptiles including the American alligator, Alligator mississippiensis, do not appear to possess heteromorphic sex chromosomes, and sex is determined by the incubation temperature of the egg during embryonic development. Mapping of homologues of mammalian X-linked genes in reptiles could lead to a greater understanding of the evolution of vertebrate sex chromosomes. One of the genes used in the mammalian mapping studies was ZFX, an X-linked copy of the human ZFY gene which was originally isolated as a candidate for the mammalian testis-determining factor (TDF). ZFX is X-linked in eutherians, but maps to two autosomal locations in marsupials and monotremes, close to other genes associated with the eutherian X. The alligator homologue of the ZFY/ZFX genes, Zfc, has been isolated and described previously. A detailed karyotype of A. mississippiensis is presented, together with chromosomal in situ hybridisation data localising the Zfc gene to chromosome 3. Further chromosomal mapping studies using eutherian X-linked genes may reveal conserved chromosomal regions in the alligator that have become part of the eutherian X chromosome during evolution.
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Affiliation(s)
- E M Valleley
- School of Biological Sciences, University of Manchester, UK
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17
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Lang JW, Aggarwal RK, Majumdar KC, Singh L. Individualization and estimation of relatedness in crocodilians by DNA fingerprinting with a Bkm-derived probe. MOLECULAR & GENERAL GENETICS : MGG 1993; 238:49-58. [PMID: 8479440 DOI: 10.1007/bf00279530] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Individual-specific DNA fingerprints of crocodilians were obtained by the use of Bkm-2(8) probe. Pedigree analyses of Crocodylus palustris, C. porosus and Caiman crocodilus revealed that the multiple bands (22-23 bands with Aludigest) thus obtained were inherited stably in a Mendelian fashion. Unique fingerprints permitted us to identify individuals, assign parentage, and reconstruct the DNA profile of a missing parent. Average band sharing between unrelated crocodiles was found to be 0.37. Band sharing between animals of known pedigrees increased predictably with relatedness and provided a basis for distinguishing relatives from non-relatives. Similar results obtained in other species/genera, using the same probe, suggest that this approach may be applicable to all species of crocodilians, and could facilitate genetic studies of wild and captive populations.
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Affiliation(s)
- J W Lang
- Department of Biology, University of North Dakota, Grand Forks
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18
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King M, Contreras N, Honeycutt RL. Variation within and between nucleolar organizer regions in Australian hylid frogs (Anura) shown by 18S + 28S in-situ hybridization. Genetica 1990; 80:17-29. [PMID: 2323563 DOI: 10.1007/bf00120116] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Five distinct classes of secondary constriction are found in the hylid frogs from the genera Litoria and Cyclorana, each of which is defined by its C-banding pattern and morphology (King, 1980, 1987). In-situ hybridization experiments utilizing 18S + 28S copy RNA probes derived from Xenopus and Drosophila rDNA templates, were made on nine species of frogs possessing the major constriction types. Types 1, 2, 4, and 5 are confirmed as being NORs. These results also indicate that type 1 and 2 constriction types are not differentially despiralized as previously suggested, but show absolute differences in the quantity of ribosomal DNA present. This variation took two forms, deletion polymorphism and amplification polymorphism. These differences were observed between homologues within cells and between cells within individuals. Animals possessing these 'despiralized' constrictions are therefore mosaics for both deletion and amplification polymorphisms. Polymorphism frequencies vary greatly between constriction types. Some specimens have a higher level of presence/absence heterozygosity, (L. moorei, type 2, L. nannotis type 5, L. raniformis (animal A, pair 8 type 2), than do others (L. peronii, L. rothii, L. caerulea). The above species also vary markedly in the degree and frequency of amplification of the NORs. The type 4 constrictions analysed (L. coplandi, L. lesueuri and C. novaehollandiae) have a particularly low frequency of presence/absence heterozygosity, and they have fewer size heteromorphisms between homologues. The type 3 ephemeral constrictions did not hybridize to cRNA probes at any stage. In all but one of the species studied, a single pair of chromosomes possessed an NOR. However, in L. raniformis these occurred on two pairs of chromosomes.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M King
- Natural Sciences Division, Museum of Arts and Sciences of the Northern Territory, Darwin, Australia
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