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Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution. Cells 2021; 10:cells10071707. [PMID: 34359877 PMCID: PMC8303610 DOI: 10.3390/cells10071707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.
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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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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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Figuet E, Ballenghien M, Romiguier J, Galtier N. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol Evol 2014; 7:240-50. [PMID: 25527834 PMCID: PMC4316630 DOI: 10.1093/gbe/evu277] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.
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Affiliation(s)
- Emeric Figuet
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Marion Ballenghien
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Jonathan Romiguier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Nicolas Galtier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
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Kohno S, Parrott BB, Yatsu R, Miyagawa S, Moore BC, Iguchi T, Guillette L. Gonadal Differentiation in Reptiles Exhibiting Environmental Sex Determination. Sex Dev 2014; 8:208-26. [DOI: 10.1159/000358892] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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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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Moore BC, Milnes MR, Kohno S, Katsu Y, Iguchi T, Guillette LJ. Influences of sex, incubation temperature, and environmental quality on gonadal estrogen and androgen receptor messenger RNA expression in juvenile American alligators (Alligator mississippiensis). Biol Reprod 2009; 82:194-201. [PMID: 19759368 DOI: 10.1095/biolreprod.109.077305] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Gonadal steroid hormone receptors play a vital role in transforming ligand signals into gene expression. We have shown previously that gonads from wild-caught juvenile alligators express greater levels of estrogen receptor 1 (ESR1) than estrogen receptor 2 (ESR2). Furthermore, sexually dimorphic ESR2 mRNA expression (female > male) observed in animals from the reference site (Lake Woodruff, FL, USA) was lost in alligators from the contaminated Lake Apopka (FL, USA). We postulated that environmental contaminant exposure could influence gonadal steroid hormone receptor expression. Here, we address questions regarding gonadal estrogen and androgen receptor (AR) mRNA expression in 1-yr-old, laboratory-raised alligators. What are relative expression levels within gonads? Do these levels vary between sexes or incubation temperatures? Can contaminant exposure change these levels? We observed a similar pattern of expression (ESR1 > AR > ESR2) in ovary and testis. However, both incubation temperature and environment modulated expression. Males incubated at 33.5 degrees C expressed greater AR levels than females incubated at 30 degrees C; dimorphic expression was not observed in animals incubated at 32 degrees C. Compared to Lake Woodruff alligators, Lake Apopka animals of both sexes showed lesser ESR2 mRNA expression levels. Employing cluster analyses, we integrated these receptor expression patterns with those of steroidogenic factors. Elevated ESR2 and CYP19A1 expressions were diagnostic of alligator ovary, whereas elevated HSD3B1, CYP11A1, and CYP17A1 expressions were indicative of testis. In contrast, AR, ESR1, and NR5A1 showed variable expressions that were not entirely associated with sex. These findings demonstrate that the mRNA expression of receptors required for steroid hormone signaling are modified by exposure to environmental factors, including temperature and contaminants.
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Affiliation(s)
- Brandon C Moore
- Department of Biology, University of Florida, Gainesville, Florida, USA.
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Chapus C, Edwards SV. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird. BMC Genomics 2009; 10 Suppl 2:S8. [PMID: 19607659 PMCID: PMC2966332 DOI: 10.1186/1471-2164-10-s2-s8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. RESULTS From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. CONCLUSION Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.
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Affiliation(s)
- Charles Chapus
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Spotila LD, Spotila JR, Hall SE. Sequence and expression analysis of WT1 and Sox9 in the red-eared slider turtle, Trachemys scripta. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 1998; 281:417-27. [PMID: 9662829 DOI: 10.1002/(sici)1097-010x(19980801)281:5<417::aid-jez7>3.0.co;2-r] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Temperature-dependent sex-determination (TSD) is a phenomenon that has been characterized at the ecological, morphological, and endocrinological levels in some reptilian species. We have begun to investigate TSD at the level of molecular development by cloning, sequencing, and analyzing the expression of two genes, WT1 and Sox9, in the red-eared slider turtle Trachemys scripta. We obtained almost full-length cDNA clones for WT1 and Sox9 that were greater than 73% identical to the human homologues at the nucleotide level. WT1 was expressed in urogenital tissue at all developmental stages examined (Yntema stages 12-20) at incubation temperatures that produce males (26 degrees C) or females (32 degrees C). Sox9 was also expressed throughout these same stages, but some differences were observed. At both 26 degrees C and 32 degrees C Sox9 was expressed in the mesonephroi and the undifferentiated gonads until Yntema stage 20, when only the gonad from the 26 degrees C embryos expressed a high level. In addition, there were two transcripts of Sox9 at all stages, but the relative proportion of the two transcripts differed at the two temperatures. Although the similarities in gene expression between a TSD species and other species with genotypically determined sex probably reflect the common features of organogenesis, differences may illustrate unique mechanisms for TSD.
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Affiliation(s)
- L D Spotila
- Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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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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