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Genomic Organization of Microsatellites and LINE-1-like Retrotransposons: Evolutionary Implications for Ctenomys minutus (Rodentia: Ctenomyidae) Cytotypes. Animals (Basel) 2022; 12:ani12162091. [PMID: 36009681 PMCID: PMC9405301 DOI: 10.3390/ani12162091] [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: 06/08/2022] [Revised: 07/28/2022] [Accepted: 08/13/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary In animals, several species contain substantial chromosomal and genomic variation among their populations, but as to what could have driven such diversification is still a puzzle for most cases. Here, we used molecular cytogenetic analysis to expose the main genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae), which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoint regions (EBRs) and highlight their direct impact in promoting chromosomal rearrangements. Abstract The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)30, (C)30, (CA)15, (CAC)10, (CAG)10, (CGG)10, (GA)15, and (GAG)10 could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements.
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Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species. Genes (Basel) 2020; 11:genes11020170. [PMID: 32041215 PMCID: PMC7073582 DOI: 10.3390/genes11020170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.
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Viana Ferreira AM, Marajó L, Matoso DA, Ribeiro LB, Feldberg E. Chromosomal Mapping of Rex Retrotransposons in Tambaqui (Colossoma macropomum Cuvier, 1818) Exposed to Three Climate Change Scenarios. Cytogenet Genome Res 2019; 159:39-47. [PMID: 31593951 DOI: 10.1159/000502926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 11/19/2022] Open
Abstract
Greenhouse gas emissions are known to influence the planet's temperature, mainly due to human activities. To allow hypothesis testing, as well as to seek viable alternatives for mitigation, the Intergovernmental Panel on Climate Change (IPCC) suggested 3 main scenarios for changes projected for the year 2100. In this paper, we subjected Colossoma macropomum Cuvier, 1818 (tambaqui) individuals in a microcosm to IPCC scenarios B1 (mild), A1B (intermediate), and A2 (extreme) to test possible impacts on their genome. We found chromosome heterochromatinization in specimens exposed to the A2 scenario, where terminal blocks and interstitial bands were detected on several chromosome pairs. The behavior of Rex1 and Rex3 sequences differed between the test scenarios. Hybridization of Rex1 resulted in diffuse signals which showed a gradual increase in the tested scenarios. For Rex3, an increase was observed in the A2 scenario with blocks on several chromosomes, some of which coincided with heterochromatin. Heterochromatinization is an epigenetic process, which may have occurred as a mechanism for regulating Rex3 activity. The signal pattern of Rex6 did not change, suggesting that other mechanisms are acting to regulate its activity.
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Laporte M, Le Luyer J, Rougeux C, Dion-Côté AM, Krick M, Bernatchez L. DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species. SCIENCE ADVANCES 2019; 5:eaaw1644. [PMID: 31663013 PMCID: PMC6795504 DOI: 10.1126/sciadv.aaw1644] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 09/19/2019] [Indexed: 05/05/2023]
Abstract
The genomic shock hypothesis stipulates that the stress associated with divergent genome admixture can cause transposable element (TE) derepression, which could act as a postzygotic isolation mechanism. TEs affect gene structure, expression patterns, and chromosome organization and may have deleterious consequences when released. For these reasons, they are silenced by heterochromatin formation, which includes DNA methylation. Here, we show that a significant proportion of TEs are differentially methylated between the "dwarf" (limnetic) and the "normal" (benthic) whitefish, two nascent species that diverged some 15,000 generations ago within the Coregonus clupeaformis species complex. Moreover, TEs are overrepresented among loci that were demethylated in hybrids, indicative of their transcriptional derepression. These results are consistent with earlier studies in this system that revealed TE transcriptional derepression causes abnormal embryonic development and death of hybrids. Hence, this supports a role of DNA methylation reprogramming and TE derepression in postzygotic isolation of nascent animal species.
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Taboada X, Rey M, Bouza C, Viñas A. Cytogenomic analysis of several repetitive DNA elements in turbot (Scophthalmus maximus). Gene 2018; 644:4-12. [PMID: 29246535 DOI: 10.1016/j.gene.2017.12.013] [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: 05/16/2017] [Revised: 11/23/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome. In this work, the in silico analysis of H1 histone, 5S rDNA, telomeric and Rex repetitive sequences, was compared to their chromosomal mapping by fluorescent in situ hybridization (FISH), providing a more comprehensive picture of these elements in the turbot genome. FISH assays confirmed the location of H1 in LG8; 5S rDNA in LG4 and LG6; telomeric sequences at the end of all chromosomes whereas Rex elements were dispersed along most chromosomes. The discrepancies found between both approaches could be related to the sequencing methodology applied in this species and also to the resolution limitations of the FISH technique. Turbot cytogenomic analyses have proven to add new chromosomal landmarks in the karyotype of this species, representing a powerful tool to investigate targeted genomic sequences or regions in the genetic and physical maps of this species.
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Affiliation(s)
- Xoana Taboada
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Magalí Rey
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Ana Viñas
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Chalopin D, Volff JN. Analysis of the spotted gar genome suggests absence of causative link between ancestral genome duplication and transposable element diversification in teleost fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:629-637. [PMID: 28921831 DOI: 10.1002/jez.b.22761] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 11/08/2022]
Abstract
Teleost fish have been shown to contain many superfamilies of transposable elements (TEs) that are absent from most tetrapod genomes. Since theories predict an increase in TE activity following polyploidization, such diversity might be linked to the 3R whole-genome duplication that occurred approximately 300 million years ago before the teleost radiation. To test this hypothesis, we have analyzed the genome of the spotted gar Lepisosteus oculatus, which diverged from the teleost lineage before the 3R duplication. Our results indicate that TE diversity and copy numbers are similar in gar and teleost genomes, suggesting that TE diversity was ancestral and not linked to the 3R whole-genome duplication. We propose that about 25 distinct superfamilies of TEs were present in the last ancestor of gars and teleost fish about 300 million years ago in the ray-finned fish lineage.
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Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
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Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 2017; 9:161-177. [PMID: 28158585 PMCID: PMC5381603 DOI: 10.1093/gbe/evw264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.
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Affiliation(s)
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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Nascimento J, Baldo D, Lourenço LB. First insights on the retroelement Rex1 in the cytogenetics of frogs. Mol Cytogenet 2015; 8:86. [PMID: 26550032 PMCID: PMC4635592 DOI: 10.1186/s13039-015-0189-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 11/22/2022] Open
Abstract
Background While some transposable elements (TEs) have been found in the sequenced genomes of frog species, detailed studies of these elements have been lacking. In this work, we investigated the occurrence of the Rex1 element, which is widespread in fish, in anurans of the genus Physalaemus. We isolated and characterized the reverse transcriptase (RT)-coding sequences of Rex1 elements of five species of this genus. Results The amino acid sequences deduced from the nucleotide sequences of the isolated fragments allowed us to unambiguously identify regions corresponding to domains 3–7 of RT. Some of the nucleotide sequences isolated from Physlaemus ephippifer and P. albonotatus had internal deletions, suggesting that these fragments are likely not active TEs, despite being derived from a Rex1 element. When hybridized with metaphase chromosomes, Rex1 probes were revealed at the pericentromeric heterochromatic region of the short arm of chromosome 3 of the P. ephippifer karyotype. Neither other heterochromatin sites of the P. ephippifer karyotype nor any chromosomal regions of the karyotypes of P. albonotatus, P. spiniger and P. albifrons were detected with these probes. Conclusions Rex1 elements were found in the genomes of five species of Physalaemus but clustered in only the P. ephippifer karyotype, in contrast to observations in some species of fish, where large chromosomal sites with Rex1 elements are typically present. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0189-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juliana Nascimento
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas São Paulo, Brazil
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, Félix de Azara 1552, CPA N3300LQF Posadas, Misiones Argentina
| | - Luciana Bolsoni Lourenço
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas São Paulo, Brazil
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Dynamics of Rex3 in the genomes of endangered Iberian Leuciscinae (Teleostei, Cyprinidae) and their natural hybrids. Mol Cytogenet 2015; 8:81. [PMID: 26512297 PMCID: PMC4623273 DOI: 10.1186/s13039-015-0180-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/01/2015] [Indexed: 02/08/2023] Open
Abstract
Background Iberian Leuciscinae are greatly diverse comprising taxa of hybrid origin. With highly conservative karyotypes, Iberian Chondrostoma s.l. have recently demonstrated sub-chromosomal differentiation and rapid genome restructuring in natural hybrids, which was confirmed by ribosomal DNA (rDNA) transposition and/or multiplication. To understand the role of repetitive DNAs in the differentiation of their genomes, a genetic and molecular cytogenetic survey was conducted in Achondrostoma oligolepis, Anaecypris hispanica, Iberochondrostoma lemmingii, I. lusitanicum, Pseudochondrostoma duriense, P. polylepis, Squalius pyrenaicus and hybrids between A. oligolepis x (P. duriense/P. polylepis), representing ‘alburnine’, chondrostomine and Squalius lineages. Results Partial Rex3 sequences evidenced high sequence homology among Leuciscinae (≥98 %) and different fish families (80–95 %) proposing a relatively recent activity of these elements in the species inspected. Low nucleotide substitution rates (<20 %) and intact ORFs suggests that Rex3 may in fact be active in these genomes. The chromosomal distribution of Rex3 retroelement was found highly concentrated at pericentromeric and moderately at subtelomeric blocks, co-localizing with 5S rDNA loci, and correlating with blocks of heterochromatin and C0t-1 DNA. This accumulation was evident in at least 10 chromosome pairs, a pattern that seemed to be shared among the different species, likely pre-dating their divergence. Nevertheless, species-specific clusters were detected in I. lusitanicum, P. duriense, P. polylepis and S. pyrenaicus demonstrating rapid and independent differentiation. Natural hybrids followed the same patterns of accumulation and association with repetitive sequences. An increased number of Rex3 clusters now associating also with translocated 45S rDNA clusters vouched for other genomic rearrangements in hybrids. Rex3 sequence phylogeny did not agree with its hosts’ phylogeny but the observed distribution pattern is congruent with an evolutionary tendency to protect its activity, a robust regulatory system and/or events of horizontal transfer. Conclusions This is the first report directed at retroelement physical mapping in Cyprinidae. It helped outlining conceivable ancestral homologies and recognizing retrotransposon activation in hybrids, being possibly associated with genome diversification within the subfamily. The extensive diversity of Iberian Leuciscinae makes them excellent candidates to explore the processes and mechanisms behind the great plasticity distinguishing vertebrate genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0180-1) contains supplementary material, which is available to authorized users.
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Staton SE, Burke JM. Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. BMC Genomics 2015; 16:623. [PMID: 26290182 PMCID: PMC4546089 DOI: 10.1186/s12864-015-1830-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of Utricularia gibba to more than 80% in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants. RESULTS Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of Gypsy retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in Gypsy abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner. CONCLUSIONS We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions.
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Affiliation(s)
- S Evan Staton
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Current address: Beaty Biodiversity Research Centre and Department of Botany, 3529-6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Belyayev A. Bursts of transposable elements as an evolutionary driving force. J Evol Biol 2014; 27:2573-84. [PMID: 25290698 DOI: 10.1111/jeb.12513] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 12/25/2022]
Abstract
A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process.
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Affiliation(s)
- A Belyayev
- Institute of Botany, Czech Academy of Sciences, Pruhonice near Prague, Czech Republic
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Barbosa CM, Mareco EA, Silva MDP, Martins C, Alves-Costa FA. Differential expression of a retrotransposable element, Rex6, in Colossoma macropomum fish from different Amazonian environments. Mob Genet Elements 2014; 4:e30003. [PMID: 25089227 PMCID: PMC4113519 DOI: 10.4161/mge.30003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences that have the ability to move and replicate within the genomes. TEs can be classified according to their intermediates of transposition, RNA (retrotransposons) or DNA. In some aquatic organisms, it has been observed that environmental factors such as pH, temperature and pollution may stimulate differential transcription and mobilization of retrotransposons. In light of this information, the present study sought to evaluate the expression of Rex6 TE transcripts in Colossoma macropomum, which is a very commercially exploited fish in Brazil. In order to establish a comparative analysis using real-time PCR, the samples were collected from Amazonian rivers with different physical and chemical characteristics (distinguished by clear water and black water). Quantitative RT-PCR analyses revealed a differential pattern of expression between tissues collected from different types of water (clear and black waters). When it came to the hepatic and muscle tissues sampled, the levels of Rex6 transcripts were significantly different between the two Amazonian water types. These results suggest that environmental conditions operate differently in the regulation of Rex6 transcription in C. macropomum, results which have implications in the reshaping of the genome against environmental variations.
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Affiliation(s)
- Cassiane Martins Barbosa
- UNESP—São Paulo State University (Universidade Estadual Paulista); Instituto de Biociências de Botucatu; Departamento de Morfologia; Botucatu, SP, Brazil
| | - Edson Assunção Mareco
- UNESP—São Paulo State University (Universidade Estadual Paulista); Instituto de Biociências de Botucatu; Departamento de Morfologia; Botucatu, SP, Brazil
| | - Maeli Dal Pai Silva
- UNESP—São Paulo State University (Universidade Estadual Paulista); Instituto de Biociências de Botucatu; Departamento de Morfologia; Botucatu, SP, Brazil
| | - Cesar Martins
- UNESP—São Paulo State University (Universidade Estadual Paulista); Instituto de Biociências de Botucatu; Departamento de Morfologia; Botucatu, SP, Brazil
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Voltolin TA, Mendonça BB, Ferreira DC, Senhorini JA, Foresti F, Porto-Foresti F. Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei: Characiformes. Mob Genet Elements 2013; 3:e25846. [PMID: 24195015 PMCID: PMC3812791 DOI: 10.4161/mge.25846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/13/2013] [Accepted: 07/22/2013] [Indexed: 01/14/2023] Open
Abstract
Transposable elements are repetitive DNA sequences comprising a group of segments able to move and carry sequences within the genome. Studies involving comparative genomics have revealed that most vertebrates have different populations of transposable elements with significant differences among species of the same lineage. Few studies have been conducted in fish, the most diverse group of vertebrates, with the objective to locate different types of transposable elements. Therefore, this study proposed to map the retrotransposable element Rex1 applying Fluorescent in situ Hybridization (FISH) in five species of the genus Prochilodus (Prochilodus argenteus, Prochilodus brevis, Prochilodus costatus, Prochilodus lineatus and Prochilodus nigricans). After the application of the Rex1 probe, scattered markings were found throughout the genome of analyzed species, and also the presence of small clusters located in the centromeric and telomeric regions coincident with the heterochromatin distribution pattern. This was the first description of the retrotransposable element Rex1 in Prochilodus genome seeking for a better understanding of the distribution pattern of these retrotransposons in the genome of teleost fish.
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Affiliation(s)
- Tatiana Aparecida Voltolin
- Departamento Ciências Biológicas; Faculdade de Ciências; Universidade Estadual Paulista (UNESP); Campus de Bauru; Bauru, São Paulo Brazil
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Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications. BMC Evol Biol 2013; 13:42. [PMID: 23410024 PMCID: PMC3585787 DOI: 10.1186/1471-2148-13-42] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 02/11/2013] [Indexed: 01/07/2023] Open
Abstract
Background Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution. Results Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8–10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. Conclusion We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation. Such causal interplay between genome differentiation, retrotransposons (re)activation and environmental conditions may become a topic to be explored in a broader genomic context in future evolutionary studies.
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Ferreira DC, Porto-Foresti F, Oliveira C, Foresti F. Transposable elements as a potential source for understanding the fish genome. Mob Genet Elements 2011; 1:112-117. [PMID: 22016858 DOI: 10.4161/mge.1.2.16731] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 05/11/2011] [Accepted: 05/30/2011] [Indexed: 12/24/2022] Open
Abstract
Transposable elements are repetitive sequences with the capacity tomove inside of the genome. They constitute the majority of the eukaryotic genomes, and are extensively present in the human genome, representing more than 45% of the genome sequences. The knowledge of the origin and function of these elements in the fish genome is still reduced and fragmented, mainly with regard to its structure and organization in the chromosomes of the representatives of this biological group, with data currently available for very few species that represent the great variety of forms and existing diversity. Comparative analyses ascertain differences in the organization of such elements in the species studied up to the present. They can be part of the heterochromatic regions in some species or be spread throughout the genome in others. The main objective of the present revision is to discuss the aspects of the organization of transposable elements in the fish genome.
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Affiliation(s)
- Daniela Cristina Ferreira
- Departamento de Morfologia; Instituto de Biociência; Universidade Estadual Paulista; Bauru, SP Brazil
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16
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Novikova OS, Blinov AG. Origin, evolution, and distribution of different groups of non-LTR retrotransposons among eukaryotes. RUSS J GENET+ 2009. [DOI: 10.1134/s102279540902001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Genomic organization of repetitive DNAs in the cichlid fish Astronotus ocellatus. Genetica 2008; 136:461-9. [DOI: 10.1007/s10709-008-9346-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 12/11/2008] [Indexed: 01/20/2023]
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18
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Kuraku S, Meyer A. Genomic analysis of cichlid fish 'natural mutants'. Curr Opin Genet Dev 2008; 18:551-8. [PMID: 19095433 DOI: 10.1016/j.gde.2008.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/03/2008] [Indexed: 11/24/2022]
Abstract
In the lakes of East Africa, cichlid fishes have formed adaptive radiations that are each composed of hundreds of endemic, morphologically stunningly diverse, but genetically extremely similar species. In the past 20 years, it became clear that their extreme phenotypic diversity arose within very short time spans, and that phenotypically radically different species are exceptionally similar genetically; hence, they could be considered to be 'natural mutants'. Many species can be hybridized and, therefore, provide a unique opportunity to study the genetic underpinnings of phenotypic diversification. Comparative large-scale genomic analyses are beginning to unravel the patterns and processes that led to the formation of the cichlid species flocks. Cichlids are an emerging evolutionary genomic model system for fundamental questions on the origin of phenotypic diversity.
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Affiliation(s)
- Shigehiro Kuraku
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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19
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Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Res 2008; 16:203-15. [DOI: 10.1007/s10577-007-1202-6] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Terrat Y, Bonnivard E, Higuet D. GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species. Mol Genet Genomics 2007; 279:63-73. [PMID: 17929059 DOI: 10.1007/s00438-007-0295-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 09/19/2007] [Indexed: 11/25/2022]
Abstract
Crustacean species have not been examined in great detail for their transposable elements content. Here we focus on galatheid crabs, which are one of the most diverse and widespread taxonomic groups of Decapoda. Ty1/copia retrotransposons are a diverse and taxonomically dispersed group. Using degenerate primers, we isolated several DNA fragments that show homology with Ty1/copia retroelements reverse transcriptase gene. We named the corresponding elements from which they originated GalEa1 to GalEa3 and analyzed one of them further by isolating various clones containing segments of GalEa1. This is the first LTR retrotransposon described in crustacean genome. Nucleotide sequencing of the clones revealed that GalEa1 has LTRs (124 bp) and that the internal sequence (4,421 bp) includes a single large ORF containing gag and pol regions. Further screening identified highly related elements in six of the nine galatheid species studied. By performing BLAST searches on genome databases, we could also identify GalEa-like elements in some fishes and Urochordata genomes. These elements define a new clade of Ty1/copia retrotransposons that differs from all other Ty1/copia elements and that seems to be restricted to aquatic species.
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Affiliation(s)
- Yves Terrat
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre and Marie Curie Paris 6, Case 5, Bât A, porte 427, 7 quai St-Bernard, 75252, Paris Cedex 05, France
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21
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Dreyer C, Hoffmann M, Lanz C, Willing EM, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D. ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata. BMC Genomics 2007; 8:269. [PMID: 17686157 PMCID: PMC1994688 DOI: 10.1186/1471-2164-8-269] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 08/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available. RESULTS With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes. CONCLUSION Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.
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Affiliation(s)
- Christine Dreyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Margarete Hoffmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Eva-Maria Willing
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Markus Riester
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Andrea Sprecher
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Namita Tripathi
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Stefan R Henz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
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22
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Schultheis C, Zhou Q, Froschauer A, Nanda I, Selz Y, Schmidt C, Matschl S, Wenning M, Veith AM, Naciri M, Hanel R, Braasch I, Dettai A, Böhne A, Ozouf-Costaz C, Chilmonczyk S, Ségurens B, Couloux A, Bernard-Samain S, Schmid M, Schartl M, Volff JN. Molecular Analysis of the Sex-Determining Region of the PlatyfishXiphophorus maculatus. Zebrafish 2006; 3:299-309. [DOI: 10.1089/zeb.2006.3.299] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Qingchun Zhou
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
- Present address: Department of Zoology and Stephenson Research and Technology Center, University of Oklahoma, Norman, Oklahoma
| | - Alexander Froschauer
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
- Present address: Institut für Zoologie, Technische Universität Dresden, Dresden, Germany
| | - Indrajit Nanda
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Yvonne Selz
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Cornelia Schmidt
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Sabine Matschl
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Marina Wenning
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Anne-Marie Veith
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Mariam Naciri
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
- Present address: Université Mohamed V, Faculté des Sciences, Rabat, Morocco
| | - Reinhold Hanel
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
- Present address: Leibniz Institut für Meereswissenschaften, IFM-GEOMAR, Kiel, Germany
| | - Ingo Braasch
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Agnès Dettai
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Astrid Böhne
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Catherine Ozouf-Costaz
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Stefan Chilmonczyk
- Laboratoire de Virologie et Immunologie Molécularies, INRA, Jouy en Josas, France
| | | | - Arnaud Couloux
- Genoscope/Centre National de Séquençage, CNRS-UMR, Evry, France
| | | | - Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Manfred Schartl
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
| | - Jean-Nicolas Volff
- Physiologische Chemie I, Biozentrum , University of Würzburg, Würzburg, Germany
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23
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Mank JE, Avise JC. Cladogenetic correlates of genomic expansions in the recent evolution of actinopterygiian fishes. Proc Biol Sci 2006; 273:33-8. [PMID: 16519231 PMCID: PMC1560015 DOI: 10.1098/rspb.2005.3295] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 08/13/2005] [Indexed: 11/12/2022] Open
Abstract
Genomic expansions via regional gene duplications and polyploidization events have been implicated as catalysts for rapid cladogenetic speciation in some fish taxa, but any general relationships between genome sizes and patterns of evolutionary radiation remain poorly characterized. Here we examine empirical correlations between genome size and species richness (number of extant species within a given clade) both across Actinopterygii (ray-finned fishes) and within several large actinopterygiian clades. We conducted the analyses both without and with correction (by independent contrasts) for phylogenetic effects. Across the full suite of 461 surveyed genera, relatively small but significant positive correlations were present between species richness and evolutionary increases in C-value. Although many variables (including ecological and behavioural factors) clearly can influence speciation rates, the current results are consistent with the notion that genomic architecture may play a role in species proliferation as well.
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Affiliation(s)
- Judith E Mank
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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24
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Yamagami S, Suzuki N. Diverse Forms of Guanylyl Cyclases in Medaka Fish – Their Genomic Structure and Phylogenetic Relationships to those in Vertebrates and Invertebrates. Zoolog Sci 2005; 22:819-35. [PMID: 16141695 DOI: 10.2108/zsj.22.819] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fish species such as medaka fish, fugu, and zebrafish contain more guanylyl cyclases (GCs) than do mammals. These GCs can be divided into two types: soluble GCs and membrane GCs. The latter are further divided into four subfamilies: (i) natriuretic peptide receptors, (ii) STa/guanylin receptors, (iii) sensory-organ-specific membrane GCs, and (iv) orphan receptors. Phylogenetic analyses of medaka fish GCs, along with those of fugu and zebrafish, suggest that medaka fish is a much closer relative to fugu than to zebrafish. Analyses of nucleotide data available on a web site (http://www.ncbi. nlm.nih.gov/) of GCs from a range of organisms from bacteria to vertebrates suggest that gene duplication, and possibly chromosomal duplication, play important roles in the divergence of GCs. In particular, the membrane GC genes were generated by chromosomal duplication before the divergence of tetrapods and teleosts.
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Affiliation(s)
- Sayaka Yamagami
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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25
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Fischer C, Bouneau L, Coutanceau JP, Weissenbach J, Ozouf-Costaz C, Volff JN. Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis. Cytogenet Genome Res 2005; 110:522-36. [PMID: 16093705 DOI: 10.1159/000084985] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 03/25/2004] [Indexed: 12/15/2022] Open
Abstract
We report the characterization and chromosomal distribution of retroelements in the compact genome of the pufferfish Tetraodon nigroviridis. We have reconstructed partial/complete retroelement sequences, established their phylogenetic relationship to other known eukaryotic retrotransposons, and performed double-color FISH analyses to gain new insights into their patterns of chromosomal distribution. We could identify 43 different reverse transcriptase retrotransposons belonging to the three major known subclasses (14 non-LTR retrotransposons from seven clades, 25 LTR retrotransposons representing the five major known groups, and four Penelope-like elements), and well as two SINEs (non-autonomous retroelements). Such a diversity of retrotransposable elements, which seems to be relatively common in fish but not in mammals, is astonishing in such a compact genome. The total number of retroelements was approximately 3000, roughly representing only 2.6% of the genome of T. nigroviridis. This is much less than in other vertebrate genomes, reflecting the compact nature of the genome of this pufferfish. Major differences in copy number were observed between different clades, indicating differential success in invading and persisting in the genome. Some retroelements displayed evidence of recent activity. Finally, FISH analysis showed that retrotransposable elements preferentially accumulate in specific heterochromatic regions of the genome of T. nigroviridis, revealing a degree of genomic compartmentalization not observed in the human genome.
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Affiliation(s)
- C Fischer
- Genoscope/Centre National de Séquençage, CNRS-UMR 8030, Evry, France.
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26
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Abstract
Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.
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Affiliation(s)
- J-N Volff
- BioFuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, D-97074 Würzburg, Germany.
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27
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Matsuo MY, Nonaka M. Repetitive elements in the major histocompatibility complex (MHC) class I region of a teleost, medaka: identification of novel transposable elements. Mech Dev 2005; 121:771-7. [PMID: 15210184 DOI: 10.1016/j.mod.2004.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 03/11/2004] [Accepted: 03/22/2004] [Indexed: 11/27/2022]
Abstract
The repetitive elements of medaka (Oryzias latipes) are poorly characterized in spite of recent rapid progress in the medaka genome analysis. Here we report the characterization of the repetitive elements in the major histocompatibility complex (MHC) class I region, which spans about 400 kb and is one of the best characterized regions of the medaka genome. Microsatellite, low complexity regions, transposable elements, and other repeats occupied 0.68, 0.98, 7.0 and 2.9%, respectively, of the MHC class I region. Eleven transposable elements, three LTR-type, six LINE-type and two DNA-type, including several novel ones, were identified. Genomic Southern hybridization analysis indicated that these LINE-type and DNA-type elements have many copies in the medaka genome, whereas the LTR-type elements have only several copies. The comparison of the medaka MHC class I region with those of zebrafish and fugu shows the presence of three medaka lineage-specific tandem duplications of the PSMB (proteasome beta-type subunit) 8 and class Ia genes. Since eight of the 11 transposable elements were located in this region, these elements may have played a role in the medaka-specific DNA rearrangement.
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Affiliation(s)
- Megumi Y Matsuo
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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28
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Fischer C, Bouneau L, Coutanceau JP, Weissenbach J, Volff JN, Ozouf-Costaz C. Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis. Gene 2004; 336:175-83. [PMID: 15246529 DOI: 10.1016/j.gene.2004.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Revised: 03/31/2004] [Accepted: 04/13/2004] [Indexed: 11/24/2022]
Abstract
Because of its unusual high degree of compaction and paucity of repetitive sequences, the genome of the smooth pufferfish Tetraodon nigroviridis is the subject of a well-advanced sequencing project. An astonishing diversity of transposable elements not found in the human and the mouse has been observed in the genome of T. nigroviridis. Due to the difficulty of assembling repeat-rich regions, the whole genome shotgun sequencing approach will probably fail to reveal the general organisation of this compact vertebrate genome. Therefore, in order to gain new insights into the global distribution pattern of repeated DNA in the genome of T. nigroviridis, we have reconstructed partial/complete repetitive sequences from data generated by the genome project and performed double-colour fluorescent in situ hybridization (FISH) analysis for representatives of three major categories of repeated sequences including two minisatellites (ms100 and ms104), two DNA transposons (Tol2 and Buffy1) and two non-long terminal repeat (LTR) retrotransposons (Rex3 and Babar). We show that DNA transposons and retroelements very frequently colocalize with minisatellites and mostly accumulate within heterochromatic regions. These results, which have not been reported so far for the fugu Takifugu rubripes, show that repeated elements are generally excluded from gene-rich regions in T. nigroviridis and underline the extreme degree of compartmentalization of this compact genome. The genome organization of the pufferfish is clearly different from that observed in humans, where repeated sequences make up an important fraction of euchromatic DNA, and is more similar to that observed in the fruit fly Drosophila melanogaster.
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Affiliation(s)
- Cécile Fischer
- Genoscope/Centre National de Séquençage and CNRS-UMR 8030, F-91057, Evry Cedex 06, France
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29
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Bouneau L, Fischer C, Ozouf-Costaz C, Froschauer A, Jaillon O, Coutanceau JP, Körting C, Weissenbach J, Bernot A, Volff JN. An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis. Genome Res 2003; 13:1686-95. [PMID: 12805276 PMCID: PMC403742 DOI: 10.1101/gr.726003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR retrotransposons from nematodes. Zebulon was detected in the pufferfishes Tetraodon nigroviridis and Takifugu rubripes, as well as in the zebrafish Danio rerio. Structural analysis suggested that Zebulon, in contrast to most non-LTR retrotransposons, might be able to retrotranspose as a partial tandem array. Zebulon was active relatively recently in the compact genome of T. nigroviridis, in which it contributed to the extension of intergenic and intronic sequences, and possibly to the formation of genomic rearrangements. Accumulation of Zebulon together with other retrotransposons was observed in some heterochromatic chromosomal regions of the genome of T. nigroviridis that might serve as reservoirs for active elements. Hence, pufferfish compact genomes are not evolutionarily inert and contain active retrotransposons, suggesting the presence of mechanisms allowing accumulation of retrotransposable elements in heterochromatin, but minimizing their impact on euchromatic regions. Homologous recombination between partial tandem sequences eliminating active copies of Zebulon and reducing the size of insertions in intronic and intragenic regions might represent such a mechanism.
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Affiliation(s)
- Laurence Bouneau
- Genoscope/Centre National de Séquençage and CNRS-UMR 8030, F-91057 Evry Cedex 06, France
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30
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Abstract
Vasa is the most extensively characterized germ cell-specific marker in metazoans. We determined the sequence of the zebrafish vasa locus, which - together with the flanking regions - is 25 kb long. It contains 26 + 1 exons, with an average length of 83 bp. The 5' end of zebrafish vasa is rich in repeats; it includes a peculiar tandem repeat with three units spanning a total of eight exons, each unit containing several tandemly arranged RNA-binding motifs (RGG boxes). The presence of various, nonmicrosatellite type repeats in vasa seems to be universal among the species studied, and could have functional importance during the evolution of the gene, due to the increase in the number of RGG boxes located in these repeats. Analysis of vasa transcripts in zebrafish identified numerous isoforms resulting from alternative splicing (seven) and polyadenylation (four). Mapping to two radiation hybrid panels strengthened the position of the gene on LG10 of zebrafish.
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Affiliation(s)
- Richárd Bártfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
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31
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Froschauer A, Körting C, Katagiri T, Aoki T, Asakawa S, Shimizu N, Schartl M, Volff JN. Construction and initial analysis of bacterial artificial chromosome (BAC) contigs from the sex-determining region of the platyfish Xiphophorus maculatus. Gene 2002; 295:247-54. [PMID: 12354660 DOI: 10.1016/s0378-1119(02)00684-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Despite the major importance of sex determination in aquaculture, no master sex-determining gene has been identified so far in teleost fish. In the platyfish Xiphophorus maculatus, this master gene is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene responsible for melanoma formation in some Xiphophorus interspecific hybrids, and its proto-oncogenic counterpart. Both Xmrk genes, which have already been characterised at the molecular level, delimit a region of about 1 Mb that contains other gene loci involved in sexual maturity, pigmentation and melanoma formation. We have constructed a genomic bacterial artificial chromosome (BAC) library of X. maculatus with a tenfold coverage of the haploid genome and walked on both X and Y sex chromosomes starting from both Xmrk genes. This led to the assembly of BAC contigs from the sex-determining region covering approximately 950 kb of the X and 750 kb of the Y chromosome. To our knowledge, these are the largest contigs reported so far for sex chromosomes in fish. Molecular analysis suggests that the sex-determining region of X. maculatus frequently undergoes retrotranspositions and other kinds of rearrangements. This genomic plasticity might be related to the high genetic variability observed in Xiphophorus for sex determination, sexual maturity, pigmentation and melanoma formation, which are encoded by gene loci located in the sex-determining region.
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Affiliation(s)
- Alexander Froschauer
- Lehrstuhl Physiologische Chemie I, Biozentrum, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
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32
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Abstract
Poeciliids are one of the best-studied groups of fishes with respect to sex determination. They present an amazing variety of mechanisms, which span from simple XX-XY or ZZ-ZW systems to polyfactorial sex determination. The gonosomes of poeciliids generally are homomorphic, but very early stages of sex chromosome differentiation have been occasionally detected in some species. In the platyfish Xiphophorus maculatus, gene loci involved in melanoma formation, in different pigmentation patterns and in sexual maturity are closely linked to the sex-determining locus in the subtelomeric region of the X- and Y- chromosomes. The majority of traits encoded by these loci are highly polymorphic. This phenomenon might be explained by the high level of genomic plasticity apparently affecting the sex-determining region, where frequent rearrangements such as duplications, deletions, amplifications, and transpositions frequently occur. We propose that the high plasticity of the sex-determining region might explain the variability of sex determination in Xiphophorus and other poeciliids.
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Affiliation(s)
- J N Volff
- Physiologische Chemie I, Biozentrum der Universität Würzburg, Germany.
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Casaregola S, Neuvéglise C, Bon E, Gaillardin C. Ylli, a non-LTR retrotransposon L1 family in the dimorphic yeast Yarrowia lipolytica. Mol Biol Evol 2002; 19:664-77. [PMID: 11961100 DOI: 10.1093/oxfordjournals.molbev.a004125] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side of this zone of homology allowed the definition of an element over 6 kb long. The conceptual translation of this sequence revealed two open reading frames (ORFs) that displayed several characteristics of non-LTR retrotransposons: a Cys-rich motif in the ORF1, an N-terminal endonuclease, a central RT, and a C-terminal zinc finger domain in the ORF2. We called this element Ylli (for Y. lipolytica LINE). A total of 19 distinct repeats carrying the 3' untranslated region (UTR) and all ending with a poly-A tail were detected. Most of them were very short, 17 being 134 bp long or less. The number of copies of Ylli was estimated to be around 100 if these short repeats are 5' truncations. No 5' UTR was clearly identified, indicating that entire and therefore active elements might be very rare in the Y. lipolytica strain tested. Ylli does not seem to have any insertion specificity. Phylogenetic analysis of the RT domain unambiguously placed Ylli within the L1 clade. It forms a monophyletic group with the Zorro non-LTR retrotransposons discovered in another dimorphic yeast Candida albicans. BLAST comparisons showed that ORF2 of Ylli is closely related to that of the slime mold Dictyostelium discoideum L1 family, TRE.
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Affiliation(s)
- Serge Casaregola
- Collection de Levures d'Intérêt Biotechnologique, Laboratoire de Génétique Moleculaire et Cellulaire, INRA UR216, CNRS URA1925, INA-PG, F-78850 Thiverval-Grignon, France.
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