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Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation? Life (Basel) 2022; 12:life12040522. [PMID: 35455013 PMCID: PMC9025612 DOI: 10.3390/life12040522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes.
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Aroh O, Halanych KM. Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi. BMC Genomics 2021; 22:466. [PMID: 34157969 PMCID: PMC8220671 DOI: 10.1186/s12864-021-07749-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid. Results We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity. Conclusions Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07749-1.
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Affiliation(s)
- Oluchi Aroh
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, College of Science and Mathematics, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA.
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, College of Science and Mathematics, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA
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Non-neutral evolution of H3.3-encoding genes occurs without alterations in protein sequence. Sci Rep 2019; 9:8472. [PMID: 31186448 PMCID: PMC6560044 DOI: 10.1038/s41598-019-44800-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
Histone H3.3 is a developmentally essential variant encoded by two independent genes in human (H3F3A and H3F3B). While this two-gene arrangement is evolutionarily conserved, its origins and function remain unknown. Phylogenetics, synteny and gene structure analyses of H3.3 genes from 32 metazoan genomes indicate independent evolutionary paths for H3F3A and H3F3B. While H3F3B bears similarities with H3.3 genes in distant organisms and with canonical H3 genes, H3F3A is sarcopterygian-specific and evolves under strong purifying selection. Additionally, H3F3B codon-usage preferences resemble those of broadly expressed genes and 'cell differentiation-induced' genes, while codon-usage of H3F3A resembles that of 'cell proliferation-induced' genes. We infer that H3F3B is more similar to the ancestral H3.3 gene and likely evolutionarily adapted for a broad expression pattern in diverse cellular programs, while H3F3A adapted for a subset of gene expression programs. Thus, the arrangement of two independent H3.3 genes facilitates fine-tuning of H3.3 expression across cellular programs.
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Thomas-Bulle C, Piednoël M, Donnart T, Filée J, Jollivet D, Bonnivard É. Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics. BMC Genomics 2018; 19:821. [PMID: 30442098 PMCID: PMC6238403 DOI: 10.1186/s12864-018-5200-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023] Open
Abstract
Background The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested that Copia LTR-retrotransposons display specific dynamic compared to the more abundant and diverse Gypsy elements. Indeed, Copia elements show a relative scarcity and the prevalence of only a few clades in specific hosts. Thus, BEL/Pao seems to be the second most abundant superfamily. However, the generality of these assumptions remains to be assessed. Therefore, we carried out the first large-scale comparative genomic analysis of LTR-retrotransposons in molluscs. The aim of this study was to analyse the diversity, copy numbers, genomic proportions and distribution of LTR-retrotransposons in a large host phylum. Results We compare nine genomes of molluscs and further added LTR-retrotransposons sequences detected in databases for 47 additional species. We identified 1709 families, which enabled us to define 31 clades. We show that clade richness was highly dependent on the considered superfamily. We found only three Copia clades, including GalEa and Hydra which appear to be widely distributed and highly dominant as they account for 96% of the characterised Copia elements. Among the seven BEL/Pao clades identified, Sparrow and Surcouf are characterised for the first time. We find no BEL or Pao elements, but the rare clades Dan and Flow are present in molluscs. Finally, we characterised 21 Gypsy clades, only five of which had been previously described, the C-clade being the most abundant one. Even if they are found in the same number of host species, Copia elements are clearly less abundant than BEL/Pao elements in copy number or genomic proportions, while Gypsy elements are always the most abundant ones whatever the parameter considered. Conclusions Our analysis confirms the contrasting dynamics of Copia and Gypsy elements in metazoans and indicates that BEL/Pao represents the second most abundant superfamily, probably reflecting an intermediate dynamic. Altogether, the data obtained in several taxa highly suggest that these patterns can be generalised for most metazoans. Finally, we highlight the importance of using database information in complement of genome analyses when analyzing transposable element diversity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5200-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camille Thomas-Bulle
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France. .,Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, 29688, Roscoff, France.
| | - Mathieu Piednoël
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
| | - Tifenn Donnart
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
| | - Jonathan Filée
- Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, 29688, Roscoff, France
| | - Éric Bonnivard
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
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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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Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian. Genetica 2016; 144:325-33. [PMID: 27178280 DOI: 10.1007/s10709-016-9901-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.
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8
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Glukhov IA, Kotnova AP, Stefanov YE, Ilyin YV. The first complete Mag family retrotransposons discovered in Drosophila. DOKL BIOCHEM BIOPHYS 2016; 466:1-4. [PMID: 27025475 DOI: 10.1134/s1607672916010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 11/23/2022]
Abstract
A retrotransposon of the Mag family was found in the Drosophila simulans genome for the first time. We also identified novel transposable elements representing the Mag family in seven Drosophila species. The high similarity between the 3' and 5' long terminal repeats in the found copies of transposable elements indicates that their retrotransposition has occurred relatively recently. Thus, the Mag family of retrotransposons is quite common for the genus Drosophila.
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Affiliation(s)
- I A Glukhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia.
| | - A P Kotnova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia
| | - Y E Stefanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia
| | - Y V Ilyin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia.,Institute of Gene Biology, Russian Academy of Sciences, ul. Vavilova 34/5, Moscow, 119334, Russia
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Gao B, Shen D, Xue S, Chen C, Cui H, Song C. The contribution of transposable elements to size variations between four teleost genomes. Mob DNA 2016; 7:4. [PMID: 26862351 PMCID: PMC4746887 DOI: 10.1186/s13100-016-0059-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/11/2016] [Indexed: 11/23/2022] Open
Abstract
Background Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained. Results In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome. Conclusion Overall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bo Gao
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Dan Shen
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Songlei Xue
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Cai Chen
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Hengmi Cui
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Chengyi Song
- Institute of Epigenetics & Epigenomics, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009 China
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Qiu GH. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:31-41. [DOI: 10.1016/j.mrrev.2016.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/22/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
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Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae). Genetica 2015; 143:353-60. [PMID: 25792372 DOI: 10.1007/s10709-015-9834-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45%) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25%). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family.
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Lee A, Nolan A, Watson J, Tristem M. Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120503. [PMID: 23938752 PMCID: PMC3758187 DOI: 10.1098/rstb.2012.0503] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host-parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104-110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum 'lookback' times, with subsequent implications for the field of paleovirology.
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Affiliation(s)
- Adam Lee
- Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Alison Nolan
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Jason Watson
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Michael Tristem
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
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Bohne A, Zhou Q, Darras A, Schmidt C, Schartl M, Galiana-Arnoux D, Volff JN. Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish. Mol Biol Evol 2011; 29:631-45. [DOI: 10.1093/molbev/msr208] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Böhne A, Schultheis C, Galiana-Arnoux D, Froschauer A, Zhou Q, Schmidt C, Selz Y, Ozouf-Costaz C, Dettai A, Segurens B, Couloux A, Bernard-Samain S, Barbe V, Chilmonczyk S, Brunet F, Darras A, Tomaszkiewicz M, Semon M, Schartl M, Volff JN. Molecular analysis of the sex chromosomes of the platyfish Xiphophorus maculatus: Towards the identification of a new type of master sexual regulator in vertebrates. Integr Zool 2011; 4:277-84. [PMID: 21392300 DOI: 10.1111/j.1749-4877.2009.00166.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In contrast to mammals and birds, fish display an amazing diversity of genetic sex determination systems, with frequent changes during evolution possibly associated with the emergence of new sex chromosomes and sex-determining genes. To better understand the molecular and evolutionary mechanisms driving this diversity, several fish models are studied in parallel. Besides the medaka (Oryzias latipes Temminck and Schlegel, 1846) for which the master sex-determination gene has been identified, one of the most advanced models for studying sex determination is the Southern platyfish (Xiphophorus maculatus, Günther 1966). Xiphophorus maculatus belongs to the Poeciliids, a family of live-bearing freshwater fish, including platyfish, swordtails and guppies that perfectly illustrates the diversity of genetic sex-determination mechanisms observed in teleosts. For X. maculatus, bacterial artificial chromosome contigs covering the sex-determination region of the X and Y sex chromosomes have been constructed. Initial molecular analysis demonstrated that the sex-determination region is very unstable and frequently undergoes duplications, deletions, inversions and other rearrangements. Eleven gene candidates linked to the master sex-determining gene have been identified, some of them corresponding to pseudogenes. All putative genes are present on both the X and the Y chromosomes, suggesting a poor degree of differentiation and a young evolutionary age for platyfish sex chromosomes. When compared with other fish and tetrapod genomes, syntenies were detected only with autosomes. This observation supports an independent origin of sex chromosomes, not only in different vertebrate lineages but also between different fish species.
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Affiliation(s)
- Astrid Böhne
- Institute of Functional Genomics, Ecole Normale Supérieure de Lyon / Université de Lyon, Lyon, France
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Villarreal LP. The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 2009; 1178:194-232. [PMID: 19845639 DOI: 10.1111/j.1749-6632.2009.05020.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both virus persistence but will also destroy cells that interrupt this module and thereby prevent infection by competitors. Previously, I have generalized this concept to also include persistent and lytic states of virus infection, which can be considered as a virus addiction module. Such states often involve defective viruses. In this report, I examine the origin of the adaptive immune system from the perspective of a virus addiction module. The likely role of both endogenous and exogenous retroviruses, DNA viruses, and their defective elements is considered in the origin of all the basal components of adaptive immunity (T-cell receptor, RAG-mediated gene rearrangement, clonal lymphocyte proliferation, antigen surface presentation, apoptosis, and education of immune cells). It is concluded that colonization by viruses and their defectives provides a more coherent explanation for the origin of adaptive immunity.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.
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Barthélémy RM, Casanova JP, Faure E. Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons. Open Virol J 2008; 2:44-60. [PMID: 19440464 PMCID: PMC2678813 DOI: 10.2174/1874357900802010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 01/04/2023] Open
Abstract
Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats.
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Affiliation(s)
- Roxane M Barthélémy
- LATP, CNRS-UMR 6632, Evolution biologique et modélisation, case 5, Université de Provence, Place Victor Hugo, 13331 Marseille cedex 3, France
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17
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Literature watch. Xiphophorus. Zebrafish 2008; 3:105-10. [PMID: 18248251 DOI: 10.1089/zeb.2006.3.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Wang S, Bao Z, Hu X, Shao M, Zhang L, Hu J. Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis). Genetica 2007; 133:37-46. [PMID: 17694394 DOI: 10.1007/s10709-007-9180-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2007] [Accepted: 07/16/2007] [Indexed: 11/28/2022]
Abstract
Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons were cloned from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis). The total length of the CFG1 element is 4826 bp, including 5'-LTR (192 bp), the entire ORF (4047 bp) and 3'-LTR (189 bp). The entire ORFs of both CFG1 and PYG1 elements are composed of 1348 aa and do not have any frameshifts. Their closest relative is Jule element from the poeciliid fish (Xiphophorus maculatus). On average, the diploid genome of C. farreri contains approximately 84 copies of CFG1 elements. We summarize the major features of CFG1, PYG1 and other elements of Mag lineage of the Ty3/Gypsy group. mRNA expression of CFG1 element in larvae increases gradually before the gastrulae stage and decreases gradually afterward, whereas in adductor such expression in adductor muscle and digestive gland are lower than those in other tissues. Overall, mRNA expression of CFG1 element in the early larvae is significantly higher than that in adult tissues. In muscle tissue, while the promoter and partial GAG domain of CFG1 element are unmethylated, the partial RT domain is highly methylated. These results suggest that CFG1 expression may be controlled by a post-transcriptional gene silencing mechanism that is associated with coding-region (RT domain) methylation.
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Affiliation(s)
- Shi Wang
- Lab of Molecular Genetics and Breeding of Mollusk, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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19
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Horth L. A sex-linked allele, autosomal modifiers and temperature-dependence appear to regulate melanism in male mosquitofish (Gambusia holbrooki). ACTA ACUST UNITED AC 2007; 209:4938-45. [PMID: 17142682 DOI: 10.1242/jeb.02599] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
About 1% of male mosquitofish (Gambusia holbrooki) express melanic (mottled-black) body coloration, which differs dramatically from the wild-type, silvery-gray coloration. Here, I report on the genetic inheritance pattern of melanic coloration, which indicates Y-linkage, and at least one autosomal modifier. Phenotypic expression of melanism is also affected by temperature. Expression is constitutive (temperature insensitive) in some populations, inducible (temperature sensitive) in others. Constitutive and inducible expression occur among geographically proximal populations. However, males from any single population demonstrate the same constitutive or inducible expression pattern as one another. The F1 males from inter-population crosses demonstrate temperature-related expression patterns like their sires'. As well, the sex ratio of melanic males' progeny differs among populations. Here, inter-population crosses demonstrate a sex-ratio bias in the same direction as intra-population crosses of the sire population. About 20% of the male progeny of melanic sires express the wild-type phenotype. These silver F1 males sire only silver offspring, suggestive of loss of the melanin gene in F1 males from crossover between sex chromosomes, or control by additional modifiers, or involvement of additional factors. In nature, melanic males persist at very low frequencies. The data collected here on heritability indicate that genetic factors contribute to the rarity of melanic male mosquitofish.
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Affiliation(s)
- Lisa Horth
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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20
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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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21
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Zhou Q, Froschauer A, Schultheis C, Schmidt C, Bienert GP, Wenning M, Dettai A, Volff JN. Helitron Transposons on the Sex Chromosomes of the PlatyfishXiphophorus maculatusand Their Evolution in Animal Genomes. Zebrafish 2006; 3:39-52. [DOI: 10.1089/zeb.2006.3.39] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Qingchun Zhou
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
- Present address: Department of Zoology and Stephenson Research & Technology Center, University of Oklahoma, Norman, Oklahoma
| | - Alexander Froschauer
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
- Present address: Institut für Zoologie, Technische Universität Dresden, Dresden, Germany
| | - Christina Schultheis
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Cornelia Schmidt
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Gerd P. Bienert
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Marina Wenning
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Agnès Dettai
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
- Present address: Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Jean-Nicolas Volff
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
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22
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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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23
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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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24
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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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25
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Tubío JMC, Naveira H, Costas J. Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol 2004; 22:29-39. [PMID: 15356275 DOI: 10.1093/molbev/msh251] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The recent availability of the genome of Anopheles gambiae offers an extraordinary opportunity for comparative studies of the diversity of transposable elements (TEs) and their evolutionary dynamics between two related species, taking advantage of the existing information from Drosophila melanogaster. To this goal, we screened the genome of A. gambiae for elements belonging to the Ty3/gypsy group of long-terminal repeat (LTR) retrotransposons. The A. gambiae genome displays a rich diversity of LTR retrotransposons, clearly greater than D. melanogaster. We have characterized in detail 63 families, belonging to five of the nine main lineages of the Ty3/gypsy group. The Mag lineage is the most diverse and abundant, with more than 30 families. In sharp contrast with this finding, a single family belonging to this lineage has been found in D. melanogaster, here reported for the first time in the literature, most probably consisting of old inactive elements. The CsRn1 lineage is also abundant in A. gambiae but almost absent from D. melanogaster. Conversely, the Osvaldo lineage has been detected in Drosophila but not in Anopheles. Comparison of structural characteristics of different families led to the identification of several lineage-specific features such as the primer-binding site (PBS), the gag-pol translational recoding signal (TRS), which is extraordinarily diverse within the Ty3/gypsy retrotransposons of A. gambiae, or the presence/absence of specific amino acid motifs. Interestingly, some of these characteristics, although in general well conserved within lineages, may have evolved independently in particular branches of the phylogenetic tree. We also show evidence of recent activity for around 75% of the families. Nevertheless, almost all families contain a high proportion of degenerate members and solitary LTRs (solo LTRs), indicative of a lower turnover rate of retrotransposons belonging to the Ty3/gypsy group in A. gambiae than in D. melanogaster. Finally, we have detected significant overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.
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Affiliation(s)
- Jose Manuel C Tubío
- Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Spain
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26
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Volff JN, Körting C, Froschauer A, Zhou Q, Wilde B, Schultheis C, Selz Y, Sweeney K, Duschl J, Wichert K, Altschmied J, Schartl M. The xmrk oncogene can escape nonfunctionalization in a highly unstable subtelomeric region of the genome of the fish xiphophorus☆. Genomics 2003; 82:470-9. [PMID: 13679027 DOI: 10.1016/s0888-7543(03)00168-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Xmrk oncogene involved in melanoma formation in the fish Xiphophorus was formed relatively recently by duplication of the epidermal growth factor co-orthologue egfrb. In the platyfish X. maculatus, Xmrk is located close to the major sex-determining locus in a subtelomeric region of the X and Y sex chromosomes that frequently undergoes duplications and other rearrangements. This region accumulates repetitive sequences: more than 80% of the 33-kb region 3' of Xmrk is constituted by retrotransposable elements. The high degree of nucleotide identity between X- and Y-linked sequences and the rarity of gonosome-specific rearrangements indicated that the instability observed was not a manifestation of gonosome-specific degeneration. Seven other duplicated genes were found, all corresponding, in contrast to Xmrk, to pseudogenes (nonfunctionalization). Functional persistence of Xmrk in a highly unstable region in divergent Xiphophorus species suggests a beneficial function under certain conditions for this dispensable and potentially injurious gene.
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Affiliation(s)
- Jean-Nicolas Volff
- Physiologische Chemie I, Biozentrum der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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27
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Ota K, Tateno Y, Gojobori T. Highly differentiated and conserved sex chromosome in fish species (Aulopus japonicus: Teleostei, Aulopidae). Gene 2003; 317:187-93. [PMID: 14604807 DOI: 10.1016/s0378-1119(03)00702-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While highly differentiated and long-conserved sex chromosomes such as XY and ZW chromosomes are observed, respectively, in mammalian and avian species, no counterparts to such chromosomes were observed in fish until we reported in the previous study that well-conserved and highly differentiated ZW sex chromosomes existed in the family of Synodontidae. Then, the problem was if the evolutionary history of the fish ZW chromosomes was long enough to be comparable to the mammalian and avian counterparts. To tackle the problem, we had to extend our finding of the fish sex chromosomes further than a family alone. For this purpose, we chose Aulopus japonicus that belonged to one of the related families to Synodontidae. Our cytogenetic and fluorescence in situ hybridization (FISH) analyses have clearly demonstrated that A. japonicus also has ZW chromosomes. We have also found that 5S rDNA clusters are located on the Z and W chromosomes in this species. Using nontranscribed intergenic sequences in the 5S rDNA clusters as PCR primers, we successfully amplified a 6-kb-long female-specific sequence on the W chromosome. The 6-kb-long sequence contained one transposable element and two tRNA sequences. The function of the sequence remains to be studied. Our Southern blot analysis confirmed that the 6-kb sequence was located only on the W chromosome.Therefore, it is now said that highly differentiated ZW chromosomes have been conserved over two fish families. As these families were reported to have been diverged 30-60 million years ago, the fish ZW chromosomes have an evolutionary history corresponding to the history of the families. This is perhaps the first case that fish sex chromosomes are shown to have such a long evolutionary lineage.
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Affiliation(s)
- Kinya Ota
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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28
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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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29
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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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30
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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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