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Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
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Etchegaray E, Dechaud C, Barbier J, Naville M, Volff JN. Diversity of Harbinger-like Transposons in Teleost Fish Genomes. Animals (Basel) 2022; 12:ani12111429. [PMID: 35681893 PMCID: PMC9179366 DOI: 10.3390/ani12111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The study of transposable elements, which are repeated DNA sequences that can insert into new locations in genomes, is of particular interest to genome evolution, as they are sources of mutations but also of new regulatory and coding sequences. Teleost fish are a species-rich clade presenting a high diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger-like DNA transposons, which are widespread from plants to vertebrates but absent from mammalian genomes. These elements code for both a transposase and a Myb-like protein. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish. While Harbinger transposons might have been present in a common ancestor of all the fish species studied, ISL2EU elements were possibly gained by horizontal transfer at the base of teleost fish. Transposase and Myb-like protein phylogenies of Harbinger transposons indicated unique origins of the association between both genes and suggests recombination was rare between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish. Abstract Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.
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Dechaud C, Miyake S, Martinez-Bengochea A, Schartl M, Volff JN, Naville M. Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes. Genome Biol Evol 2021; 13:6384576. [PMID: 34623422 PMCID: PMC8633743 DOI: 10.1093/gbe/evab230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Although genes with similar expression patterns are sometimes found in the same genomic regions, almost nothing is known about the relative organization in genomes of genes and transposable elements (TEs), which might influence each other at the regulatory level. In this study, we used transcriptomic data from male and female gonads of the Japanese medaka Oryzias latipes to define sexually biased genes and TEs and analyze their relative genomic localization. We identified 20,588 genes expressed in the adult gonads of O. latipes. Around 39% of these genes are differentially expressed between male and female gonads. We further analyzed the expression of TEs using the program SQuIRE and showed that more TE copies are overexpressed in testis than in ovaries (36% vs. 10%, respectively). We then developed a method to detect genomic regions enriched in testis- or ovary-biased genes. This revealed that sex-biased genes and TEs are not randomly distributed in the genome and a part of them form clusters with the same expression bias. We also found a correlation of expression between TE copies and their closest genes, which increases with decreasing intervening distance. Such a genomic organization suggests either that TEs hijack the regulatory sequences of neighboring sexual genes, allowing their expression in germ line cells and consequently new insertions to be transmitted to the next generation, or that TEs are involved in the regulation of sexual genes, and might therefore through their mobility participate in the rewiring of sex regulatory networks.
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Affiliation(s)
- Corentin Dechaud
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Sho Miyake
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | | | - Manfred Schartl
- Entwicklungsbiochemie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
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Helmprobst F, Kneitz S, Klotz B, Naville M, Dechaud C, Volff JN, Schartl M. Differential expression of transposable elements in the medaka melanoma model. PLoS One 2021; 16:e0251713. [PMID: 34705830 PMCID: PMC8550402 DOI: 10.1371/journal.pone.0251713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish.
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Affiliation(s)
- Frederik Helmprobst
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Neuropathology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (FH); (MS)
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
- Developmental Biochemistry, University of Würzburg, Würzburg, Germany
- * E-mail: (FH); (MS)
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Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff JN, Cabau C, Klopp C, Møller PR, Bernatchez L, García-Machado E, Rétaux S, Casane D. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals. Mol Biol Evol 2021; 38:589-605. [PMID: 32986833 PMCID: PMC7826195 DOI: 10.1093/molbev/msaa249] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.
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Affiliation(s)
- Maxime Policarpo
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Fumey
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Lafargeas
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Cedric Cabau
- SIGENAE, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Christophe Klopp
- INRAE, SIGENAE, Genotoul Bioinfo, MIAT UR875, Castanet Tolosan, France
| | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | - Louis Bernatchez
- Department of Biology, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Erik García-Machado
- Department of Biology, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Centro de Investigaciones Marinas, Universidad de La Habana, La Habana, Cuba
| | - Sylvie Rétaux
- CNRS, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Casane
- CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France.,UFR Sciences du Vivant, Université de Paris, Paris, France
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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 2021; 590:284-289. [PMID: 33461212 PMCID: PMC7875771 DOI: 10.1038/s41586-021-03198-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023]
Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
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Affiliation(s)
- Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Wai Yee Wong
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Peiwen Xiong
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Herman P Spaink
- Faculty of Science, Universiteit Leiden, Leiden, The Netherlands
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | | | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
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Abstract
Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called "exaptation" events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.
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Affiliation(s)
- Ema Etchegaray
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France.
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
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Fouret J, Brunet FG, Binet M, Aurine N, Enchéry F, Croze S, Guinier M, Goumaidi A, Preininger D, Volff JN, Bailly-Bechet M, Lachuer J, Horvat B, Legras-Lachuer C. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front Microbiol 2020; 11:1807. [PMID: 32849415 PMCID: PMC7403528 DOI: 10.3389/fmicb.2020.01807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/09/2020] [Indexed: 11/20/2022] Open
Abstract
Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.
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Affiliation(s)
- Julien Fouret
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Binet
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Noémie Aurine
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Francois Enchéry
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Séverine Croze
- Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | | | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Joël Lachuer
- Cancer Research Center of Lyon, INSERM 1052/CNRS 5286, Université de Lyon, Lyon, France.,Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | - Branka Horvat
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine Legras-Lachuer
- Viroscan3D, Trévoux, France.,Ecologie Microbienne, CNRS UMR 5557, LEM, INRA, VetAgro Sup, Université Claude Bernard Lyon 1, Villeurbanne, France
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10
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Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Res 2020; 48:D668-D675. [PMID: 31680137 PMCID: PMC7145539 DOI: 10.1093/nar/gkz955] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.
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Affiliation(s)
| | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Faure
- Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | | | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kai Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | | | | | - Shigeki Fujiwara
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi-shi, Kochi, Japan
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Hugues Roest Crollius
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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11
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Dechaud C, Volff JN, Schartl M, Naville M. Sex and the TEs: transposable elements in sexual development and function in animals. Mob DNA 2019; 10:42. [PMID: 31700550 PMCID: PMC6825717 DOI: 10.1186/s13100-019-0185-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 12/23/2022] Open
Abstract
Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of sexual development genes, and how, reciprocally, they are tightly controlled in gonads. We also review how transposable elements contribute to the organization, expression and evolution of sexual development genes and sex chromosomes. This underscores the intricate co-evolution between host functions and transposable elements, which regularly shift from a parasitic to a domesticated status useful to the host.
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Affiliation(s)
- Corentin Dechaud
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
| | - Manfred Schartl
- Entwicklungsbiochemie, Biozentrum, Universität Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX USA
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
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12
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown CT, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2019; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.,Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d'Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA.,Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA.,Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d'Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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13
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Salis P, Lorin T, Lewis V, Rey C, Marcionetti A, Escande ML, Roux N, Besseau L, Salamin N, Sémon M, Parichy D, Volff JN, Laudet V. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish. Pigment Cell Melanoma Res 2019; 32:391-402. [PMID: 30633441 DOI: 10.1111/pcmr.12766] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022]
Abstract
Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leucophores. We used the clownfish Amphiprion ocellaris, which has a color pattern consisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars exhibits similarities with that of zebrafish iridophores. We further show by pharmacological treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for iridophore development in zebrafish. Our analyses provide clues to the genomic underpinning of color diversity and allow identification of new iridophore genes in fish.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Thibault Lorin
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Victor Lewis
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France.,LBBE, CNRS, Université Lyon 1, Villeurbanne, France
| | - Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Laurence Besseau
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France
| | - David Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Jean-Nicolas Volff
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
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14
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Mommert M, Tabone O, Oriol G, Cerrato E, Guichard A, Naville M, Fournier P, Volff JN, Pachot A, Monneret G, Venet F, Brengel-Pesce K, Textoris J, Mallet F. LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs. BMC Genomics 2018; 19:522. [PMID: 29976163 PMCID: PMC6034278 DOI: 10.1186/s12864-018-4901-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/27/2018] [Indexed: 12/29/2022] Open
Abstract
Background Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to be essentially silent except in cancer, autoimmunity and placental development. Their Long Terminal Repeats (LTRs) constitute putative promoter or polyA regulatory sequences. In this study, we used a recently described high-density microarray which can be used to study HERV/MaLR transcriptome including 353,994 HERV/MaLR loci and 1559 immunity-related genes. Results We described, for the first time, the HERV transcriptome in peripheral blood mononuclear cells (PBMCs) using a cellular model mimicking inflammatory response and monocyte anergy observed after septic shock. About 5.6% of the HERV/MaLR repertoire is transcribed in PBMCs. Roughly one-tenth [5.7–13.1%] of LTRs exhibit a putative constitutive promoter or polyA function while one-quarter [19.5–27.6%] may shift from silent to active. Evidence was given that some HERVs/MaLRs and genes may share similar regulation control under lipopolysaccharide (LPS) stimulation conditions. Stimulus-dependent response confirms that HERV expression is tightly regulated in PBMCs. Altogether, these observations make it possible to integrate 62 HERVs/MaLRs and 26 genes in 11 canonical pathways and suggest a link between HERV expression and immune response. The transcriptional modulation of HERVs located close to genes such as OAS2/3 and IFI44/IFI44L or at a great distance from genes was discussed. Conclusion This microarray-based approach revealed the expression of about 47,466 distinct HERV loci and identified 951 putative promoter LTRs and 744 putative polyA LTRs in PBMCs. HERV/MaLR expression was shown to be tightly modulated under several stimuli including high-dose and low-dose LPS and Interferon-γ (IFN-γ). HERV incorporation at the crossroads of immune response pathways paves the way for further functional studies and analyses of the HERV transcriptome in altered immune responses in vivo such as in sepsis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4901-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marine Mommert
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France. .,EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France.
| | - Olivier Tabone
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France
| | - Guy Oriol
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Elisabeth Cerrato
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France
| | - Audrey Guichard
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France.,EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon, 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Paola Fournier
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon, 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Alexandre Pachot
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France
| | - Guillaume Monneret
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France.,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Fabienne Venet
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France.,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Karen Brengel-Pesce
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Julien Textoris
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France.,Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, Université Claude Bernard Lyon 1, Lyon, France
| | - François Mallet
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France. .,EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon, Cedex 3, France.
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15
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Brunet FG, Audit B, Drillon G, Argoul F, Volff JN, Arneodo A. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. Biophys J 2018; 114:2308-2316. [PMID: 29580552 PMCID: PMC6028776 DOI: 10.1016/j.bpj.2018.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022] Open
Abstract
Nucleosome-depleted regions around which nucleosomes order following the "statistical" positioning scenario were recently shown to be encoded in the DNA sequence in human. This intrinsic nucleosomal ordering strongly correlates with oscillations in the local GC content as well as with the interspecies and intraspecies mutation profiles, revealing the existence of both positive and negative selection. In this letter, we show that these predicted nucleosome inhibitory energy barriers (NIEBs) with compacted neighboring nucleosomes are indeed ubiquitous to all vertebrates tested. These 1 kb-sized chromatin patterns are widely distributed along vertebrate chromosomes, overall covering more than a third of the genome. We have previously observed in human deviations from neutral evolution at these genome-wide distributed regions, which we interpreted as a possible indication of the selection of an open, accessible, and dynamic nucleosomal array to constitutively facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner. As a first, very appealing observation supporting this hypothesis, we report evidence of a strong association between NIEB borders and the poly(A) tails of Alu sequences in human. These results suggest that NIEBs provide adequate chromatin patterns favorable to the integration of Alu retrotransposons and, more generally to various transposable elements in the genomes of primates and other vertebrates.
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Affiliation(s)
- Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Guénola Drillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Françoise Argoul
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Alain Arneodo
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France.
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16
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Warren WC, García-Pérez R, Xu S, Lampert KP, Chalopin D, Stöck M, Loewe L, Lu Y, Kuderna L, Minx P, Montague MJ, Tomlinson C, Hillier LW, Murphy DN, Wang J, Wang Z, Garcia CM, Thomas GWC, Volff JN, Farias F, Aken B, Walter RB, Pruitt KD, Marques-Bonet T, Hahn MW, Kneitz S, Lynch M, Schartl M. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Nat Ecol Evol 2018; 2:669-679. [PMID: 29434351 PMCID: PMC5866774 DOI: 10.1038/s41559-018-0473-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022]
Abstract
The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.
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Affiliation(s)
- Wesley C. Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | | | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Kathrin P. Lampert
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon I, Lyon, France
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Laurence Loewe
- Laboratory of Genetics and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Yuan Lu
- Texas State University, Department of Chemistry and Biochemistry, San Marcos, TX 78666, USA
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Michael J. Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - LaDeana W. Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Daniel N. Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - John Wang
- Biodiversity Research Center, Academica Sinica Taipei, Taiwan
| | - Zhongwei Wang
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany; present address: Institute of Hydrobiology, Chinese Academy of Sciences, China
| | - Constantino Macias Garcia
- Instituto de Ecología, Universidad Nacional Autónoma de México, CP 04510, Ciudad Universitaria, México DF
| | | | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon I, Lyon, France
| | - Fabiana Farias
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ronald B. Walter
- Texas State University, Department of Chemistry and Biochemistry, San Marcos, TX 78666, USA
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Center for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, and Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Matthew W. Hahn
- Indiana University, Department of Biology, Bloomington, IN 47405, USA
| | - Susanne Kneitz
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Michael Lynch
- Indiana University, Department of Biology, Bloomington, IN 47405, USA
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX 77843, USA, and Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany
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17
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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. J Exp Zool B Mol Dev Evol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Sarkar A, Volff JN, Vaury C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation? FASEB J 2016; 31:436-446. [PMID: 27799346 DOI: 10.1096/fj.201600637rr] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/14/2016] [Indexed: 01/12/2023]
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement. In this review, we discuss some of these recently reported roles. Data on these new roles are often rudimentary, and the involvement of piRNAs in these processes is yet to be definitely established. What is interesting is that the reports are on animals widely separated on the phylogenetic tree of life and that piRNAs were also found outside the gonadal tissues. Some of these piRNAs map to TE sequences, prompting us to hypothesize that genomes may have co-opted the TE-derived piRNA system for their own regulation.-Sarkar, A., Volff, J.-N., Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation?
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Affiliation(s)
- Arpita Sarkar
- Laboratoire de Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique, INSERM, Université Clermont Auvergne, Clermont-Ferrand,France; and
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chantal Vaury
- Laboratoire de Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique, INSERM, Université Clermont Auvergne, Clermont-Ferrand,France; and
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19
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Lesage P, Bétermier M, Bridier-Nahmias A, Chandler M, Chambeyron S, Cristofari G, Gilbert N, Quesneville H, Vaury C, Volff JN. International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany. Mob DNA 2016; 7:19. [PMID: 30044887 PMCID: PMC5072296 DOI: 10.1186/s13100-016-0075-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/12/2016] [Indexed: 11/18/2022] Open
Abstract
The third international conference on Transposable Elements (ICTE) was held 16–19 April 2016 in Saint Malo, France. Organized by the French Transposition Community (Research group of the CNRS: “Mobile genetic elements: from mechanism to populations, an integrative approach”) and the French Society of Genetics, the conference’s goal was to bring together researchers who study transposition in diverse organisms, using multiple experimental approaches. The meeting gathered 180 participants from all around the world. Most of them contributed through poster presentations, invited talks and short talks selected from poster abstracts. The talks were organized into six scientific sessions: “Taming mobile DNA: self and non-self recognition”; “Trans-generational inheritance”; “Mobile DNA genome structure and organization, from molecular mechanisms to applications”; “Remembrance of (retro)transposon past: mobile DNA in genome evolution”; and finally “The yin and the yang of mobile DNA in human health”.
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Affiliation(s)
- Pascale Lesage
- Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital Saint Louis, 75010 Paris, France
| | - Mireille Bétermier
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Antoine Bridier-Nahmias
- Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital Saint Louis, 75010 Paris, France.,Department CASER Conservatoire national des arts et métiers (Cnam), 75003 Paris, France
| | - Michael Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique, Unité Mixte de Recherche 5100, 118 Rte de Narbonne, 31062 Toulouse Cedex, France
| | - Séverine Chambeyron
- Institut de Génétique Humaine, CNRS, UPR1142, 34396 Montpellier Cedex 5, France
| | - Gael Cristofari
- Institute for Research on Cancer and Aging in Nice (IRCAN), CNRS UMR 7284, Inserm U1081, Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Nicolas Gilbert
- Institute for Regenerative Medicine and Biotherapy, INSERM, U1183 Montpellier, France
| | - Hadi Quesneville
- INRA, UR 1164, URGI, Unité de Recherche en Génomique-Info, 78026 Versailles Cedex, France
| | - Chantal Vaury
- Laboratoire GReD, Université Clermont Auvergne, CNRS, Inserm, BP 10448, 63000 Clermont-Ferrand, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
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20
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Pérot P, Mullins CS, Naville M, Bressan C, Hühns M, Gock M, Kühn F, Volff JN, Trillet-Lenoir V, Linnebacher M, Mallet F. Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes. Oncotarget 2016; 6:40095-111. [PMID: 26517682 PMCID: PMC4741882 DOI: 10.18632/oncotarget.5539] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/13/2015] [Indexed: 01/02/2023] Open
Abstract
Background Expression of the human endogenous retrovirus (HERV)-H family has been associated with colorectal carcinomas (CRC), yet no individual HERV-H locus expression has been thoroughly correlated with clinical data. Here, we characterized HERV-H reactivations in clinical CRC samples by integrating expression profiles, molecular patterns and clinical data. Expression of relevant HERV-H sequences was analyzed by qRT-PCR on two well-defined clinical cohorts (n = 139 pairs of tumor and adjacent normal colon tissue) including samples from adenomas (n = 21) and liver metastases (n = 16). Correlations with clinical and molecular data were assessed. Results CRC specific HERV-H sequences were validated and found expressed throughout CRC disease progression. Correlations between HERV-H expression and lymph node invasion of tumor cells (p = 0.0006) as well as microsatellite instable tumors (p < 0.0001) were established. No association with regard to age, tumor localization, grading or common mutations became apparent. Interestingly, CRC expressed elements belonged to specific young HERV-H subfamilies and their 5′ LTR often presented active histone marks. Conclusion These results suggest a functional role of HERV-H sequences in colorectal carcinogenesis. The pronounced connection with microsatellite instability warrants a more detailed investigation. Thus, HERV-H sequences in addition to tumor specific mutations may represent clinically relevant, truly CRC specific markers for diagnostic, prognostic and therapeutic purposes.
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Affiliation(s)
- Philippe Pérot
- Cancer Biomarkers Research Group, Joint Unit Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre Bénite, France.,Current address: Institut Pasteur, Laboratory for Pathogen Discovery, Paris, France
| | - Christina Susanne Mullins
- Cancer Biomarkers Research Group, Joint Unit Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre Bénite, France.,Centre d'Investigation des Thérapeutiques en Oncologie et Hématologie, EMR 3738 Lyon Claude Bernard University, Institut de Cancérologie des Hospices Civils de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS/Université Lyon I, Lyon, France
| | - Cédric Bressan
- Cancer Biomarkers Research Group, Joint Unit Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Maja Hühns
- Institute of Pathology, University Medicine Rostock, Rostock, Germany
| | - Michael Gock
- Department of General, Thoracic, Vascular and Transplantation Surgery, University Medicine Rostock, Rostock, Germany
| | - Florian Kühn
- Department of General, Thoracic, Vascular and Transplantation Surgery, University Medicine Rostock, Rostock, Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS/Université Lyon I, Lyon, France
| | - Véronique Trillet-Lenoir
- Centre d'Investigation des Thérapeutiques en Oncologie et Hématologie, EMR 3738 Lyon Claude Bernard University, Institut de Cancérologie des Hospices Civils de Lyon, Lyon, France
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University Medicine Rostock, Rostock, Germany
| | - François Mallet
- Cancer Biomarkers Research Group, Joint Unit Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre Bénite, France
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21
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Warren IA, Naville M, Chalopin D, Levin P, Berger CS, Galiana D, Volff JN. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 2016; 23:505-31. [PMID: 26395902 DOI: 10.1007/s10577-015-9493-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.
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Affiliation(s)
- Ian A Warren
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Perrine Levin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chloé Suzanne Berger
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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22
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Abstract
In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.
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Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, GA, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jennifer L Anderson
- INRA, Fish Physiology and Genomics (UR1037), Campus de Beaulieu, Rennes, France.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Manfred Schartl
- Department Physiological Chemistry, Biozentrum, University of Wuerzburg, and Comprehensive Cancer Center Mainfranken, University Clinic Wuerzburg, Wuerzburg, Germany.
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Naville M, Volff JN. Endogenous Retroviruses in Fish Genomes: From Relics of Past Infections to Evolutionary Innovations? Front Microbiol 2016; 7:1197. [PMID: 27555838 PMCID: PMC4977317 DOI: 10.3389/fmicb.2016.01197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/19/2016] [Indexed: 12/16/2022] Open
Abstract
The increasing availability of fish genome sequences has allowed to gain new insights into the diversity and host distribution of retroviruses in fish and other vertebrates. This distribution can be assessed through the identification and analysis of endogenous retroviruses, which are proviral remnants of past infections integrated in genomes. Retroviral sequences are probably important for evolution through their ability to induce rearrangements and to contribute regulatory and coding sequences; they may also protect their host against new infections. We argue that the current mass of genome sequences will soon strongly improve our understanding of retrovirus diversity and evolution in aquatic animals, with the identification of new/re-emerging elements and host resistance genes that restrict their infectivity.
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Affiliation(s)
- Magali Naville
- Génomique Évolutive des Poissons, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1 Lyon, France
| | - Jean-Nicolas Volff
- Génomique Évolutive des Poissons, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1 Lyon, France
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Abstract
The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75% after 1R/2R, 64.4% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.
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Affiliation(s)
- Frédéric G Brunet
- 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
| | - Manfred Schartl
- Physiologische Chemie, Biozentrum, University of Würzburg, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo¨ldi J, Lindblad-Toh K, Postlethwait JH. Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:700. [DOI: 10.1038/ng0616-700c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fraune J, Brochier-Armanet C, Alsheimer M, Volff JN, Schücker K, Benavente R. Evolutionary history of the mammalian synaptonemal complex. Chromosoma 2016; 125:355-60. [PMID: 26968413 DOI: 10.1007/s00412-016-0583-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 12/29/2022]
Abstract
The synaptonemal complex (SC), a key structure of meiosis that assembles during prophase I, has been initially described 60 years ago. Since then, the structure has been described in many sexually reproducing organisms. However, the SC protein components were characterized in only few model organisms. Surprisingly, they lacked an apparent evolutionary relationship despite the conserved structural organization of the SC. For better understanding of this obvious discrepancy, the evolutionary history of the SC and its individual components has been investigated in Metazoa in detail. The results are consistent with the notion of a single origin of the metazoan SC and provide evidence for a dynamic evolutionary history of the SC components. In this mini review, we recapitulate and discuss new insights into metazoan SC evolution.
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Affiliation(s)
- Johanna Fraune
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Céline Brochier-Armanet
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 bd du 11 novembre 1918, Villeurbanne, 69622, France
| | - Manfred Alsheimer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Lyon, France
| | - Katharina Schücker
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff JN, Postlethwait JH, Schartl M, Minx P, Warren WC, Walter RB. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics 2016; 17:37. [PMID: 26742787 PMCID: PMC4705583 DOI: 10.1186/s12864-015-2361-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/30/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. RESULTS We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. CONCLUSIONS Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
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Affiliation(s)
- Yingjia Shen
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, A316 Environment and Ecology Bldg., Xiamen, Fujian, 361102, China.
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Tzintzuni Garcia
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Sergey A Shiryev
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Richa Agarwala
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR, 97403, USA.
| | - Manfred Schartl
- Universität Würzburg, Physiologische Chemie I, Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany.
| | - Patrick Minx
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
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Regneri J, Volff JN, Schartl M. Transcriptional control analyses of the Xiphophorus melanoma oncogene. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:116-127. [PMID: 26348392 PMCID: PMC4662873 DOI: 10.1016/j.cbpc.2015.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/25/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Melanoma development in interspecific hybrids of Xiphophorus is induced by the overexpression of the mutationally activated receptor tyrosine kinase Xmrk in pigment cells. Based on the melanocyte specificity of the transcriptional upregulation, a pigment cell-specific promoter region was postulated for xmrk, the activity of which is controlled in healthy purebred fish by the molecularly still unidentified regulator locus R. However, as yet the xmrk promoter region is still poorly characterized. In order to contribute to a better understanding of xmrk expression regulation, we performed a functional analysis of the entire putative gene regulatory region of the oncogene using conventional plasmid-based reporter systems as well as a newly established method employing BAC-derived luciferase reporter constructs in melanoma and non-melanoma cell lines. Using the melanocyte-specific mitfa promoter as control, we could demonstrate that our in vitro system is able to reliably monitor regulation of transcription through cell type-specific regulatory sequences. We found that sequences within 200kb flanking the xmrk oncogene do not lead to any specific transcriptional activation in melanoma compared to control cells. Hence, xmrk reporter constructs fail to faithfully reproduce the endogenous transcriptional regulation of the oncogene. Our data therefore strongly indicate that the melanocyte-specific transcription of xmrk is not the consequence of pigment cell-specific cis-regulatory elements in the promoter region. This hints at additional regulatory mechanisms involved in transcriptional control of the oncogene, thereby suggesting a key role for epigenetic mechanisms in oncogenic xmrk overexpression and thereby in tumor development in Xiphophorus.
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Affiliation(s)
- Janine Regneri
- Physiological Chemistry, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionelle de Lyon, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon cedex 07, France
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany; Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.
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29
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Naville M, Chalopin D, Casane D, Laurenti P, Volff JN. The coelacanth: Can a "living fossil" have active transposable elements in its genome? Mob Genet Elements 2015; 5:55-59. [PMID: 26442185 DOI: 10.1080/2159256x.2015.1052184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 01/24/2023] Open
Abstract
The coelacanth has long been regarded as a "living fossil," with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a "living fossil." Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a "non-fossil" vertebrate species.
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Affiliation(s)
- Magali Naville
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Domitille Chalopin
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Didier Casane
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Patrick Laurenti
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Jean-Nicolas Volff
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
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30
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Henriet S, Sumic S, Doufoundou-Guilengui C, Jensen MF, Grandmougin C, Fal K, Thompson E, Volff JN, Chourrout D. Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline. Nucleic Acids Res 2015; 43:3701-11. [PMID: 25779047 PMCID: PMC4402516 DOI: 10.1093/nar/gkv169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
Selective pressure to maintain small genome size implies control of transposable elements, and most old classes of retrotransposons are indeed absent from the very compact genome of the tunicate Oikopleura dioica. Nonetheless, two families of retrotransposons are present, including the Tor elements. The gene organization within Tor elements is similar to that of LTR retrotransposons and retroviruses. In addition to gag and pol, many Tor elements carry a third gene encoding viral envelope-like proteins (Env) that may mediate infection. We show that the Tor family contains distinct classes of elements. In some classes, env mRNA is transcribed from the 5′LTR as in retroviruses. In others, env is transcribed from an additional promoter located downstream of the 5′LTR. Tor Env proteins are membrane-associated glycoproteins which exhibit some features of viral membrane fusion proteins. Whereas some elements are expressed in the adult testis, many others are specifically expressed in embryonic somatic cells adjacent to primordial germ cells. Such embryonic expression depends on determinants present in the Tor elements and not on their surrounding genomic environment. Our study shows that unusual modes of transcription and expression close to the germline may contribute to the proliferation of Tor elements.
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Affiliation(s)
- Simon Henriet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Sara Sumic
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | | | - Marit Flo Jensen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Camille Grandmougin
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Kateryna Fal
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Eric Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway Department of Biology, University of Bergen, Bergen, N-5020, Norway
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon - CNRS UMR 5242 - INRA USC 1370, Lyon, 69364 Lyon cedex 07, France
| | - Daniel Chourrout
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
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Chalopin D, Naville M, Plard F, Galiana D, Volff JN. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 2015; 7:567-80. [PMID: 25577199 PMCID: PMC4350176 DOI: 10.1093/gbe/evv005] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.
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Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Floriane Plard
- Laboratoire "Biométrie et Biologie Évolutive," Unité Mixte de Recherche 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
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Valdivia K, Jouanno E, Volff JN, Galiana-Arnoux D, Guyomard R, Helary L, Mourot B, Fostier A, Quillet E, Guiguen Y. High temperature increases the masculinization rate of the all-female (XX) rainbow trout "Mal" population. PLoS One 2014; 9:e113355. [PMID: 25501353 PMCID: PMC4264747 DOI: 10.1371/journal.pone.0113355] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 10/27/2014] [Indexed: 02/06/2023] Open
Abstract
Salmonids are generally considered to have a robust genetic sex determination system with a simple male heterogamety (XX/XY). However, spontaneous masculinization of XX females has been found in a rainbow trout population of gynogenetic doubled haploid individuals. The analysis of this masculinization phenotype transmission supported the hypothesis of the involvement of a recessive mutation (termed mal). As temperature effect on sex differentiation has been reported in some salmonid species, in this study we investigated in detail the potential implication of temperature on masculinization in this XX mal-carrying population. Seven families issued from XX mal-carrying parents were exposed from the time of hatching to different rearing water temperatures ((8, 12 and 18°C), and the resulting sex-ratios were confirmed by histological analysis of both gonads. Our results demonstrate that masculinization rates are strongly increased (up to nearly two fold) at the highest temperature treatment (18°C). Interestingly, we also found clear differences between temperatures on the masculinization of the left versus the right gonads with the right gonad consistently more often masculinized than the left one at lower temperatures (8 and 12°C). However, the masculinization rate is also strongly dependent on the genetic background of the XX mal-carrying families. Thus, masculinization in XX mal-carrying rainbow trout is potentially triggered by an interaction between the temperature treatment and a complex genetic background potentially involving some part of the genetic sex differentiation regulatory cascade along with some minor sex-influencing loci. These results indicate that despite its rather strict genetic sex determinism system, rainbow trout sex differentiation can be modulated by temperature, as described in many other fish species.
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Affiliation(s)
- Karina Valdivia
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
| | - Elodie Jouanno
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
| | - Jean-Nicolas Volff
- IGFL, UMR5242 CNRS/INRA/Université Claude Bernard Lyon I/ENS, Lyon, Cedex 07, France
| | | | - René Guyomard
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Louise Helary
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
| | - Brigitte Mourot
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
| | - Alexis Fostier
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
| | - Edwige Quillet
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Yann Guiguen
- INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000, Rennes, France
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Naville M, Chalopin D, Volff JN. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths. PLoS One 2014; 9:e114382. [PMID: 25470617 PMCID: PMC4255032 DOI: 10.1371/journal.pone.0114382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/10/2014] [Indexed: 01/29/2023] Open
Abstract
Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.
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Affiliation(s)
- Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
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McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SMJ, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC. The cavefish genome reveals candidate genes for eye loss. Nat Commun 2014; 5:5307. [PMID: 25329095 PMCID: PMC4218959 DOI: 10.1038/ncomms6307] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022] Open
Abstract
Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.
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Affiliation(s)
- Suzanne E McGaugh
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Bronwen Aken
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maryline Blin
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Richard Borowsky
- Department of Biology, New York University, New York, New York 10003-6688, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d'Italie, Lyon F-69364, France
| | - Hélène Hinaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Alex Keene
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Patrick Minx
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Daniel Murphy
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly E O'Quin
- Department of Biology, Centre College, 600 West Walnut St, Danville, Kentucky 40422, USA
| | - Sylvie Rétaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Nicolas Rohner
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Steve M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bethany A Stahl
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Cliff Tabin
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d'Italie, Lyon F-69364, France
| | - Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wesley C Warren
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
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Stolfi A, Sasakura Y, Chalopin D, Satou Y, Christiaen L, Dantec C, Endo T, Naville M, Nishida H, Swalla BJ, Volff JN, Voskoboynik A, Dauga D, Lemaire P. Guidelines for the nomenclature of genetic elements in tunicate genomes. Genesis 2014; 53:1-14. [PMID: 25220678 DOI: 10.1002/dvg.22822] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 01/23/2023]
Abstract
Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines.
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Affiliation(s)
- Alberto Stolfi
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, New York
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Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, Song W, An N, Chalopin D, Volff JN, Hong Y, Li Q, Sha Z, Zhou H, Xie M, Yu Q, Liu Y, Xiang H, Wang N, Wu K, Yang C, Zhou Q, Liao X, Yang L, Hu Q, Zhang J, Meng L, Jin L, Tian Y, Lian J, Yang J, Miao G, Liu S, Liang Z, Yan F, Li Y, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao Y, Schartl M, Tang Q, Wang J. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 2014; 46:253-60. [DOI: 10.1038/ng.2890] [Citation(s) in RCA: 551] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
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Forconi M, Chalopin D, Barucca M, Biscotti MA, De Moro G, Galiana D, Gerdol M, Pallavicini A, Canapa A, Olmo E, Volff JN. Transcriptional activity of transposable elements in coelacanth. J Exp Zool B Mol Dev Evol 2013; 322:379-89. [PMID: 24038780 DOI: 10.1002/jez.b.22527] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 07/14/2013] [Indexed: 01/22/2023]
Abstract
The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity.
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Affiliation(s)
- Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy; Institut de Génomique Fonctionnelle de Lyon, ENS Lyon, France
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Chalopin D, Fan S, Simakov O, Meyer A, Schartl M, Volff JN. Evolutionary active transposable elements in the genome of the coelacanth. J Exp Zool (Mol Dev Evol ) 2013; 322:322-33. [DOI: 10.1002/jez.b.22521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/22/2013] [Accepted: 06/17/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
| | - Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Oleg Simakov
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- European Molecular Biology Laboratory; Heidelberg Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Manfred Schartl
- Department Physiological Chemistry, Biocenter; University of Wuerzburg; Wuerzburg Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
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Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SMJ, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. The African coelacanth genome provides insights into tetrapod evolution. Nature 2013; 496:311-6. [PMID: 23598338 PMCID: PMC3633110 DOI: 10.1038/nature12027] [Citation(s) in RCA: 464] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 02/20/2013] [Indexed: 01/28/2023]
Abstract
It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
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Affiliation(s)
- Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.
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Valdivia K, Mourot B, Jouanno E, Volff JN, Galiana-Arnoux D, Guyomard R, Cauty C, Collin B, Rault P, Helary L, Fostier A, Quillet E, Guiguen Y. Sex differentiation in an all-female (XX) rainbow trout population with a genetically governed masculinization phenotype. Sex Dev 2013; 7:196-206. [PMID: 23485832 DOI: 10.1159/000348435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 11/19/2022] Open
Abstract
Sex determination is known to be male heterogametic in the rainbow trout, Oncorhynchus mykiss; however, scattered observations that deviate from this rather strict genetic control have been reported. Here, we provide a detailed morphological and histological characterization of the gonadal differentiation and development (from 43 days postfertilization to 11 months of age) in an all-female (XX) population with a genetically governed masculinization phenotype. In comparison with control males and females, the gonadal differentiation in these animals was characterized by many perturbations, including significantly fewer germ cells. This decrease in germ cells was confirmed by the significantly decreased expression of 2 germ cell maker genes (vasa and sycp3) in the masculinized XX populations as compared with the control females and control males. Although only a proportion of the total adult population was partially or fully masculinized, this early differentiating phenotype affected nearly all the sampled animals. This suggests that the adult masculinization phenotype is the consequence of an early functional imbalance in ovarian differentiation in the entire population. We hypothesize that the lower number of germ cells that we observed in this population could be one cause of their masculinization.
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Affiliation(s)
- K Valdivia
- INRA, UR1037 LPGP Fish Physiology and Genomics, Rennes, France
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Berbejillo J, Martinez-Bengochea A, Bedo G, Brunet F, Volff JN, Vizziano-Cantonnet D. Expression and phylogeny of candidate genes for sex differentiation in a primitive fish species, the Siberian sturgeon, Acipenser baerii. Mol Reprod Dev 2012; 79:504-16. [DOI: 10.1002/mrd.22053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 05/11/2012] [Indexed: 11/12/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Böhne A, Darras A, D'Cotta H, Baroiller JF, Galiana-Arnoux D, Volff JN. The vertebrate makorin ubiquitin ligase gene family has been shaped by large-scale duplication and retroposition from an ancestral gonad-specific, maternal-effect gene. BMC Genomics 2010; 11:721. [PMID: 21172006 PMCID: PMC3022923 DOI: 10.1186/1471-2164-11-721] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, invertebrates and vertebrates including human, almost nothing is known about their structural and functional evolution. RESULTS Via partial sequencing of a testis cDNA library from the poeciliid fish Xiphophorus maculatus, we have identified a new member of the makorin gene family, that we called mkrn4. In addition to the already described mkrn1 and mkrn2, mkrn4 is the third example of a makorin gene present in both tetrapods and ray-finned fish. However, this gene was not detected in mouse and rat, suggesting its loss in the lineage leading to rodent murids. Mkrn2 and mkrn4 are located in large ancient duplicated regions in tetrapod and fish genomes, suggesting the possible involvement of ancestral vertebrate-specific genome duplication in the formation of these genes. Intriguingly, many mkrn1 and mkrn2 intronless retrocopies have been detected in mammals but not in other vertebrates, most of them corresponding to pseudogenes. The nature and number of zinc fingers were found to be conserved in Mkrn1 and Mkrn2 but much more variable in Mkrn4, with lineage-specific differences. RT-qPCR analysis demonstrated a highly gonad-biased expression pattern for makorin genes in medaka and zebrafish (ray-finned fishes) and amphibians, but a strong relaxation of this specificity in birds and mammals. All three mkrn genes were maternally expressed before zygotic genome activation in both medaka and zebrafish early embryos. CONCLUSION Our analysis demonstrates that the makorin gene family has evolved through large-scale duplication and subsequent lineage-specific retroposition-mediated duplications in vertebrates. From the three major vertebrate mkrn genes, mkrn4 shows the highest evolutionary dynamics, with lineage-specific loss of zinc fingers and even complete gene elimination from certain groups of vertebrates. Comparative expression analysis strongly suggests that the ancestral E3 ubiquitin ligase function of the single copy mkrn gene before duplication in vertebrates was gonad-specific, with maternal expression in early embryos.
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Affiliation(s)
- Astrid Böhne
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France.
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Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 2010; 330:1381-5. [PMID: 21097902 DOI: 10.1126/science.1194167] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
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Affiliation(s)
- France Denoeud
- Commissariat à l'Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
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Lampert KP, Schmidt C, Fischer P, Volff JN, Hoffmann C, Muck J, Lohse MJ, Ryan MJ, Schartl M. Determination of onset of sexual maturation and mating behavior by melanocortin receptor 4 polymorphisms. Curr Biol 2010; 20:1729-34. [PMID: 20869245 DOI: 10.1016/j.cub.2010.08.029] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 07/16/2010] [Accepted: 08/13/2010] [Indexed: 11/30/2022]
Abstract
Polymorphisms in reproductive strategies are among the most extreme and complex in nature. A prominent example is male body size and the correlated reproductive strategies in some species of platyfish and swordtails of the genus Xiphophorus. This polymorphism is controlled by a single Mendelian locus (P) that determines the onset of sexual maturity of males. Because males cease growth after reaching puberty, this results in a marked size polymorphism. The different male size classes show pronounced behavioral differences (e.g., courtship versus sneak mating), and females prefer large over small males. We show that sequence polymorphisms of the melanocortin receptor 4 gene (mc4r) comprise both functional and non-signal-transducing versions and that variation in copy number of mc4r genes on the Y chromosome underlies the P locus polymorphism. Nonfunctional Y-linked mc4r copies in larger males act as dominant-negative mutations and delay the onset of puberty. Copy number variation, as a regulating mechanism, endows this system with extreme genetic flexibility that generates extreme variation in phenotype. Because Mc4r is critically involved in regulation of body weight and appetite, a novel link between the physiological system controlling energy balance and the regulation of reproduction becomes apparent.
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Affiliation(s)
- Kathrin P Lampert
- Physiological Chemistry I, Biocenter, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
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Zhou Q, Braasch I, Froschauer A, Böhne A, Schultheis C, Schartl M, Volff JN. A novel marker for the platyfish (Xiphophorus maculatus) W chromosome is derived from a Polinton transposon. J Genet Genomics 2010; 37:181-8. [PMID: 20347827 DOI: 10.1016/s1673-8527(09)60036-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 11/13/2009] [Accepted: 11/25/2009] [Indexed: 01/18/2023]
Abstract
A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa in length, contains a DNA_pol_B_2 domain and a DTDS motif. The DNA polymerase type B gene has about 10 copies in the haploid X. maculatus genome with one Y-specific copy. Interestingly, it has specific copies on the W chromosome in the X. maculatus Usumacinta strain (sex determination with female heterogamety), which represent new markers for this type of sex chromosome in platyfish. This marker with W- and Y-specific copies suggests relationship between different types of gonosomes and allows comparing male and female heterogameties in the platyfish. Further molecular analysis of the DNA polymerase type B gene in X. maculatus will shed new light on the evolution of sex chromosomes in platyfish.
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Affiliation(s)
- Qingchun Zhou
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg 97074, Germany.
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Affiliation(s)
- Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France.
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48
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Abstract
Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate
lineage, but their evolutionary significance for phenotypic evolution remains
elusive. Here, we have investigated the impact of the fish-specific genome
duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes.
Pigmentation and color patterning are among the most diverse traits in teleosts,
and their pigmentary system is the most complex of all vertebrate groups. Using a comparative genomic approach including phylogenetic and synteny analyses,
the evolution of 128 vertebrate pigmentation genes in five teleost genomes
following the FSGD has been reconstructed. We show that pigmentation genes have
been preferentially retained in duplicate after the FSGD, so that teleosts have
30% more pigmentation genes compared with tetrapods. This is significantly
higher than genome-wide estimates of FSGD gene duplicate retention in teleosts.
Large parts of the melanocyte regulatory network have been retained in two
copies after the FSGD. Duplicated pigmentation genes follow general evolutionary
patterns such as the preservation of protein complex stoichiometries and the
overrepresentation of developmental genes among retained duplicates. These
results suggest that the FSGD has made an important contribution to the
evolution of teleost-specific features of pigmentation, which include novel
pigment cell types or the division of existing pigment cell types into distinct
subtypes. Furthermore, we have observed species-specific differences in
duplicate retention and evolution that might contribute to pigmentary diversity
among teleosts. Our study therefore strongly supports the hypothesis that WGDs have promoted the
increase of complexity and diversity during vertebrate phenotypic evolution.
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Affiliation(s)
- Ingo Braasch
- Physiological Chemistry I, University of Würzburg, Biozentrum, Würzburg, Germany.
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49
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Affiliation(s)
- Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, Supérieure de Lyon, France.
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Schultheis C, Böhne A, Schartl M, Volff JN, Galiana-Arnoux D. Sex determination diversity and sex chromosome evolution in poeciliid fish. Sex Dev 2009; 3:68-77. [PMID: 19684452 DOI: 10.1159/000223072] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Accepted: 02/11/2009] [Indexed: 11/19/2022] Open
Abstract
Poeciliids, a family of live-bearing freshwater fish, including among others platyfish, swordtails and guppies, fully illustrate the diversity of genetic sex determination mechanisms observed in teleosts. Besides unisexuality, a variety of sex-determining systems has been described in this group of fish, including male and female heterogamety with or without autosomal influence, as well as more complicated situations such as multichromosomal and polyfactorial sex determination. Due to the presence of different mechanisms in closely related species or even between populations within a same species, poeciliids are a very attractive model to study the evolutionary dynamics of sex determination. For one species, the Southern platyfish Xiphophorus maculatus, positional cloning of the master sex-determining gene has been initiated through the construction and sequencing of bacterial artificial chromosome contigs covering the region differentiating the X from the Y chromosome. Initial analysis revealed a high plasticity of the sex-determining region and the absence of synteny with other fish and vertebrate sex chromosomes, indicating an independent evolutionary origin.
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Affiliation(s)
- C Schultheis
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
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