Author: "Romain Feron" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Romain Feron"' showing total 33 results

Start Over Author "Romain Feron"

33 results on '"Romain Feron"'

1. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

Author: Heiner Kuhl, Peter T. Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A. Larson, John H. Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, and Yann Guiguen
Subjects: Sex-determination, Genome, Perches, Pikeperches, Sex chromosomes, Biology (General), QH301-705.5
Abstract: Abstract Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. Results We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19–27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. Conclusions Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Published: 2024
Full Text: View/download PDF

2. A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

Author: Heiner Kuhl, Wen Hui Tan, Christophe Klopp, Wibke Kleiner, Baturalp Koyun, Mitica Ciorpac, Romain Feron, Martin Knytl, Werner Kloas, Manfred Schartl, Christoph Winkler, and Matthias Stöck
Subjects: Science
Abstract: Abstract Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5′-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.
Published: 2024
Full Text: View/download PDF

3. Anopheles mosquitoes reveal new principles of 3D genome organization in insects

Author: Varvara Lukyanchikova, Miroslav Nuriddinov, Polina Belokopytova, Alena Taskina, Jiangtao Liang, Maarten J. M. F. Reijnders, Livio Ruzzante, Romain Feron, Robert M. Waterhouse, Yang Wu, Chunhong Mao, Zhijian Tu, Igor V. Sharakhov, and Veniamin Fishman
Subjects: Science
Abstract: Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
Published: 2022
Full Text: View/download PDF

4. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

Author: Mateus C. Adolfi, Kang Du, Susanne Kneitz, Cédric Cabau, Margot Zahm, Christophe Klopp, Romain Feron, Rômulo V. Paixão, Eduardo S. Varela, Fernanda L. de Almeida, Marcos A. de Oliveira, Rafael H. Nóbrega, Céline Lopez-Roques, Carole Iampietro, Jérôme Lluch, Werner Kloas, Sven Wuertz, Fabian Schaefer, Matthias Stöck, Yann Guiguen, and Manfred Schartl
Subjects: Medicine, Science
Abstract: Abstract Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
Published: 2021
Full Text: View/download PDF

5. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758)

Author: Ming Wen, Romain Feron, Qiaowei Pan, Justine Guguin, Elodie Jouanno, Amaury Herpin, Christophe Klopp, Cedric Cabau, Margot Zahm, Hugues Parrinello, Laurent Journot, Shawn M. Burgess, Yoshihiro Omori, John H. Postlethwait, Manfred Schartl, and Yann Guiguen
Subjects: Goldfish, RADseq, Poolseq, Sex determination, Sex markers, Male genome assembly, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. Here we used sequencing approaches to better characterize sex determination and sex-chromosomes in an experimental strain of goldfish. Results Our results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18 °C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (~ 11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the coding DNA sequence of the goldfish amh gene. Conclusions These results show that our goldfish strain has a relatively large sex locus on LG22, which is likely the Y chromosome of this experimental population. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers, which will be important tools for future research on sex determination in our experimental goldfish population. However, additional work would be needed to explore whether this sex locus is conserved in other populations of goldfish.
Published: 2020
Full Text: View/download PDF

6. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author: Robert M. Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Livio Ruzzante, Maarten J. M. F. Reijnders, Romain Feron, Sèverine Bérard, Phillip George, Matthew W. Hahn, Paul I. Howell, Maryam Kamali, Sergey Koren, Daniel Lawson, Gareth Maslen, Ashley Peery, Adam M. Phillippy, Maria V. Sharakhova, Eric Tannier, Maria F. Unger, Simo V. Zhang, Max A. Alekseyev, Nora J. Besansky, Cedric Chauve, Scott J. Emrich, and Igor V. Sharakhov
Subjects: Genome assembly, Gene synteny, Comparative genomics, Mosquito genomes, Orthology, Bioinformatics, Biology (General), QH301-705.5
Abstract: Abstract Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
Published: 2020
Full Text: View/download PDF

7. The rise and fall of the ancient northern pike master sex-determining gene

Author: Qiaowei Pan, Romain Feron, Elodie Jouanno, Hugo Darras, Amaury Herpin, Ben Koop, Eric Rondeau, Frederick W Goetz, Wesley A Larson, Louis Bernatchez, Mike Tringali, Stephen S Curran, Eric Saillant, Gael PJ Denys, Frank A von Hippel, Songlin Chen, J Andrés López, Hugo Verreycken, Konrad Ocalewicz, Rene Guyomard, Camille Eche, Jerome Lluch, Celine Roques, Hongxia Hu, Roger Tabor, Patrick DeHaan, Krista M Nichols, Laurent Journot, Hugues Parrinello, Christophe Klopp, Elena A Interesova, Vladimir Trifonov, Manfred Schartl, John Postlethwait, and Yann Guiguen
Subjects: fish, pikes, mudminnows, esociforms, esocidae, umbridae, Medicine, Science, Biology (General), QH301-705.5
Abstract: The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2021
Full Text: View/download PDF

8. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation.

Author: Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, Estelle Vigouroux, Ming Wen, Jean-Mickaël Busnel, Julien Bobe, Jean-Paul Concordet, Hugues Parrinello, Laurent Journot, Christophe Klopp, Jérôme Lluch, Céline Roques, John Postlethwait, Manfred Schartl, Amaury Herpin, and Yann Guiguen
Subjects: Genetics, QH426-470
Abstract: Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.
Published: 2019
Full Text: View/download PDF

9. Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation

Author: Kang Du, Martin Pippel, Susanne Kneitz, Romain Feron, Irene da Cruz, Sylke Winkler, Brigitta Wilde, Edgar G. Avila Luna, Gene Myers, Yann Guiguen, Constantino Macias Garcia, and Manfred Schartl
Subjects: Genetics, Genetics (clinical)
Abstract: Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin, Girardinichthys multiradiatus. The assembly is chromosome level and includes the X and Y Chromosomes. A large male-specific region on the Y was identified covering 80% of Chromosome 20, allowing some first inferences on the recent origin and a candidate male sex determining gene. Genome-wide transcriptomics uncovered sex-specific differences in brain gene expression with an enrichment for neurosteroidogenesis and testis genes in males. The expression signatures of the splitfin embryonal and maternal placenta showed overlap with homologous tissues including human placenta, the ovarian follicle epithelium of matrotrophic poeciliid fish species and the brood pouch epithelium of the seahorse. Our comparative analyses on the evolution of embryonal and maternal placenta indicate that the evolutionary novelty of maternal provisioning development repeatedly made use of genes that already had the same function in other tissues. In this way, preexisting modules are assembled and repurposed to provide the molecular changes for this novel trait.
Published: 2022

10. First Optical Seismometer at the Top of La Soufrière Volcano, Guadeloupe

Author: Mathieu Feuilloy, Philippe Menard, Romain Feron, Pascal Bernard, Sébastien Deroussi, Guy Plantier, Thierry Kitou, Alexandre Nercessian, ESEO-GSII (GSII), ESEO-Tech, Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Observatoire Volcanologique et Sismologique de Guadeloupe (OVSG), and Institut de Physique du Globe de Paris
Subjects: Seismometer, geography, geography.geographical_feature_category, 010504 meteorology & atmospheric sciences, Geophone, 010502 geochemistry & geophysics, 01 natural sciences, Seismic wave, Fumarole, [SPI]Engineering Sciences [physics], Geophysics, Volcano, 13. Climate action, Archipelago, [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, Stratovolcano, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Phreatic, Seismology, Geology, 0105 earth and related environmental sciences
Abstract: Accurate monitoring of volcanic activity demands expertise in fields including geophysics, geology, and geochemistry. Data obtained from the most recent technical advances are particularly vital in pre-eruptive phases. In particular, seismic monitoring in near real time is essential to locating and discriminating early signs among different sources of seismic waves, especially those related to movement and overpressure in underground fluids. Among the major indicators of volcanic restlessness are fumaroles, or gas and steam vents, often located near a volcanic summit. Their activity could be monitored by seismometers in their vicinity, but today’s standard instruments cannot last very long when exposed to the high temperatures and the billowing, sulfurous, acidic gases near a fumarole. Conventional gear may also not be accessible for emergency deployment, or repair, even in pre-eruptive phases. La Soufrière de Guadeloupe Volcano in the Caribbean typifies such challenges. Its last significant event was a phreatic (gas and steam) eruption in 1976 that prompted evacuation of the archipelago’s nearby capital. Since early 2018, the 1467-meter-high stratovolcano has shown signs of increased activity. To provide a hardy, high-resolution monitoring system, we installed a recently developed type of seismometer just 10 m from a vigorous summit fumarole. The sensor is a purely opto-mechanical geophone that is interrogated through a 1.5 km fiber-optic cable by a remote, and thus it is a much safer optic-electronic system down the volcano’s flank. The ESEO Group and the Institut de Physique du Globe de Paris (IPGP) started development of this novel seismometer in 2008. The 2019 Guadeloupe installation is part of the HIgh PERformance SeISmometer (HIPERSIS) project (French Agence Nationale de la Recherche [ANR]). It is, to our knowledge, the first high-resolution optical seismometer ever installed on an active volcano or other active, hazardous zone. We report here the details of this installation, the means we are using for measurements, and our implementation strategy, and we share some of the first results. Such an optical seismometer, as well as a variety of other geophysical sensors built on the same principle, can be installed in a wide variety of sites with fibers up to 50 km long.
Published: 2020

11. Nature Communications

Author: Varvara Lukyanchikova, Miroslav Nuriddinov, Polina Belokopytova, Alena Taskina, Jiangtao Liang, Maarten J. M. F. Reijnders, Livio Ruzzante, Romain Feron, Robert M. Waterhouse, Yang Wu, Chunhong Mao, Zhijian Tu, Igor V. Sharakhov, and Veniamin Fishman
Subjects: architecture, Multidisciplinary, Asian malaria mosquito, General Physics and Astronomy, alignment, малярийные комары, prediction, General Chemistry, Chromatin, General Biochemistry, Genetics and Molecular Biology, гены, Anopheles, map, evolution, Animals, Anopheles/genetics, Chromatin/genetics, геном комаров, chromatin, хроматин, комары, Hi-C reveals, polycomb, inversion breakpoints
Abstract: Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for similar to 100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin. NSF [MCB-1715207]; NIH NIAID [R21AI135298, R21AI159382]; USDA National Institute of Food and Agriculture Hatch project [223822]; RFBR [19-34-50051]; University of Lausanne Department of Ecology and Evolution; NIH [AI133571, AI121284]; Novartis Foundation [18B116]; Swiss National Science Foundation [PP00P3_170664, PP00P3_202669]; Fulbright Foreign Student Program [15161026]; Ministry of Education and Science of Russian Federation [2019-0546 (FSUS-2020-0040)]; [121031800061-7] Published version The following reagents were obtained through BEI Resources, NIAID, NIH: An. coluzzii, Strain MOPTI, Eggs, MRA-763, contributed by Gregory C. Lanzaro; An. merus, Strain MAF, MRA-1156, contributed by Maureen Coetzee; An. atroparvus, Strain EBRO, Eggs, MRA-493, contributed by Carlos Aranda and Mark Q. Benedict; An. albimanus, Strain STECLA, Eggs, MRA-126, contributed by Mark Q. Benedict. All computations were performed using nodes of the high-throughput cluster of the Novosibirsk State University, and bioinformatics resource center of the Institute of Cytology and Genetics. We are sincerely grateful to Nariman Battulin for fruitful discussions. This work was supported by the NSF grant MCB-1715207, NIH NIAID grants R21AI135298 and R21AI159382, and the USDA National Institute of Food and Agriculture Hatch project 223822 to IVS. The reported study of An. atroparvus was partly funded by RFBR according to the research project no 19-34-50051 to IVS and VL. PacBio sequencing of An. merus was funded by a grant from the University of Lausanne Department of Ecology and Evolution to RMW and NIH grants AI133571 and AI121284 to Z.T. M.J.M.F.R., L.R., R.F., and R.M.W. were supported by Novartis Foundation for medical-biological research grant #18B116 and Swiss National Science Foundation grants PP00P3_170664 and PP00P3_202669. V.L. was partly supported by the Fulbright Foreign Student Program, Grantee ID: 15161026. Hi-C data analysis was supported by the Ministry of Education and Science of Russian Federation, grant #2019-0546 (FSUS-2020-0040). ChIP-seq data analysis was supported by project 121031800061-7 (Mechanisms of genetic control of development, physiological processes and behavior in animals).
Published: 2022

12. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Author: Romain Feron and Robert M. Waterhouse
Subjects: Workflow, Resource (project management), Phylum, media_common.quotation_subject, Data quality, Quality (business), Benchmarking, Data science, Genome, DNA sequencing, media_common
Abstract: Ambitious initiatives to coordinate genome sequencing of Earth’s biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.
Published: 2021

13. A supernumerary 'B-sex' chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Author: Séverine Beille, Sylvie Rétaux, John H. Postlethwait, Claire Kuchly, Hugues Parrinello, Amaury Herpin, Tomáš Pavlica, Ahmed Al-Rikabi, Christophe Klopp, Cécile Donnadieu, Jorge Torres-Paz, Manfred Schartl, Lisa Gil, Thomas Liehr, Joerg Bohlen, Adrien Castinel, Romain Feron, Yann Guiguen, Céline Lopez-Roques, Margot Zahm, Cédric Cabau, Boudjema Imarazene, Frédéric Veyrunes, Thomas D. Mueller, Elodie Jouanno, Alexandr Sember, Kang Du, Sergey A. Simanovsky, Qiaowei Pan, Julie Perez, Laurent Journot, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Texas State University, Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institute of Animal Physiology and Genetics of the Czech Academy of Sciences (IAPG / CAS), Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), Jena University Hospital [Jena], A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Würzburg = Universität Würzburg, University of Oregon [Eugene], This project was supported by funds from the 'Agence Nationale de la Recherche' (ANR/DFG, PhyloSex project, 2014-2016) to Y.G. and M.S. S.R. was supported by grants from an Equipe FRM (Fondation pour la Recherche Médicale, DEQ20150331745) and MITI CNRS (Mission pour les Initiatives Transverses et Interdisciplinaires). J.H.P. was supported by an NIH grant (R35 GM139635). Sequencing was supported by France Génomique as part of an 'Investissement d’avenir' program managed by ANR (contract ANR-10-INBS-09) and by the GET-PACBIO program (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020). The CytoEvol platform at ISEM was supported by the Labex CeMEB. J.B., T.P., and A.S. were supported by RVO: 67985904 of IAPG CAS, Liběchov. T.P. was supported by the projects of the Czech Ministry of Education (SVV 260571/2021). S.A.S. was supported by the Russian Foundation for Basic Research (RFBR) (18-34-00638). B.I.’s PhD fellowship was supported by the Doctoral School of Ecology, Geosciences, Agronomy, Nutrition of the University of Rennes 1 and INRAE. We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help, computing, and storage resources. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), University of Lausanne (UNIL), Université de Lausanne (UNIL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Guiguen, Yann, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, and Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID
Subjects: Male, [SDV]Life Sciences [q-bio], Male sex determination, sex determination, Cavefish, B chromosome, Biology, Genome, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Animals, gonads, Gene, genome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Sexual differentiation, Characidae, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], sex chromosomes, Chromosome, Sex reversal, Biological Evolution, [SDV] Life Sciences [q-bio], Caves, cavefish, gdf6, sex differentiation, Female, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.(1,2) B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species(3,4) that have often been considered as selfish genetic elements that behave as genome parasites.(5,6) The observation that in some species Bs can be either restricted or predominant in one sex(7–14) raised the interesting hypothesis that Bs could play a role in sex determination.(15) The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a “B-sex” chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
Published: 2021

14. The bowfin genome illuminates the developmental evolution of ray-finned fishes

Author: Hugues Roest Crollius, Dustin J. Wcisel, Matthew P. Harris, Brett Racicot, Elise Parey, Jérôme Montfort, Solomon R. David, Quenton C. Fontenot, Kazuhiko Kawasaki, Allyse M. Ferrara, Yann Guiguen, Tatsuya Ota, Mauricio Losilla, Ingo Braasch, M. Brent Hawkins, Olivia E Fitch, Romain Feron, Andrew W. Thompson, Marine Milhes, Amy R. McCune, Qiaowei Pan, Emily Funk, Jeffrey A. Yoder, Camille Berthelot, Alex Dornburg, Alexandra Louis, Kevin L. Childs, Michigan State University [East Lansing], Michigan State University System, Harvard Medical School [Boston] (HMS), Boston Children's Hospital, Harvard University [Cambridge], Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Pennsylvania State University (Penn State), Penn State System, Cornell University [New York], University of California [Davis] (UC Davis), University of California, University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nicholls State University, University of North Carolina [Charlotte] (UNC), We are thankful for grant support from NIH R01OD011116 (I.B.), NSF DDIG DEB-1600920 (M.B.H.), NSF IOS-1755242 (A.D.) and NSF IOS-1755330 (J.A.Y.). Parts of this work have been supported by the Agence Nationale de la Recherche, France (ANR GenoFish project, 2016-2021, ANR-16-CE12-0035) to H.R.C., C.B., E.P., A.L. and Y.G. E.P., C.B. and H.R.C. received support under the program ‘Investissements d’Avenir’ launched by the French government and implemented by ANR with references ANR–10–LABX–54 MEMOLIFE and ANR-10-IDEX-0001-02 PSL* Université Paris. We thank F. Feng for access to Oneida Lake bowfin spawning habitats, the Bauer Core at Harvard University for sequencing fin transcriptomes and M. Gundappa (FISH & LINES) for species illustrations. Species silhouettes were obtained from http://PhyloPic.org. We are exceedingly grateful to the late J.L. Gómez-Skarmeta for his guidance on establishing ATAC-seq in holosteans., ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Scale (anatomy), [SDV]Life Sciences [q-bio], Sequence assembly, Vertebrate Biology, Genome, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, biology.animal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Developmental biology, Genetics, Animals, 14. Life underwater, Skates, Fish, Bowfin, ComputingMilieux_MISCELLANEOUS, Amia calva, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, biology, Whole Genome Sequencing, Fishes, Vertebrate, Genomics, biology.organism_classification, Biological Evolution, Chromatin, Body plan, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Amiidae, Evolutionary biology, Zoology, 030217 neurology & neurosurgery
Abstract: The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era., Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.
Published: 2021

15. Functional constraints on insect immune system components govern their evolutionary trajectories

Author: Maarten J.M.F. Reijnders, Thiebaut A, Livio Ruzzante, Romain Feron, Robert M. Waterhouse, and Leitner, Thomas (ed.)
Subjects: Comparative genomics, Genome, Insecta, gene families, AcademicSubjects/SCI01130, Population genetics, Genomics, Biology, AcademicSubjects/SCI01180, Anopheles mosquito, Animals, Evolution, Molecular, Immune System, Insecta/genetics, evolutionary profiling, gene expression, innate immunity, Phenotype, Evolutionary biology, Gene duplication, Gene family, Gene, Discoveries, Synteny
Abstract: The role of constraints in shaping evolutionary outcomes is often investigated in the contexts of developmental biology and population genetics, in terms of the capacity to generate new variants as well as how selection either limits or promotes consequent phenotypic change. Comparative genomics also recognises the role of constraints, in terms of shaping the evolution of gene and genome architectures, sequence evolutionary rates, and gene gains and losses, as well as on molecular phenotypes. Characterising patterns of genomic change where putative functions and interactions of system components are relatively well-described offers opportunities to explore whether genes with similar or analogous roles exhibit similar evolutionary trajectories, possibly governed by common constraints. Using insect innate immunity as our study system, we hypothesise that quantitative characterisation of gene evolutionary histories can define distinct dynamics associated with different functional roles. We develop metrics that quantify gene evolutionary histories, employ these to characterise evolutionary features of immune gene repertoires, and explore relationships between gene family evolutionary profiles and their roles in immunity to understand how different constraints may relate to distinct dynamics. We identified three main axes of evolutionary trajectories characterised by gene duplication and synteny, maintenance/stability and sequence conservation, and loss and sequence divergence, highlighting similar and contrasting patterns across these axes amongst subsets of immune genes. Our results indicate that where and how genes participate in immune responses limit the range of possible evolutionary scenarios they exhibit. Comparative genomics approaches therefore offer opportunities to characterise how functional constraints on different components of biological systems govern their evolutionary trajectories.
Published: 2021

16. Genome biology of the darkedged splitfin

Author: Kang, Du, Martin, Pippel, Susanne, Kneitz, Romain, Feron, Irene, da Cruz, Sylke, Winkler, Brigitta, Wilde, Edgar G, Avila Luna, Gene, Myers, Yann, Guiguen, Constantino, Macias Garcia, and Manfred, Schartl
Subjects: Male, Cyprinodontiformes, Genome, Sex Chromosomes, Pregnancy, Animals, Female, Biology, Placentation
Abstract: Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin
Published: 2021

17. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

Author: Ørjan Karlsen, Susanne Kneitz, Rafael Henrique Nóbrega, Qiaowei Pan, Masatoshi Nakamoto, Elodie Jouanno, Thomas Desvignes, John H. Postlethwait, Ato Takanashi, Braedan M. McCluskey, Amaury Herpin, Matthias Stöck, Alvaro S. Roco, Boudjema Imarazene, Manfred Schartl, Zhongwei Wang, Mateus Contar Adolfi, Romain Feron, Catherine Wilson, Hugues Parrinello, Takashi Sakamoto, Ingo Braasch, Christophe Klopp, Marcos Antonio de Oliveira, Frederick W. Goetz, Harry William Detrich, Robert M. Waterhouse, Ming Wen, Yann Guiguen, Mari Kawaguchi, Angel Amores, Laurent Journot, Anna Wargelius, Verena A. Kottler, Kang Du, Jennifer L. Anderson, IINRAE, Univ Lausanne, Swiss Inst Bioinformat, Hunan Normal Univ, Uppsala Univ, Univ Montpellier, INRAE, Univ Wurzburg, Texas State Univ, Univ Oregon, NOAA, Sophia Univ, Northeastern Univ, Universidade Estadual Paulista (Unesp), Tokyo Univ Marine Sci & Technol, Inst Marine Res, Chinese Acad Sci, IGB, Michigan State Univ, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution, University of Lausanne, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiological Chemistry, Biocenter, University of Würzburg = Universität Würzburg, The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Institute of Neuroscience, University of Oregon, Eugene, University of Oregon [Eugene], Tokyo University of Marine Science and Technology (TUMSAT), Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Sophia University, Tokyo, Faculty of Science and Technology, Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Institute of Hydrobiology [Wuhan], Chinese Academy of Sciences [Beijing] (CAS), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Integrative Biology, Michigan State University, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project,2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grant R01GM085318, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Department of Ecology and Evolution [Lausanne], Institute of Neuroscience, University of Oregon, Eugene, Oregon, Department of Materials and Life Sciences, Sophia University [Tokyo], Department of Structural and Functional Biology, Department of Aquatic Marine Biosciences, Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grants R01GM085318 and R35GM139635, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW.
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Sex Determination Analysis, Computer science, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), Computational biology, Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Computational workflow, DNA sequencing, Article, Workflow, 03 medical and health sciences, Sex-determination system, Genetics, Animals, Sequencing, RAD&#8208, Computational Biology, DNA, Female, Fishes/genetics, Sequence Analysis, DNA, Sex Chromosomes, Software, RAD-Sequencing, computational workflow, fish, visualization, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Visualization, 0303 health sciences, Fishes, Japanese Medaka, Sex determination, Restriction site, 030104 developmental biology, Fish, Identification (biology), Biotechnology
Abstract: Made available in DSpace on 2021-06-25T11:54:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-09 National Institute of Health (USA) Deutsche Forschungsgemeinschaft National Science Foundation (USA) Office of Polar Programs Agence Nationale de la Recherche Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish. IINRAE, LPGP, Rennes, France Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Changsha, Peoples R China Uppsala Univ, Dept Organismal Biol, Systemat Biol, Uppsala, Sweden Univ Montpellier, Inst Genom Fonct, INSERM, IGF,CNRS, Montpellier, France INRAE, Math & Informat Appl Toulouse, SIGENAE, Castanet Tolosan, France Univ Wurzburg, Physiol Chem, Bioctr, Wurzburg, Germany Texas State Univ, Xiphophorus Genet Stock Ctr, Dept Chem & Biochem, San Marcos, TX USA Univ Wurzburg, Dev Biochem, Bioctr, Wurzburg, Germany Univ Oregon, Inst Neurosci, Eugene, OR USA NOAA, Environm & Fisheries Sci Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA USA Sophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Tokyo, Japan Northeastern Univ, Ctr Marine Sci, Dept Marine & Environm Sci, Nahant, MA 01908 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil Tokyo Univ Marine Sci & Technol, Dept Aquat Marine Biosci, Tokyo, Japan Inst Marine Res, Bergen, Norway Chinese Acad Sci, Inst Hydrobiol, Beijing, Peoples R China IGB, Leibniz Inst Freshwater Ecol & Inland Fishe, Berlin, Germany Michigan State Univ, Dept Integrat Biol, Ecol Evolut & Behav Program, E Lansing, MI 48824 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil National Institute of Health (USA): R01GM085318 National Institute of Health (USA): R35GM139635 Deutsche Forschungsgemeinschaft: SCHA 408/10-1 National Science Foundation (USA) Office of Polar Programs: OPP-1543383 National Science Foundation (USA) Office of Polar Programs: PLR-1247510 National Science Foundation (USA) Office of Polar Programs: PLR-1444167 Agence Nationale de la Recherche: SCHA 408/10-1 Agence Nationale de la Recherche: ANR-10-INBS-09 Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung: PP00P3_170664
Published: 2021

18. A Supernumerary 'B-Sex' Chromosome Drives Male Sex Determination in the Pachón Cavefish, Astyanax mexicanus

Author: Claire Kuchly, Adrien Castinel, Séverine Beille, Romain Feron, Yann Guiguen, Kang Du, Jorge Torres-Paz, Sylvie Rétaux, Alexandr Sember, Boudjema Imarazene, Margot Zham, Sergey A. Simanovsky, Cédric Cabau, Tomáš Pavlica, Joerg Bohlen, Qiaowei Pan, Cécile Donnadieu, Céline Lopez-Roques, John H. Postlethwait, Manfred Schartl, Elodie Jouanno, Julie Perez, Thomas Liehr, Frédéric Veyrunes, Hugues Parrinello, Lisa Gil, Ahmed Al-Rikabi, Christophe Klopp, Laurent Journot, Amaury Herpin, and Thomas D. Mueller
Subjects: Genetics, B chromosome, GDF6, Male sex determination, Cavefish, Chromosome, Sex reversal, Biology, Gene, Genome
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now. B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species, that have often been considered as selfish genetic elements that behave as genome parasites. The observation that in some species Bs can be either restricted or predominant in one sex raised the interesting hypothesis that Bs could play a role in sex determination. The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachon cave, we show that Bs are strongly male-predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachon cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b gdf6b). Supporting its role as an MSD gene, we found that the Pachon cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachon cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachon cavefish B is a “B-sex” chromosome containing duplicated copies of the gdf6b gene acting as an MSD gene promoting male sex determination in this species.
Published: 2021

19. Author response: The rise and fall of the ancient northern pike master sex-determining gene

Author: Christophe Klopp, E. A. Interesova, Songlin Chen, Laurent Journot, Amaury Herpin, René Guyomard, Wesley A. Larson, Manfred Schartl, Louis Bernatchez, Vladimir A. Trifonov, Eric Saillant, Eric Rondeau, Hugo Verreycken, Patrick W. DeHaan, Stephen S. Curran, Yann Guiguen, Hongxia Hu, Hugo Darras, Romain Feron, Qiaowei Pan, J. Andrés López, Jérôme Lluch, Gael Pj Denys, Céline Roques, Mike Tringali, Camille Eché, Roger A. Tabor, Frederick W. Goetz, Hugues Parrinello, Elodie Jouanno, Krista M. Nichols, John H. Postlethwait, Konrad Ocalewicz, Ben F. Koop, and Frank A. von Hippel
Subjects: Geography, Zoology, computer, Gene, Pike, computer.programming_language
Published: 2020

20. The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

Author: Qiaowei Pan, Mauricio Losilla, Allyse M. Ferrara, Alex Dornburg, Tatsuya Ota, Kevin L. Childs, Yann Guiguen, Marine Milhes, Amy R. McCune, Ingo Braasch, Michael Brent Hawkins, Andrew W. Thompson, Emily Funk, Olivia E Fitch, Hugues Roest Crollius, Dustin J. Wcisel, Quenton C. Fontenot, Romain Feron, Brett Racicot, Elise Parey, Solomon R. David, Matthew P. Harris, Kazuhiko Kawasaki, Camille Berthelot, and Jeffrey A. Yoder
Subjects: biology, Evolutionary biology, Bowfin, biology.organism_classification, Genome
Abstract: The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.
Published: 2020

21. Independent origin of XY and ZW sex determination mechanisms in Mosquitofish sister species

Author: Susanne Kneitz, Frederik Helmprobst, Hugues Parrinello, Céline Lopez-Roques, Kang Du, Indrajit Nanda, Romain Feron, Verena A. Kottler, Dunja K. Lamatsch, Christophe Klopp, Laurent Journot, Manfred Schartl, Jérôme Lluch, Yann Guiguen, University of Würzburg = Universität Würzburg, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Bioinformatics, GSF - Research Institute for Environment and Health, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Innsbruck, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM), Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, This project was supported by funds to Y.G. and M.S. from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016). V.A.K. was supported through a SCIENTIA fellowship of the Free State of Bavaria. The GeT, Toulouse (C.L.-R., J.L.), and the Montpellier GenomiX (MGX) France (L.J., H.P.) core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Male, 0106 biological sciences, X Chromosome, Genetic Linkage, 46, XX Testicular Disorders of Sex Development, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), sox9b, Investigations, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Gambusia, Cyprinodontiformes, 03 medical and health sciences, Y Chromosome, Genetics, Animals, gipc1, Cell Lineage, [INFO]Computer Science [cs], Allele, Phylogeny, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genome, Sex Chromosomes, Autosome, biology, Mosquitofish, Pigmentation, Chromosome Mapping, Chromosome, Eastern mosquitofish, Sex Determination Processes, biology.organism_classification, W chromosome, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, Female, pool sequencing
Abstract: Fish are known for the outstanding variety of their sex determination mechanisms and sex chromosome systems. The western (Gambusia affinis) and eastern mosquitofish (G. holbrooki) are sister species for which different sex determination mechanisms have been described: ZZ/ZW for G. affinis and XX/XY for G. holbrooki. Here, we carried out restriction-site associated DNA (RAD-) and pool sequencing (Pool-seq) to characterize the sex chromosomes of both species. We found that the ZW chromosomes of G. affinis females and the XY chromosomes of G. holbrooki males correspond to different linkage groups, and thus evolved independently from separate autosomes. In interspecific hybrids, the Y chromosome is dominant over the W chromosome, and X is dominant over Z. In G. holbrooki, we identified a candidate region for the Y-linked melanic pigmentation locus, a rare male phenotype that constitutes a potentially sexually antagonistic trait and is associated with other such characteristics, e.g., large body size and aggressive behavior. We developed a SNP-based marker in the Y-linked allele of GIPC PDZ domain containing family member 1 (gipc1), which was linked to melanism in all tested G. holbrooki populations. This locus represents an example for a color locus that is located in close proximity to a putative sex determiner, and most likely substantially contributed to the evolution of the Y.
Published: 2020

22. BMC Biology

Author: Eric Tannier, Igor V. Sharakhov, Sèverine Bérard, Robert M. Waterhouse, Matthew W. Hahn, Maria F. Unger, Maria V. Sharakhova, Sergey Koren, Scott J. Emrich, Yoann Anselmetti, Adam M. Phillippy, Ashley Peery, Jiyoung Lee, Sergey Aganezov, Cedric Chauve, Livio Ruzzante, Max A. Alekseyev, Paul I. Howell, Daniel Lawson, Simo V. Zhang, Romain Feron, Nora J. Besansky, Maarten J.M.F. Reijnders, Phillip George, Maryam Kamali, Gareth Maslen, Université de Lausanne (UNIL), Princeton University, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Virginia Polytechnic Institute and State University [Blacksburg], Virginia Tech [Blacksburg], Indiana University [Bloomington], Indiana University System, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Wellcome Trust Sanger Institute [Cambridge], Department of Entomology [Blacksburg], National Human Genome Research Institute (NHGRI), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), University of Notre Dame [Indiana] (UND), Georgetown University [Washington] (GU), Department of Mathematics [Burnaby] (SFU), Simon Fraser University (SFU.ca), Department of Computer Science. University of Tennessee, Tennessee State University, Physical mapping and PacBio sequencing of A. funestus were supported by the US National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) grant R21 AI112734 to NJB, with SJE and IVS as co-investigators. IVS was supported by the US NIH NIAID grants R21AI099528 and R21AI135298 and by the US Department of Agriculture National Institute of Food and Agriculture Hatch project 223822. SA and MAA were supported by the US National Science Foundation (NSF) grant IIS-1462107. SA was supported by the US NSF grants CCF-1053753 and DBI-1350041 and by US NIH grants U24CA211000 and R01-HG006677. YA, SB, and ET were supported by the French Agence Nationale pour la Recherche Ancestrome project ANR10-BINF-01-01. SK and AMP were supported by the Intramural Research Program of the NIH National Human Genome Research Institute 1ZIAHG200398. CC was supported by a Mitacs Globalink grant, the Natural Sciences and Engineering Research Council of Canada Discovery Grant RGPIN-249834, and a resource allocation from Compute Canada. MWH and SVZ were supported by US NSF grant DEB-1249633. RMW, LR, MJMFR, and RF were supported by Novartis Foundation for medical-biological research grant #18B116 and SwissNational Science Foundation grant PP00P3_170664., Université de Lausanne = University of Lausanne (UNIL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Entomology
Subjects: Bioinformatics, Computational biology, Biology, Genome, Synteny, Chromosomes, Mosquito genomes, 03 medical and health sciences, 0302 clinical medicine, Chromosome (genetic algorithm), Gene synteny, Biotechnology, Plant Science, General Biochemistry, Genetics and Molecular Biology, Developmental Biology, Cell Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, General Agricultural and Biological Sciences, Orthology, Anopheles, Animals, Comparative genomic analysis, lcsh:QH301-705.5, Gene, 030304 developmental biology, Whole genome sequencing, Comparative genomics, 0303 health sciences, Genome assembly, Chromosome Mapping, Genomics, 06 Biological Sciences, biology.organism_classification, Computational evolutionary biology, Biological Evolution, lcsh:Biology (General), Genetic Techniques, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Research Article, Physical mapping
Abstract: BackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.ResultsWe employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.ConclusionsExperimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
Published: 2020

23. The rise and fall of the ancient northern pike master sex-determining gene

Author: Mike Tringali, Hongxia Hu, Amaury Herpin, Patrick W. DeHaan, Eric Rondeau, Louis Bernatchez, Wesley A. Larson, Manfred Schartl, Elodie Jouanno, E. A. Interesova, Yann Guiguen, Eric Saillant, Stephen S. Curran, Hugo Verreycken, Gaël P.J. Denys, Roger A. Tabor, Vladimir A. Trifonov, Hugo Darras, Christophe Klopp, Hugues Parrinello, Frederick W. Goetz, John H. Postlethwait, Qiaowei Pan, Céline Roques, J. Andrés López, Camille Eché, Jérôme Lluch, Laurent Journot, Frank A. von Hippel, Krista M. Nichols, Konrad Ocalewicz, Romain Feron, René Guyomard, Song-Lin Chen, Ben F. Koop, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Department of Biology, University of Victoria, Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Alaska Pacific University, Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Florida Marine Research Institute, Florida Fish and Wildlife Conservation Commission, School of Ocean Science and Technology [Mississippi] (SOST), University of Southern Mississippi (USM), Gulf Coast Research Laboratory, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Department of Biological Sciences [Flagstaff], Northern Arizona University [Flagstaff], Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, College of Fisheries and Ocean Sciences (CFOS), University of Alaska [Fairbanks] (UAF), Research Institute for Nature and Forest (INBO), Department of Marine Biology and Ecology, University of Gdansk, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Fisheries Research Institute, U.S. Fish and Wildlife Service, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Tomsk State University [Tomsk], Siberian Branch of the Russian Academy of Sciences (SB RAS), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institute of Neuroscience, University of Oregon, Eugene, Oregon, University of Oregon [Eugene], This work was supported by the Agence Nationale de la Recherche, the Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), and the U.S. National Institutes of Health (R01GM085318 to JHP). The MGX and Get-Plage core sequencing facilities were supported by France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Lausanne = University of Lausanne (UNIL), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Victoria [Canada] (UVIC), Qingdao National Laboratory for Marine Science and Technology, University of Gdańsk (UG), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Texas State University, Agence Nationale de la Recherche, Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), U.S. National Institutes of Health (R01GM085318 to JHP), France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09), Julius-Maximilians-Universität Würzburg (JMU), Corvaisier, Maryse, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, and Przeworski, Molly (ed.)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, Evolution of sexual reproduction, Lineage (evolution), [SDV]Life Sciences [q-bio], sex determination, 01 natural sciences, mudminnows, Gene Duplication, Gene duplication, Biology (General), Clade, master sex determining gene, Phylogeny, северная щука, computer.programming_language, гены, определяющие пол, 0303 health sciences, education.field_of_study, Sex Chromosomes, biology, umbridae, General Neuroscience, General Medicine, [SDV] Life Sciences [q-bio], Medicine, Female, Research Article, QH301-705.5, Demographic history, Science, Population, esocidae, Y chromosome, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Animals, education, Esox, pikes, 030304 developmental biology, Pike, fish, General Immunology and Microbiology, evolutionary biology, Sex Determination Processes, biology.organism_classification, esociforms, Sexual reproduction, 030104 developmental biology, Evolutionary biology, Other, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Sex linkage
Abstract: Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebrates and uncovered that the northern pike (Esox lucius) master sex-determining gene initiated from a 65 to 90 million-year-old gene duplication and remained sex-linked on undifferentiated sex chromosomes for at least 56 million years. Contrasting with its ancient origin, we identified several independent species- or population-specific transitions of sex determination mechanisms in this lineage, including an unexpected complete and recent Y-chromosome loss in some North American northern pike populations. These findings highlight the diversity of the evolutionary fates of master sex-determining genes and raise the importance of careful considerations of population demographic history in sex determination studies. Our study also puts forward the hypothesis that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2020

24. Sex chromosome and sex locus characterization in the goldfish, Carassius auratus

Author: Hugues Parrinello, Amaury Herpin, Margot Zahm, Romain Feron, Manfred Schartl, Ming Wen, Shawn M. Burgess, Elodie Jouanno, Qiaowei Pan, Yann Guiguen, Laurent Journot, Christophe Klopp, Justine Guguin, Cédric Cabau, John H. Postlethwait, Yoshihiro Omori, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Hunan Normal University, University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Ecology and Evolution, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), National Human Genome Research Institute (NHGRI), Nagahama Institute of Bio-Science and Technology, Osaka University, Institute of Neuroscience, University of Oregon [Eugene], University of Würzburg, Texas State University, This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016) to MS and YG. Montpellier Genomics (MGX) facility was supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). This work was also supported by Grant-in-Aid for Scientific Research (19K22426) to YO, and grants R01OD011116 and 5R01GM085318 from the USA National Institutes of Health to JHP, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ProdInra, Migration, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University (HNU), Université de Lausanne = University of Lausanne (UNIL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, male genome assembly, [SDV]Life Sciences [q-bio], marqueur génétique, sex determination, Locus (genetics), [MATH] Mathematics [math], [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Genome, reproduction, 03 medical and health sciences, poisson, cyprinidae, température, Sex-determination system, chromosome sexuel, [INFO]Computer Science [cs], 14. Life underwater, goldfish, [MATH]Mathematics [math], Gene, poolseq, 030304 developmental biology, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, détermination du sexe, génome, carassius auratus, RADseq, Sex reversal, [SDV] Life Sciences [q-bio], poisson rouge, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, espèce modèle, aquaculture, Genetic marker, facteur externe, sex markers, Heterogametic sex
Abstract: BackgroundGoldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. We used sequencing approaches to better characterize sex determination and sex-chromosomes in goldfish.ResultsOur results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18°C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (∼11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the goldfish amh gene or its 5 kb proximal promoter sequence.ConclusionsThese results show that goldfish have a relatively large sex locus on LG22, which is likely the goldfish Y chromosome. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers in goldfish, which will be important for future research on sex determination and aquaculture applications in this species.
Published: 2019
Full Text: View/download PDF

25. Innovative optical geophysical instruments at the end of plurikilometric fibers for monitoring volcanic and seismic hazard in harsh environment

Author: Bernard P., Romain Feron, Guy Plantier, Mathieu Feuilloy, Philippe Menard, Nercessiane, A., Julien Couteau, Anthony Sourice, Brunet C., Boyer D., Stéphane GAFFET, Louis Géli, Pascal Pelleau, ESEO-GSII (GSII), ESEO-Tech, Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Institut de Physique du Globe de Paris (IPGP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Géoazur (GEOAZUR 6526), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER)
Subjects: [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

26. Onland and Offshore Extrinsic Fabry–Pérot Optical Seismometer at the End of a Long Fiber

Author: D. Boyer, Frederick Boudin, Romain Feron, Han Cheng Seat, Louis Géli, Anthony Sourice, Alexandre Nercessian, Guy Plantier, Julien Couteau, Michel Cattoen, Christophe Brunet, Mathieu Feuilloy, Stéphane Gaffet, Jean Chéry, Patrick Chawah, Pascal Bernard, Pascal Pelleau, Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), ESEO-GSII (GSII), ESEO-Tech, Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO)-Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Équipe Optoélectronique pour les Systèmes Embarqués (LAAS-OSE), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire Souterrain à Bas Bruit (LSBB), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire de Recherche Impliquant la Géologie et la Mécanique (LIRIGM), Université Joseph Fourier - Grenoble 1 (UJF), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), ANR-16-CE04-0008,HIPERSIS,Sismomètre Optique à Haute Performance(2016), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Aix Marseille Université (AMU)-Avignon Université (AU)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER)
Subjects: Seismometer, Optical fiber cable, Heterodyne, Optical fiber, 010504 meteorology & atmospheric sciences, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Ambient noise level, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Geophone, 010502 geochemistry & geophysics, 7. Clean energy, 01 natural sciences, Noise floor, law.invention, [SPI.TRON]Engineering Sciences [physics]/Electronics, Interferometry, Geophysics, 13. Climate action, law, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Geology, 0105 earth and related environmental sciences, Remote sensing
Abstract: We report here the design, performance, and in situ demonstration, on‐land and offshore, of an innovative high‐resolution low‐cost optical (laser) seismometer. The instrument was developed within the Laser Interferometry for Earth Strain project (French Agence Nationale de la Recherche [ANR] program), and first tested at the low‐noise underground laboratory Laboratoire Souterrain à Bas Bruit (LSBB, France). It is based on Fabry–Pérot optical interferometry between the extremity of a probing optical fiber and a reflecting mirror secured to the mobile mass of a passive 2 Hz geophone. The detection technique is based on the wavelength modulation of the laser diode (1310 nm), which allows the separation of the optical power into two signals in quadrature, thanks to an heterodyne technique. The relative displacement of the mobile mass is retrieved in real time by the phase unwrapping of these two signals. At LSBB, the fiber was 3 km long. It recorded many teleseismic earthquakes and a few regional ones, and resolves the low‐seismic noise of the Earth for periods up to 6 s, presenting an acceleration noise floor lower than 1 ng/Hz in the 0.3–5 Hz range. A three‐component version of this fiber‐based interferometric 2 Hz geophone has been recently constructed, shielded in a hyperbaric container, and installed offshore for test in Brittany (France) in April 2018, with an improved control system. Its record of the marine ambient noise matches those of a collocated commercial broadband seismometer for periods up to 50 s. This opens promising perspectives for large‐scale ocean bottom instrumentation with up to 50‐kilometer‐long optical lines; an installation is planned for 2020, off Guadeloupe, with a 5‐kilometer‐long fiber cable. It may also prove useful for installations in other challenging and exposed environments, such as deep hot boreholes, active volcanoes, unstable landslides, for real‐time monitoring in regions with high natural hazard, but also for seismic monitoring of geoindustries.
Published: 2019

27. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

Author: Amaury Herpin, Ming Wen, Jean-Paul Concordet, Julien Bobe, Jean-Mickael Busnel, René Guyomard, Estelle Vigouroux, Ayaka Yano, Jérôme Lluch, Laurent Journot, Elodie Jouanno, Romain Feron, Manfred Schartl, Yann Guiguen, Christophe Klopp, Qiaowei Pan, Hugues Parrinello, John H. Postlethwait, Céline Roques, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Fédération d'Ille-et-Vilaine pour la pêche et la protection du milieu aquatique [Rennes] (FDPPMA 35), Structure et Instabilité des Génomes (STRING), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Plateforme Bio-Informatique - Génotoul, Institut National de la Recherche Agronomique (INRA), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Neuroscience [Eugene, OR, États-Unis], University of Oregon [Eugene], Department of Physiological Chemistry [Würzburg, Allemagne], University of Würzburg-Biocenter [Würzburg, Allemagne], Comprehensive Cancer Center Mainfranken [Würzburg, Allemagne], University Hospital of Würzburg, Department of Biology [College Station, TX, États-Unis], Hagler Institute for Advanced Study [College Station, TX, États-Unis], Texas A&M University [College Station]-Texas A&M University [College Station], This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016) to YG and MS. The GeT core facility (JL, CR), Toulouse, France and the MGX facility, Montpellier, France (LJ, HP) were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Ecology and Evolution, Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Institute of Neuroscience, Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/ DFG, PhyloSex project, 2014-2016) to YG and MS. The GeT core facility (JL, CR), Toulouse, France and the MGX facility, Montpellier, France (LJ, HP) were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09), Bodescot, Myriam, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Université de Lausanne = University of Lausanne (UNIL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Dpt of Ecology and Evolution [Lausanne], Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Plateforme Bioinformatique Genotoul [Castanet-Tolosan], Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Julius-Maximilians-Universität Würzburg (JMU), and ProdInra, Migration
Subjects: Anti-Mullerian Hormone, Male, Evolution of sexual reproduction, [SDV]Life Sciences [q-bio], gène déterminant majeur du sexe, [MATH] Mathematics [math], [SDV.GEN] Life Sciences [q-bio]/Genetics, QH426-470, Animals, Genetically Modified, mâle, Database and Informatics Methods, 0302 clinical medicine, duplication de gènes, poisson, Gene Duplication, Gene duplication, Morphogenesis, Medicine and Health Sciences, chromosome sexuel, [MATH]Mathematics [math], Phylogeny, Genetics, détermination du sexe, 0303 health sciences, education.field_of_study, Sex Chromosomes, Sexual Differentiation, Chromosome Biology, Chromosome Mapping, Animals, Anti-Mullerian Hormone/genetics, Esocidae/physiology, Female, Gene Knockdown Techniques, Sex Chromosomes/genetics, Sex Determination Processes/genetics, Synteny, Genomics, [SDV] Life Sciences [q-bio], séquençage du génome, hormone antimullérienne, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Anatomy, Sequence Analysis, Genital Anatomy, différenciation sexuelle, expression des gènes, Research Article, Bioinformatics, Population, Locus (genetics), [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], Biology, Research and Analysis Methods, DNA sequencing, Chromosomes, reproduction, 03 medical and health sciences, esox lucius, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO]Computer Science [cs], education, Molecular Biology Techniques, Gonads, Gene, Molecular Biology, 030304 developmental biology, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, Sequence Assembly Tools, génome, Gene Mapping, Reproductive System, Chromosome, Biology and Life Sciences, Computational Biology, Cell Biology, Sex Determination, Sex Determination Processes, Genome Analysis, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetic Loci, Esocidae, Sequence Alignment, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade., Author summary In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf- β family, as the male master sex determining gene in the Northern pike, Esox lucius. We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha. We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.
Published: 2019

28. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

Author: Romain Feron, Mateus Contar Adolfi, Matthias Stöck, Chad Tomlinson, Ingo Braasch, Wesley C. Warren, Kang Du, John H. Postlethwait, Dmitry Yu Prokopov, Hugues Parrinello, Heiner Kuhl, Susanne Kneitz, Petra Fischer, Manfred Schartl, Yann Guiguen, Cédric Cabau, Axel Meyer, I. G. Kichigin, Vladimir A. Trifonov, Jörn Gessner, Alexey I. Makunin, Laurent Journot, Sven Wuertz, Carole Iampietro, Christophe Klopp, Werner Kloas, Joost M. Woltering, Cornelia Schmidt, University of Würzburg = Universität Würzburg, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität Konstanz, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Novosibirsk State University (NSU), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1), Washington University School of Medecine [Saint Louis, MO], University of Oregon [Eugene], Michigan State University [East Lansing], Michigan State University System, Novosibirsk State Technical University, University of Missouri [Columbia] (Mizzou), University of Missouri System, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Texas State University, German Research Foundation (DFG) /DFG SCHA 408/14-1 /SCHA 408/10-1 / Scha408/16-1 /DFG WO-2165/2-1 /DFG Me1725/24-1Russian Science Foundation (RSF) /RSF 18-44-04007German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food / 2816ERA04G, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Lausanne = University of Lausanne (UNIL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Washington University School of Medicine [Saint Louis, MO], Naudinat, Carine, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Low protein, Lineage (evolution), Genome, Chromosomes, Article, Evolutionary genetics, Polyploidy, 03 medical and health sciences, 0302 clinical medicine, Sturgeon, ddc:570, Animals, 14. Life underwater, Acipenser ruthenus, Coelacanth, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Ecology, biology, Fishes/genetics, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], Comparative genomics, Fishes, biology.organism_classification, Evolutionary biology, Molecular evolution, 030217 neurology & neurosurgery, Ichthyology, Reference genome
Abstract: Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random., A genome assembly of the sterlet, Acipenser ruthenus, reveals a whole-genome duplication early in the evolution of the entire sturgeon lineage and provides details about the rediploidization of the genome.
Published: 2019

29. Acoustic surface waves measurements by self mixing array transducers for nondestructive testing and structure health monitoring applications

Author: Roberto Longo, Guy Plantier, Mathieu Feuilloy, Alain LeDuff, Ladji Adiaviakoye., Romain Feron, ESEO-GSII (GSII), ESEO-Tech, Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Laboratoire d'Acoustique de l'Université du Mans (LAUM), and Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], Acoustics and Ultrasonics, business.industry, Computer science, Acoustics, Context (language use), Acoustic wave, 01 natural sciences, Ray, Piezoelectricity, 03 medical and health sciences, [SPI]Engineering Sciences [physics], 0302 clinical medicine, Transducer, Signal-to-noise ratio, Arts and Humanities (miscellaneous), Surface wave, Nondestructive testing, 0103 physical sciences, Reflection (physics), 030223 otorhinolaryngology, business, 010301 acoustics, Scanning laser doppler vibrometer
Abstract: International audience; In the Non Destructive Testing (NDT) and Structure Health Monitoring (SHM) field, Surface Acoustic Waves (SAWs) are widelyemployed to detect defects and/ or to monitor the integrity of the structure to test. In this context, SAWs contactless measurements offerseveral advantages with respect to the traditional use of a recording piezoelectric transducers fixed in the structure to test. They can beeasily employed in situations of difficult access to the structure avoiding the generation of undesired reflections due to the presence of asecond transducers mass. The gold standard technique for this this kind of measurements is the scanning Laser Doppler Vibrometer(sLDV), which allows to perform contactless measurements with a high spatial resolutions and a good Signal to Noise ratio. The maindrawback is the high costs to be supported and the large acquisition time that a 2D grid of measurement points could require. Moreover,to ensure an optimal reflection of the incident light, the surface of the structure under test is often treated with reflective paint or stickers.The purpose of this article is to build a large bandwidth array transducer for NDT/SHM applications overcoming the sLDV measurements disadvantages. This technique is based on the use of Laser diodes. The principle behind this approach is the Self Mixing effectoccurring when the optical beam is back-scattered in the active cavity of the diode itself.
Published: 2017

30. The lines high resolution optical seismometer

Author: Jean Chéry, Michel Cattoen, Alexandre Nercessian, D. Boyer, Guy Plantier, Romain Feron, Frédéric Boudin, Mathieu Feuilloy, Anthony Sourice, Patrick Chawah, Pascal Bernard, Stéphane Gaffet, Han Cheng Seat, Christophe Brunet, Institut de Physique du Globe de Paris (IPGP), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), ESEO-GSII (GSII), ESEO-Tech, Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Équipe Optoélectronique pour les Systèmes Embarqués (LAAS-OSE), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Ecole Nationale Supérieure d'Electrotechnique, d'Electronique, d'Informatique, d'Hydraulique et de Télécommunications (ENSEEIHT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), École normale supérieure - Paris (ENS Paris), Géoazur (GEOAZUR 7329), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Laboratoire Souterrain à Bas Bruit (LSBB), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Université Paris sciences et lettres (PSL), Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Aix Marseille Université (AMU)-Avignon Université (AU)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO)-Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT), École normale supérieure - Paris (ENS-PSL), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Seismometer, 010504 meteorology & atmospheric sciences, Laser diode, business.industry, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Geophone, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Seismic noise, 010502 geochemistry & geophysics, 01 natural sciences, 7. Clean energy, law.invention, Interferometry, [SPI]Engineering Sciences [physics], Optics, Modulation, law, business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Noise (radio), Geology, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Diode
Abstract: We present here the performance of an innovative, high resolution, robust, and low-cost optical seismometer. The instrument was developed within the LINES project ( ANR, 2009-2012), and tested at the low noise underground laboratory of LSBB (France). It is based on a Fabry-Perot interferometry between the extremity of a laser fiber and a reflecting mirror fixed on the mobile mass of a passive geophone (2 Hz ). At the other extremity of the fiber, 3 km long, an optical system includes a laser diode (1310 nm) and the recording and control systems. A double modulation (at 50 KHz and 1 KHz ) of the intensity of the diode current produces a wavelength modulation, allowing to calculate in real-time the position on the mass, thanks to fast and innovative numerical processing. It ran more than two years, recording many teleseismic earthquakes and a few regional ones. It resolves the low seismic noise of the Earth for periods as low as 5 s, and presents an acceleration floor noise lower than 1 ng/sqrt(Hz) in the 0.2-5 Hz range. The LINEs optical seismometer is thus a promising instrument for the microseismic monitoring of deep and/or hot industrial boreholes.
Published: 2017

31. Social learning and the replication process: an experimental investigation

Author: Romain Feron, Maxime Derex, Michel Raymond, and Bernard Godelle
Subjects: Adult, Male, Adolescent, Fitness landscape, Process (engineering), General Biochemistry, Genetics and Molecular Biology, Task (project management), Random Allocation, Young Adult, Cultural Evolution, Humans, Sociocultural evolution, Research Articles, General Environmental Science, General Immunology and Microbiology, Fourier Analysis, General Medicine, Middle Aged, Social learning, Replication (computing), Social Learning, Video Games, Idealization, France, General Agricultural and Biological Sciences, Psychology, Social psychology, Mechanism (sociology), Cognitive psychology
Abstract: Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning events has not been carefully assessed. Here, we used a specifically developed computer task to evaluate (i) the extent to which social learning leads to the replication of an observed behaviour and (ii) the consequences it has for fitness landscape exploration. Our results show that social learning does not lead to a dichotomous choice between disregarding and replicating social information. Rather, it appeared that individuals combine and transform information coming from multiple sources to produce new solutions. As a consequence, landscape exploration was promoted by the use of social information. These results invite us to rethink the way social learning is commonly modelled and could question the validity of predictions coming from models considering this process as replicative.
Published: 2015

32. High resolution passive optical seismometer connected to a long fiber for onland and offshore remote applications

Author: Pascal Bernard, Romain Feron, Guy Plantier, Alexandre Nercessian, Julien Couteau, Mathieu Feuilloy, Anthony Sourice, Michel Cattoen, Han Cheng Seat, Patrick Chawah, Jean Chery, Christophe Brunet, Frédéric Boudin, Daniel Boyer, Stéphane GAFFET, Louis Geli, Pascal Pelleau, Institut de Physique du Globe de Paris (IPGP), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), ESEO-Tech, Université Bretagne Loire (UBL), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), ESEO-GSII (GSII), Université Bretagne Loire (UBL)-Université Bretagne Loire (UBL), Équipe Optoélectronique pour les Systèmes Embarqués (LAAS-OSE), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), École normale supérieure - Paris (ENS Paris), Laboratoire Souterrain à Bas Bruit (LSBB), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO)-Université Bretagne Loire (UBL)-École supérieure d'électronique de l'ouest [Angers] (ESEO), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Avignon Université (AU)-Aix Marseille Université (AMU)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Aix Marseille Université (AMU)-Avignon Université (AU)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), and Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne)
Subjects: [SPI]Engineering Sciences [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing
Abstract: International audience; In many areas with high telluric hazard (earthquakes, tsunamis, landslides etc.), our understanding of seismogenic and mechanical processes and our ability to properly asses the related hazard is still very limited by the difficulty or the impossibility to deploy arrays of high performance seismometers in areas with harsh and challenging environment (far offshore, hot/deep boreholes, mountainous regions, etc.), due to the high installations and maintaining costs, and to the risk of loss (lightning, eruptions, rock falls, power failure, etc.) or even to the absence of suitablecommercial technology (high temperature). These last few years, innovative, high-resolution, low-cost optical seismometers have been developed to provide a real-time monitoring solution for regions of interest. The application fields of these significant advances are multiple: natural areas with a high telluric hazard, geo-industries (oil and gas production, geothermy, gas or waste storage), monitoring of structures, etc.The IPGP, the ESEO Group and their partners Geosciences Montpellier and the Laboratory of Analysis and Architecture Systems (LAAS) of Toulouse developed an on-land and offshore, high resolution, low-cost optical (laser) seismometer (french ANR LINES). Campaigns have been conducted in order to test and qualify their first prototype of 2 Hz - optical seismometers, at the Low Noise Underground Laboratory (LSBB) of Rustrel (France). This allowed a first validation of all opto-mechanical functions of the involved sensors, including the dedicated signalprocessing. Thus, the acceleration floor noise level of the sensor is lower than 1ng.Hzˆ-1/2 in the 0.3-5Hz range andremains under 10ng.Hzˆ-1/2 in the 0.15-20Hz range. One of the current fields of investigation, co-financed by the Technology Transfer Accelerator Office (SATT) Ouest Valorisation, consists in adapting these technologies to the design of a 3 components remote underwater seismometer. In this campaign, the integration of optical components, electronics for analog signal conditioning and digital signal processing has significantly improved the sensor performances and allowed an important reduction of power consumption (by a factor of ten). This autonomous device has been deployed during the past 6 months directly on a platform in the Brest harbour, collaborating with IFREMER and the Sea Test Base of ISEN. Our optical geophones were packaged in a hyperbaric chamber, buried in the seafloor, 500 meters away from the platform and at a depthof about 10 meters. This presentation aims to show the results and observations collected during these campaigns, and discuss aboutthe short and long term perspectives.

33. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

Author: Adolfi, Mateus C., Du, Kang, Kneitz, Susanne, Cabau, Cédric, Zahm, Margot, Klopp, Christophe, Feron, Romain, Paixão, Rômulo V., Varela, Eduardo S., de Almeida, Fernanda L., de Oliveira, Marcos A., Nóbrega, Rafael H., Lopez-Roques, Céline, Iampietro, Carole, Lluch, Jérôme, Kloas, Werner, Wuertz, Sven, Schaefer, Fabian, Stöck, Matthias, Guiguen, Yann, Schartl, Manfred, University of Würzburg = Universität Würzburg, Texas State University, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Sport Sciences of University of Lausanne (ISSUL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), EMBRAPA Amazônia Oriental, Embrapa Pesca E Aquicultura, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Hiroshima University, University Hospital of Würzburg, University of Wuerzburg, Université de Toulouse, LPGP, and Swiss Institute of Bioinformatics, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade Estadual Paulista (UNESP), Genotoul, IGB, University Hospital, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), MATEUS C. ADOLFI, University of Wuerzburg, KANG DU, University of Wuerzburg, SUSANNE KNEITZ, University of Wuerzburg, CÉDRIC CABAU, Université de Toulouse, MARGOT ZAHM, Université de Toulouse, CHRISTOPHE KLOPP, INRA, ROMAIN FERON, INRAE, RÔMULO V. PAIXÃO, Bolsista CPAA, EDUARDO SOUSA VARELA, CNPASA, FERNANDA LOUREIRO ALMEIDA OSULLIVAN, CPAA, MARCOS A. DE OLIVEIRA, UNESP, RAFAEL H. NÓBREGA, UNESP, CÉLINE LOPEZ-ROQUES, INRAE, CAROLE IAMPIETRO, INRAE, JÉRÔME LLUCH, INRAE, WERNER KLOAS, Institute of Freshwater Ecology and Inland Fisheries, SVEN WUERTZ, Institute of Freshwater Ecology and Inland Fisheries, FABIAN SCHAEFER, Institute of Freshwater Ecology and Inland Fisheries, MATTHIAS STÖCK, Institute of Freshwater Ecology and Inland Fisheries, YANN GUIGUEN, INRAE, and MANFRED SCHARTL, Comprehensive Cancer Center Mainfranken.
Subjects: Genetic Markers, Male, Conservation of Natural Resources, Genotype, Science, [SDV]Life Sciences [q-bio], Fisheries, Polymerase Chain Reaction, Article, Evolutionary genetics, Protein Structure, Secondary, Arapaima gigas, Evolution, Molecular, Pirarucu, Gene Duplication, Y Chromosome, Animals, ddc:610, Phylogeny, Inhibitor of Differentiation Protein 2, Genome, Sex Chromosomes, Fishes, Chromosome Mapping, DNA, Sequence Analysis, DNA, Protein Structure, Tertiary, Phenotype, Medicine, Female
Abstract: Made available in DSpace on 2022-04-28T19:46:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Julius-Maximilians-Universität Würzburg Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes. Developmental Biochemistry Biocenter University of Wuerzburg, Am Hubland The Xiphophorus Genetic Stock Center Department of Chemistry and Biochemistry Texas State University, San Marcos Biochemistry and Cell Biology Biocenter University of Wuerzburg, Am Hubland Sigenae GenPhySE INRAE ENVT Université de Toulouse MIAT INRA Université de Toulouse, Chemin de Borde Rouge INRAE LPGP Department of Ecology and Evolution University of Lausanne and Swiss Institute of Bioinformatics Embrapa Amazônia Ocidental Embrapa Pesca E Aquicultura Reproductive and Molecular Biology Group Department of Morphology Institute of Biosciences UNESP GeT-PlaGe INRAE Genotoul Leibniz-Institute of Freshwater Ecology and Inland Fisheries IGB, Müggelseedamm 301 & 310 Amphibian Research Center Hiroshima University Comprehensive Cancer Center Mainfranken University Hospital Reproductive and Molecular Biology Group Department of Morphology Institute of Biosciences UNESP
Published: 2021

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources

Refine your results

33 results on '"Romain Feron"'

1. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

2. A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

3. Anopheles mosquitoes reveal new principles of 3D genome organization in insects

4. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

5. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758)

6. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

7. The rise and fall of the ancient northern pike master sex-determining gene

8. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation.

9. Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation

10. First Optical Seismometer at the Top of La Soufrière Volcano, Guadeloupe

11. Nature Communications

12. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

13. A supernumerary 'B-sex' chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

14. The bowfin genome illuminates the developmental evolution of ray-finned fishes

15. Functional constraints on insect immune system components govern their evolutionary trajectories

16. Genome biology of the darkedged splitfin

17. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

18. A Supernumerary 'B-Sex' Chromosome Drives Male Sex Determination in the Pachón Cavefish, Astyanax mexicanus

19. Author response: The rise and fall of the ancient northern pike master sex-determining gene

20. The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

21. Independent origin of XY and ZW sex determination mechanisms in Mosquitofish sister species

22. BMC Biology

23. The rise and fall of the ancient northern pike master sex-determining gene

24. Sex chromosome and sex locus characterization in the goldfish, Carassius auratus

25. Innovative optical geophysical instruments at the end of plurikilometric fibers for monitoring volcanic and seismic hazard in harsh environment

26. Onland and Offshore Extrinsic Fabry–Pérot Optical Seismometer at the End of a Long Fiber

27. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

28. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

29. Acoustic surface waves measurements by self mixing array transducers for nondestructive testing and structure health monitoring applications

30. The lines high resolution optical seismometer

31. Social learning and the replication process: an experimental investigation

32. High resolution passive optical seismometer connected to a long fiber for onland and offshore remote applications

33. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

Catalog

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

33 results on '"Romain Feron"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources