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Identification of the Master Sex Determining Gene in Northern Pike (Esox Lucius) Reveals Restricted Sex Chromosome Differentiation

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Identification of the Master Sex Determining Gene in Northern Pike (Esox Lucius) Reveals Restricted Sex Chromosome Differentiation Identification of the master sex determining genein Northern pike (Esox lucius) reveals restricted sex chromosome differentiation Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, Estelle Vigouroux, Ming Wen, Jean-Mickaël Busnel, Julien Bobe, Jean-Paul Concordet, et al. To cite this version: Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, et al.. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genetics, Public Library of Science, 2019, 15 (8), pp.e1008013. 10.1371/jour- nal.pgen.1008013. inserm-02279967 HAL Id: inserm-02279967 https://www.hal.inserm.fr/inserm-02279967 Submitted on 5 Sep 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation 1,13 1,13 1 2 1 Qiaowei PanID , Romain FeronID , Ayaka Yano , Rene Guyomard , Elodie Jouanno , 1 1 3 1 Estelle VigourouxID , Ming Wen , Jean-MickaeÈl Busnel , Julien BobeID , Jean- 4 5 5 6,7 Paul Concordet , Hugues Parrinello , Laurent Journot , Christophe KloppID , 8 8 9 10,11,12 JeÂroà me Lluch , CeÂline Roques , John PostlethwaitID , Manfred SchartlID , 1 1 Amaury HerpinID , Yann GuiguenID * a1111111111 a1111111111 1 INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France, 2 GABI, INRA, AgroParisTech, Universite Paris-Saclay, Jouy-en-Josas, France, 3 FeÂdeÂration d'Ille-et-Vilaine pour la pêche et la protection du milieu a1111111111 aquatique (FDPPMA35), CS 26713, Rennes, France, 4 INSERM U1154, CNRS UMR7196, MNHN, MuseÂum a1111111111 National d'Histoire Naturelle, France, 5 Institut de GeÂnomique Fonctionnelle, IGF, CNRS, INSERM, Universite a1111111111 de Montpellier, Montpellier, France, 6 Plate-forme bio-informatique Genotoul, MatheÂmatiques et Informatique AppliqueÂes de Toulouse, INRA, Castanet Tolosan, France, 7 SIGENAE, GenPhySE, Universite de Toulouse, INRA, ENVT, Castanet Tolosan, France, 8 INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France, 9 Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America, 10 University of Wuerzburg, Physiological Chemistry, Biocenter, WuÈrzburg, Germany, 11 Comprehensive Cancer Center Mainfranken, University Hospital, WuÈrzburg, Germany, 12 Hagler Institute for Advanced Study and Department OPEN ACCESS of Biology, Texas A&M University, College Station, Texas, United States of America, 13 Department of Ecology and Evolution, University of Lausanne,1015, Lausanne, Switzerland Citation: Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, et al. (2019) Identification * [email protected] of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genet 15(8): e1008013. https://doi.org/10.1371/journal. Abstract pgen.1008013 Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide Editor: Catherine L. Peichel, Universitat Bern, SWITZERLAND 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 Received: February 11, 2019 interplay between the sex chromosomes and the MSD genes they harbor is rather unex- Accepted: July 26, 2019 plored. We characterized a male-specific duplicate of the anti-MuÈllerian hormone (amh) as Published: August 22, 2019 the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as Copyright: © 2019 Pan et al. This is an open access well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a article distributed under the terms of the Creative family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned Commons Attribution License, which permits the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD origi- unrestricted use, distribution, and reproduction in any medium, provided the original author and nated from an ancient duplication of the autosomal amh gene, which was subsequently source are credited. translocated to LG24. Using sex-specific pooled genome sequencing and a new male Data Availability Statement: Sequencing data and genome sequence assembled using Nanopore long reads, we also characterized the differ- assembly for the Esox lucius genome can be found entiation of the X and Y chromosomes, revealing a small male-specific insertion containing under NCBI Bioproject PRJNA514887. Sequencing the MSD gene and a limited region with reduced recombination. Our study reveals an unex- data for identifying and charactering the sex locus, including RAD-seq and pool-seq reads, can be pectedly low level of differentiation between a pair of sex chromosomes harboring an old found under the NCBI Bioproject PRJNA514888. MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from Funding: This project was supported by funds the amh pathway in sex determination, as well as the importance of gene duplication as a from the ªAgence Nationale de la Rechercheº and mechanism driving the turnover of sex chromosomes in this clade. the ªDeutsche Forschungsgemeinschaftº (ANR/ DFG, PhyloSex project, 2014-2016) to YG and MS. PLOS Genetics | https://doi.org/10.1371/journal.pgen.1008013 August 22, 2019 1 / 31 Restricted sex chromosome differentiation in Northern pike The GeT core facility (JL, CR), Toulouse, France and the MGX facility, Montpellier, France (LJ, HP) were supported by France GeÂnomique National Author summary infrastructure, funded as part of ªInvestissement In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic d'avenirº program managed by Agence Nationale sex chromosomes and display a high diversity of sex determining genes. Yet, population pour la Recherche (contract ANR-10-INBS-09). The funders had no role in study design, data level knowledge of both the sex chromosome and the master sex determining gene is only collection and analysis, decision to publish, or available for the Japanese medaka, a model species. Here we identified and provided func- preparation of the manuscript. tional proofs of an old duplicate of anti-MuÈllerian hormone (Amh), a member of the Tgf- Competing interests: The authors have declared β family, as the male master sex determining gene in the Northern pike, Esox lucius. We that no competing interests exist. found that this duplicate, named amhby (Y-chromosome-specific anti-MuÈllerian hor- mone paralog b), was translocated to the sub-telomeric region of the new sex chromo- some, 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 chromo- somes in teleosts. Introduction The evolution of sex determination (SD) systems and sex chromosomes has sparked the inter- est of evolutionary biologists for decades. While initial insights on sex chromosome evolution came from detailed studies in Drosophila and in mammals [1±5], recent research on other ver- tebrate groups, such as avian [6,7], non-avian reptiles [8,9], amphibians [10±13], and teleost fishes [14±17], has provided new information that helps us understand the evolution of SD sys- tems and sex chromosomes. Teleosts display the highest diversity of genetic sex determination systems in vertebrates, including several types of monofactorial and polygenic systems [14,18]. In addition, in some species, genetic factors can interact with environmental factors, most commonly temperature, i.e. in Odontesthes bonariensis [19], generating intricate sex determination mechanisms. More- over, sex determination systems in fish can differ between very closely related species, as illus- trated by the group of Asian ricefish (genus Oryzias) [20±25], and sometimes even among different populations of one species, as in the Southern platyfish, Xiphophorus maculatus [26]. Beside this remarkable dynamic of sex determination systems, the rapid turnover of sex chro- mosomes in teleosts provides many opportunities to examine sex chromosome pairs at differ- ent stages of differentiation. Finally, recent studies on fish sex determination have revealed a dozen new master sex determining (MSD) genes [14,16,27], providing additional insight to the forces driving the turnover of SD systems and the formation of sex chromosomes. The birth of new MSD genes drives the formation of sex chromosomes and transitions of SD systems. The origin of new MSDs falls into two categories: either
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