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Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens
Romain Feron
1, 2
Margot Zahm
3
Cédric Cabau
4
Christophe Klopp
3
Céline Roques
5
Olivier Bouchez
5
Camille Eché
5
Sophie Valière
5
Cécile Donnadieu
5
Pierrick Haffray
6
Anastasia Bestin
6
Romain Morvezen
6
Hervé Acloque
7
Peter T. Euclide
8
Ming Wen
1, 9
Elodie Jouanno
1
Manfred Schartl
10, 11
John H. Postlethwait
12
Claire Schraidt
13
Mark R. Christie
13, 14
Wesley A. Larson
8
Amaury Herpin
1
Yann Guiguen
1
5
GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique
INRA - Institut National de la Recherche Agronomique : US 1426, GET - Plateforme Génome & Transcriptome
Romain Feron 1, 2
Author IdHAL : romainferon ORCID : https://orcid.org/0000-0001-5893-6184
Margot Zahm 3
Author
Cédric Cabau 4
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : cedric-cabau ORCID : https://orcid.org/0000-0001-8560-4003
Christophe Klopp 3
Author IdHAL : 0000-0001-7126-5477 ORCID : https://orcid.org/0000-0001-7126-5477
Céline Roques 5
Author
Olivier Bouchez 5
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
Camille Eché 5
Author
Sophie Valière 5
Author
Cécile Donnadieu 5
Author
Pierrick Haffray 6
Author Employer institution : Syndicat des Sélectionneurs Avicoles et Aquacoles Français IdHAL : pierrick-haffray ORCID : https://orcid.org/0000-0001-8604-4562
Anastasia Bestin 6
Author Employer institution : Syndicat des Sélectionneurs Avicoles et Aquacoles Français IdHAL : anastasia-bestin ORCID : https://orcid.org/0000-0002-1777-338X
Romain Morvezen 6
Author Employer institution : Syndicat des Sélectionneurs Avicoles et Aquacoles Français IdHAL : romain-morvezen ORCID : https://orcid.org/0000-0002-9773-9359
Hervé Acloque 7
Author IdHAL : herve-acloque ORCID : https://orcid.org/0000-0003-4761-1055
Peter T. Euclide 8
Author
Ming Wen 1, 9
Author
Elodie Jouanno 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : elodiejouanno
Manfred Schartl 10, 11
Author
John H. Postlethwait 12
Author
Claire Schraidt 13
Author
Mark R. Christie 13, 14
Author
Wesley A. Larson 8
Author
Amaury Herpin 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : amaury-herpin ResearcherId : http://www.researcherid.com/rid/B-8950-2011 ORCID : https://orcid.org/0000-0002-0630-4027
Yann Guiguen 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : yann-guiguen ORCID : https://orcid.org/0000-0001-5464-6219
1
LPGP - Laboratoire de Physiologie et Génomique des Poissons (Campus de Beaulieu - Bât. 16A - 35042 RENNES Cedex [France] - France)
- INRA - Institut National de la Recherche Agronomique : UR1037 (France)
- Biosit : Biologie - Santé - Innovation Technologique - Structure Fédérative de Recherche en Biologie et Santé de Rennes (Université Rennes 1 - Campus Santé Villejean - 2, avenue Professeur Léon Bernard 35043 Rennes cedex - France)
2
SIB - Swiss Institute of Bioinformatics [Lausanne] (Quartier UNIL-Sorge Bâtiment Génopode CH-1015 Lausanne - Switzerland)
- UNIL - Université de Lausanne (CH-1015 Lausanne - Switzerland)
3
MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse (Chemin de Borde Rouge, 31320 Castanet Tolosan - France)
- INRA - Institut National de la Recherche Agronomique : UR875 (France)
4
GenPhySE - Génétique Physiologie et Systèmes d'Elevage (INRA Auzeville -
24, chemin de Borde-Rouge -
Auzeville Tolosane
31326 Castanet Tolosan
- France)
- École nationale supérieure agronomique de Toulouse [ENSAT] (France)
- INRA - Institut National de la Recherche Agronomique : UMR1388 (France)
- ENVT - Ecole Nationale Vétérinaire de Toulouse (23 chemin des Capelles
31076 Toulouse
Cedex - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
5
GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique (Campus INRA
24 chemin de borde rouge - Auzeville
CS 52627
31326 CASTANET-TOLOSAN Cedex - France)
- INRA - Institut National de la Recherche Agronomique : US 1426 (France)
- GET - Plateforme Génome & Transcriptome (Bio5 - INSA 135 Avenue de Rangueil 31077 Toulouse Cedex 04 - France)
- GENOTOUL - Génopole Toulouse Midi-Pyrénées [Auzeville] (Chemin de Borde-Rouge Auzeville - France)
- INSA Toulouse - Institut National des Sciences Appliquées - Toulouse (135, avenue de Rangueil - 31077 Toulouse cedex 4 - France)
- UT3 - Université Toulouse III - Paul Sabatier (118 route de Narbonne - 31062 Toulouse - France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (France)
- ENVT - Ecole Nationale Vétérinaire de Toulouse (23 chemin des Capelles
31076 Toulouse
Cedex - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- INSERM - Institut National de la Santé et de la Recherche Médicale (101, rue de Tolbiac, 75013 Paris - France)
- GENOTOUL - Génopole Toulouse Midi-Pyrénées [Auzeville] (Chemin de Borde-Rouge Auzeville - France)
7
GABI - Génétique Animale et Biologie Intégrative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)
- INRA - Institut National de la Recherche Agronomique : UMR1313 (France)
- AgroParisTech (16 rue Claude Bernard F-75231 Paris Cedex 05 - France)
8
University of Wisconsin Stevens Point (United States)
- Partenaires INRAE (Cette structure regroupe l'ensemble des structures créées pour la reprise des données ProdInra - France)
9
Hunan Normal University (France)
10
University Hospital of Würzburg (Germany)
11
Texas State University (601 University Drive San Marcos, Texas 78666-4684 - United States)
12
Institute of Neuroscience (United States)
- University of Oregon [Eugene] (1585 E 13th Ave. Eugene, OR 97403 - United States)
13
Department of Forestry and Natural Resources (United States)
- Purdue University [West Lafayette] (Hovde Hall, 610 Purdue Mall, West Lafayette, IN 47907 - United States)
14
Department of Biological Sciences [Lafayette IN] (Hansen Life Sciences Research Building West Lafayette IN, 47907 - United States)
- Purdue University [West Lafayette] (Hovde Hall, 610 Purdue Mall, West Lafayette, IN 47907 - United States)
Abstract : Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture management practices. Findings: By combining Oxford Nanopore Technologies long-reads, 10X genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). Genome annotation identified 41.7% (366 Mb) of repeated elements and 24,486 genes including 16,579 genes (76.3%) significantly matching with proteins in public databases. We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping test which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by−). Conclusions: Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries, and aquaculture research. In addition, the characterization of the amhr2by gene as a candidate sex determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.
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Preprints, Working Papers, ...
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https://hal.inrae.fr/hal-02790966
Contributor : Migration Prodinra Connect in order to contact the contributor
Submitted on : Friday, June 5, 2020 - 7:03:36 AM
Last modification on : Wednesday, November 3, 2021 - 6:49:14 AM
Contributor : Migration Prodinra Connect in order to contact the contributor
Submitted on : Friday, June 5, 2020 - 7:03:36 AM
Last modification on : Wednesday, November 3, 2021 - 6:49:14 AM
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2019_Feron_BioRxiv_1.pdf
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Identifiers
- HAL Id : hal-02790966, version 1
- DOI : 10.1101/717397
- PRODINRA : 496659
Collections
INRAE | INRA | LPGP | BIOSIT | AGROPARISTECH | ANR | GENETIQUE_ANIMALE | GS-BIOSPHERA | UNIV-TLSE3 | INSA-TOULOUSE | PHASE
Citation
Romain Feron, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, et al.. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. 2019. ⟨hal-02790966⟩
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