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Pré-publication, Document de travail

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
1 LPGP - Laboratoire de Physiologie et Génomique des Poissons
2 SIB - Swiss Institute of Bioinformatics [Lausanne]
3 MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse
4 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
5 Génome et Transcriptome - Plateforme Génomique
6 SYSAAF - Syndicat des Sélectionneurs Avicoles et Aquacoles Français
7 GABI - Génétique Animale et Biologie Intégrative
8 University of Wisconsin Stevens Point
9 Hunan Normal University
10 University Hospital of Würzburg
11 Texas State University
12 Institute of Neuroscience
13 Department of Forestry and Natural Resources
14 Department of Biological Sciences [Lafayette IN]
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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https://hal.inrae.fr/hal-02790966
Déposant : Migration Prodinra <>
Soumis le : vendredi 5 juin 2020 - 07:03:36
Dernière modification le : jeudi 11 février 2021 - 12:02:02

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2019_Feron_BioRxiv_1.pdf
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INRAE | INRA | LPGP | BIOSIT | AGROPARISTECH

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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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