1
|
Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valière S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouano E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y. 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. Mol Ecol Resour 2020; 20:531-543. [PMID: 31903688 PMCID: PMC7050324 DOI: 10.1111/1755-0998.13133] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. 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). 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 assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, 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.
Collapse
Affiliation(s)
- Romain Feron
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Margot Zahm
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Camille Eché
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Pierrick Haffray
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Anastasia Bestin
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Romain Morvezen
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | - Hervé Acloque
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI 54481, USA
| | - Ming Wen
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Elodie Jouano
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
| | - Manfred Schartl
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany and The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Claire Schraidt
- Department of Forestry and Natural Resources, Purdue University; 715 W. State St., West Lafayette, Indiana 47907-2054 USA
| | - Mark R. Christie
- Department of Forestry and Natural Resources, Purdue University; 715 W. State St., West Lafayette, Indiana 47907-2054 USA
- Department of Biological Sciences, Purdue University; 915 W. State St., West Lafayette, Indiana 47907-2054 USA
| | - Wesley A. Larson
- U.S. Geological Survey Wisconsin Cooperative Fishery Research Unit, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI 54481, USA
| | - Amaury Herpin
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
| | - Yann Guiguen
- INRAE, UR 1037 Fish Physiology and Genomics, F-35000 Rennes, France
| |
Collapse
|