Paulino Martínez1, Diego Robledo2, Xoana Taboada3, Andrés Blanco4, Michel Moser5, Francesco Maroso6, Miguel Hermida7, Antonio Gómez-Tato8, Blanca Álvarez-Blázquez9, Santiago Cabaleiro10, Francesc Piferrer11, Carmen Bouza12, Sigbjørn Lien13, Ana M Viñas14. 1. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: paulino.martinez@usc.es. 2. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK. Electronic address: diego.robledo@roslin.ed.ac.uk. 3. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain. 4. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: andres.blanco.hortas@usc.es. 5. Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway. Electronic address: michel.moser@nmbu.no. 6. Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy. 7. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: miguel.hermida@usc.es. 8. Departament of Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain. Electronic address: antonio.gomez.tato@usc.es. 9. Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Vigo, Cabo Estay-Canido, 36280 Vigo, Spain. Electronic address: blanca.alvarez@ieo.es. 10. Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695 A Coruña, Spain. Electronic address: cabaleiro@cetga.org. 11. Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain. Electronic address: piferrer@icm.csic.es. 12. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain. Electronic address: mcarmen.bouza@usc.es. 13. Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway. Electronic address: sigbjorn.lien@nmbu.no. 14. Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain. Electronic address: anamaria.vinas@usc.es.
Abstract
BACKGROUND: Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. RESULTS: The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. CONCLUSIONS: The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families.
BACKGROUND: Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. RESULTS: The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. CONCLUSIONS: The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families.