A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

• Published in: Genomics
• Main Authors: Martínez Portela, Paulino, Robledo Sánchez, Diego, Taboada Penoucos, Xoana, Blanco Hortas, Andrés, Moser, Michel, Maroso, Francesco, Hermida Prieto, Miguel, Gómez Tato, Antonio, Álvarez Blázquez, Blanca, Cabaleiro, Santiago, Piferrer, Francesc, Bouza Fernández, María Carmen, Lien, Sigbjørn, Viñas Díaz, Ana María
• Other Authors: Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier
• Subjects: Turbot; Sex determination; GWAS; sox2; Interfamily variation; Genome assembly; Oxford Nanopore; Scophthalmus maximus
• Online Access: http://hdl.handle.net/10347/26042; https://doi.org/10.1016/j.ygeno.2021.04.007

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 This work was supported by the Spanish Ministry of Economy and Competitiveness, Grant: AGL2014-57065-R, by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 81792 (AQUA-FAANG) and by Consellería de Educación, Universidade e Formación Profesional. Xunta de Galicia, Grant number:ED431C 2018/28 SI