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, Paulino, Robledo, Diego, Taboada, Xoana, Blanco, Andrés, Moser, Michel, Maroso, Francesco, Hermida, Miguel, Gómez-Tato, Antonio, Álvarez-Blázquez, Blanca, Cabaleiro, Santiago, Piferrer, Francesc, Bouza, Carmen, Lien, Sigbjør, Viñas, Ana
• Other Authors: Ministerio de Economía y Competitividad (España), European Commission, Xunta de Galicia, Agencia Estatal de Investigación (España)
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier 2021
• Subjects: Turbot; Sex determination; GWAS; sox2; Interfamily variation; Genome assembly; Oxford Nanopore; Scophthalmus maximus
• Online Access: http://hdl.handle.net/10261/244431; https://doi.org/10.1016/j.ygeno.2021.04.007; https://doi.org/10.13039/501100011033; https://doi.org/10.13039/501100000780; https://doi.org/10.13039/501100003329; https://doi.org/10.13039/501100010801

14 pages, 7 figures, 2 tables, supplementary material https://doi.org/10.1016/j.ygeno.2021.04.007.-- Availability of data and materials: All dataset generated during this study are included (in this article and as supplementary information files) or are available in public repositories. Turbot Genome Sequencing data are at NCBI databases (Bioproject: PRJNA631898) (https://www.ncbi.nlm.nih.gov/genome/?term=turbot) and BioProject es PRJNA649485 (https://www.ncbi.nlm.nih.gov/bioproject/649485; Accessión numbers: SRX8843737, SRX8843739, SRX8843738) 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 ...