Draft genomes of female and male turbot Scophthalmus maximus

Abstract

turbot (Scophthalmus maximus) is a commercially important flatfish species in aquaculture. It has a drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female and male turbot genomes. The assembled female genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), and the male genome was 584 Mb (scaffold N50, 5.9 Mb, BUSCO 96.6%). Using two genetic maps, we anchored female scaffolds representing 535 Mb onto 22 chromosomes. Annotation of the female anchored genome identified 87.8 Mb transposon elements and 20,134 genes. We identified 17,936 gene families, of which 369 gene families were flatfish specific. Phylogenetic analysis showed that the turbot, Japanese flounder and Chinese tongue sole form a clade that diverged from other teleosts approximately 78 Mya. This report of female and male turbot draft genomes and annotated genes provides a new resource for identifying sex determination genes, elucidating the evolution of adaptive traits in flatfish and developing genetic techniques to increase the sustainability of turbot aquaculture. Background & Summary Turbot (Scophthalmus maximus) is an economically important flatfish with both eyes on the upper side of the body, and it is commonly found along the Atlantic coast of Europe. Aquaculture of turbot was initiated in Scotland in the 1970s and subsequently expanded into other European countries by the early 1980s 1. In the 1990s, turbot was introduced to China where its farming has since developed rapidly. China is currently the largest producer of turbot in the world 2. Turbot growth is sexually dimorphic, with females eventually attaining sizes up to 50% larger than those of males 3. An all-female stock can potentially increase the production value of turbot aquaculture. The sex determination system of turbot follows the ZW/ZZ model, and this system can be affected by environmental factors 4. Therefore, understanding the genomic architecture of female and male turbot may enable screening for sex determination loci, improve understanding of the interactions between genetic and environmental factors in sex determination, and lead to the acquisition of genomic resources for molecular breeding. Four sex-related QTLs, located on four different linkage groups, have been found in turbot 5. Though the turbot genome has been assembled, the sex-determining mechanism of turbot remains unclear 6. In this study, we sequenced, assembled and annotated the female and male turbot genomes, and conducted a phylogenetic analysis using the genome sequences of eight other closely related species. A 568 Mb female genome sequence and 584 Mb male genome sequence were assembled. The draft turbot genomes represent a valuable resource for isolating the sex determination genes, increasing our understanding of flatfish development and improving the molecular breeding techniques for turbot. Methods Turbot samples and genome sequencing. One female (ZW) and one male (ZZ) adult turbot were selected for whole genome shotgun sequenci...

Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish

“…A dot-plot alignment analysis indicated a high similarity between male and female genome assemblies perfected aligned along the diagonal (Fig. 2 ) with a completeness similar to other high-quality fish assemblies (> 95.5% complete genes) 40 , 43 , 44 .…”

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

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Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

“…Total size of this new genome was 608 Mb very close to the 600.3 Mb reported for the 85 k Illumina assembly 7 suggesting that Senegalese sole genome is a slightly bigger than other flatfish (up to 584 Mb) 2 – 4 , 48 . This assembly had a high-quality gene representativity (completeness was 96.2% similar to previous flatfish assemblies) 3 with the marker density of 886.7 SSRs per megabase (Supplementary Table S1 tab "SSR_genome"). Previous cytogenetic analyses demonstrated that most of di- and tetranucleotides appear widely distributed in subtelomeric position of metacentric, submetacentric and acrocentric chromosomes 15 and hence both of them were considered suitable for primer design and multiplex amplification in this study.…”