Abstract
BackgroundHalf-smooth tongue sole (Cynoglossus semilaevis Günther) has been exploited as a commercially important cultured marine flatfish, and female grows 2–3 times faster than male. Genetic studies, especially on the chromosomal sex-determining system of this species, have been carried out in the last decade. Although the genome of half-smooth tongue sole was relatively small (626.9 Mb), there are still some difficulties in the high-quality assembly of the next generation genome sequencing reads without the assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences. The objective of this study is to construct a bacterial artificial chromosome (BAC)-based physical map for half-smooth tongue sole with the method of high information content fingerprinting (HICF).ResultsA physical map of half-smooth tongue sole was constructed with 30, 294 valid fingerprints (7.5 × genome coverage) with a tolerance of 4 and an initial cutoff of 1e-60. A total of 29,709 clones were assembled into 1,485 contigs with an average length of 539 kb and a N50 length of 664 kb. There were 394 contigs longer than the N50 length, and these contigs will be a useful resource for future integration with linkage map and whole genome sequence assembly. The estimated physical length of the assembled contigs was 797 Mb, representing approximately 1.27 coverage of the half-smooth tongue sole genome. The largest contig contained 410 BAC clones with a physical length of 3.48 Mb. Almost all of the 676 BAC clones (99.9%) in the 21 randomly selected contigs were positively validated by PCR assays, thereby confirming the reliability of the assembly.ConclusionsA first generation BAC-based physical map of half-smooth tongue sole was constructed with high reliability. The map will promote genetic improvement programs of this fish, especially integration of physical and genetic maps, fine-mappings of important gene and/or QTL, comparative and evolutionary genomics studies, as well as whole genome sequence assembly.
Highlights
Half-smooth tongue sole (Cynoglossus semilaevis Günther) has been exploited as a commercially important cultured marine flatfish, and female grows 2–3 times faster than male
Half-smooth tongue sole (Cynoglossus semilaevis Günther) is a marine flatfish that belongs to the family Cynoglossidae in the order Pleuronectiformes, and is widely distributed in Chinese coastal water [1,2]
Microsatellite-based genetic linkage maps with different densities have been constructed, and four quantitative trait loci (QTLs) related to growth rate, seven sex-related loci and five sex-related markers have been located on the relevant chromosomes [16,17]. These studies have laid the foundation for the future genetic improvement of half-smooth tongue sole
Summary
Half-smooth tongue sole (Cynoglossus semilaevis Günther) has been exploited as a commercially important cultured marine flatfish, and female grows 2–3 times faster than male. The genome of half-smooth tongue sole was relatively small (626.9 Mb), there are still some difficulties in the high-quality assembly of the generation genome sequencing reads without the assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences. Microsatellite-based genetic linkage maps with different densities have been constructed, and four quantitative trait loci (QTLs) related to growth rate, seven sex-related loci and five sex-related markers have been located on the relevant chromosomes [16,17]. These studies have laid the foundation for the future genetic improvement of half-smooth tongue sole. No genome-wide physical map has been constructed for halfsmooth tongue sole to date, and there are still some difficulties in high-quality assembly of the generation genome sequencing reads without assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences [18,19]
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