Abstract
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.
Highlights
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry
We report the construction of an ultra-high density linkage map for pikeperch based on the most common form of genetic variation, i.e., single nucleotide polymorphisms (SNPs), and the improvement of the pikeperch genome assembly to chromosome-scale
We reported the construction of an ultra-high density SNP-based linkage map for pikeperch, and the further anchoring of the genome assembly into the first chromosome-scale assembly
Summary
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. An ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. Linkage analysis of high-density genomic markers has facilitated the assembly of reference genomes by anchoring scaffolds, produced during de novo genome assembly, into linkage groups and providing a chromosome frame[11]. In common carp (Cyprinus carpio) and yellow drum (Nibea albiflora), high-density linkage maps were built for comparative genomic analysis and identification of QTLs for growth and sex related t raits[15,16]. In channel catfish (Ictalurus punctatus), a high-density linkage map was used for the construction of chromosome maps[18]
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