An Ultra-high Density SNP-based Linkage Map for Enhancing the Pikeperch (Sander Lucioperca) Genome Assembly to Chromosome-scale

Overview

Journal Sci Rep

Specialty Science

Date 2020 Dec 19

PMID 33339898

Citations 6

Authors

Lidia De Los Rios-Perez

Julien A Nguinkal

Marieke Verleih

Alexander Rebl

Ronald M Brunner

Jan Klosa

Nadine Schafer

Marcus Stueken

Tom Goldammer

Dorte Wittenburg

Affiliations

Soon will be listed here.

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.

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