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de Los Ríos-Pérez L, Nguinkal JA, Verleih M, Rebl A, Brunner RM, Klosa J, Schäfer N, Stüeken M, Goldammer T, Wittenburg D. An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale. Sci Rep 2020; 10:22335. [PMID: 33339898 PMCID: PMC7749136 DOI: 10.1038/s41598-020-79358-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
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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Affiliation(s)
- Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Julien A Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Jan Klosa
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Marcus Stüeken
- Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries, Malchower Chaussee 1, 17194, Hohen Wangelin, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059, Rostock, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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