An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

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 lin...

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Autores principales:	Lidia de los Ríos-Pérez, Julien A. Nguinkal, Marieke Verleih, Alexander Rebl, Ronald M. Brunner, Jan Klosa, Nadine Schäfer, Marcus Stüeken, Tom Goldammer, Dörte Wittenburg
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/59f723ee76804d9c8407f7634f346358
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spelling	oai:doaj.org-article:59f723ee76804d9c8407f7634f3463582021-12-02T13:34:01ZAn ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale10.1038/s41598-020-79358-z2045-2322https://doaj.org/article/59f723ee76804d9c8407f7634f3463582020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79358-zhttps://doaj.org/toc/2045-2322Abstract 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.Lidia de los Ríos-PérezJulien A. NguinkalMarieke VerleihAlexander ReblRonald M. BrunnerJan KlosaNadine SchäferMarcus StüekenTom GoldammerDörte WittenburgNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-13 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lidia de los Ríos-Pérez Julien A. Nguinkal Marieke Verleih Alexander Rebl Ronald M. Brunner Jan Klosa Nadine Schäfer Marcus Stüeken Tom Goldammer Dörte Wittenburg An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
description	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.
format	article
author	Lidia de los Ríos-Pérez Julien A. Nguinkal Marieke Verleih Alexander Rebl Ronald M. Brunner Jan Klosa Nadine Schäfer Marcus Stüeken Tom Goldammer Dörte Wittenburg
author_facet	Lidia de los Ríos-Pérez Julien A. Nguinkal Marieke Verleih Alexander Rebl Ronald M. Brunner Jan Klosa Nadine Schäfer Marcus Stüeken Tom Goldammer Dörte Wittenburg
author_sort	Lidia de los Ríos-Pérez
title	An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
title_short	An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
title_full	An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
title_fullStr	An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
title_full_unstemmed	An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
title_sort	ultra-high density snp-based linkage map for enhancing the pikeperch (sander lucioperca) genome assembly to chromosome-scale
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/59f723ee76804d9c8407f7634f346358
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An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

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