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The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics b...

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Autores principales: Nguinkal, Julien Alban, Brunner, Ronald Marco, Verleih, Marieke, Rebl, Alexander, de los Ríos-Pérez, Lidia, Schäfer, Nadine, Hadlich, Frieder, Stüeken, Marcus, Wittenburg, Dörte, Goldammer, Tom
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770990/
https://www.ncbi.nlm.nih.gov/pubmed/31540274
http://dx.doi.org/10.3390/genes10090708
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author Nguinkal, Julien Alban
Brunner, Ronald Marco
Verleih, Marieke
Rebl, Alexander
de los Ríos-Pérez, Lidia
Schäfer, Nadine
Hadlich, Frieder
Stüeken, Marcus
Wittenburg, Dörte
Goldammer, Tom
author_facet Nguinkal, Julien Alban
Brunner, Ronald Marco
Verleih, Marieke
Rebl, Alexander
de los Ríos-Pérez, Lidia
Schäfer, Nadine
Hadlich, Frieder
Stüeken, Marcus
Wittenburg, Dörte
Goldammer, Tom
author_sort Nguinkal, Julien Alban
collection PubMed
description The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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spelling pubmed-67709902019-10-30 The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe Nguinkal, Julien Alban Brunner, Ronald Marco Verleih, Marieke Rebl, Alexander de los Ríos-Pérez, Lidia Schäfer, Nadine Hadlich, Frieder Stüeken, Marcus Wittenburg, Dörte Goldammer, Tom Genes (Basel) Article The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch. MDPI 2019-09-13 /pmc/articles/PMC6770990/ /pubmed/31540274 http://dx.doi.org/10.3390/genes10090708 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nguinkal, Julien Alban
Brunner, Ronald Marco
Verleih, Marieke
Rebl, Alexander
de los Ríos-Pérez, Lidia
Schäfer, Nadine
Hadlich, Frieder
Stüeken, Marcus
Wittenburg, Dörte
Goldammer, Tom
The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title_full The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title_fullStr The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title_full_unstemmed The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title_short The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
title_sort first highly contiguous genome assembly of pikeperch (sander lucioperca), an emerging aquaculture species in europe
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770990/
https://www.ncbi.nlm.nih.gov/pubmed/31540274
http://dx.doi.org/10.3390/genes10090708
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