Next Article in Journal
Molecular Alterations in Thyroid Cancer: From Bench to Clinical Practice
Previous Article in Journal
Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae
Open AccessArticle

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

1
Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
2
Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
3
State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(9), 708; https://doi.org/10.3390/genes10090708
Received: 23 July 2019 / Revised: 27 August 2019 / Accepted: 8 September 2019 / Published: 13 September 2019
(This article belongs to the Section Animal Genetics and Genomics)
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. View Full-Text
Keywords: genome assembly; genes annotation; pikeperch; fish; genome sequencing; aquaculture genome assembly; genes annotation; pikeperch; fish; genome sequencing; aquaculture
Show Figures

Graphical abstract

MDPI and ACS Style

Nguinkal, J.A.; Brunner, R.M.; Verleih, M.; Rebl, A.; Ríos-Pérez, L.; Schäfer, N.; Hadlich, F.; Stüeken, M.; Wittenburg, D.; Goldammer, T. The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes 2019, 10, 708.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop