The pikeperch’s genome is finally assembled

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In a study recently published in the scientific journal Genes MDPI, researchers from the "Fish Genetic Unit" of FBN's Genome Biology Institute in collaboration with colleagues from "Statistics in Genomics Unit" of FBN's Genetics and Biometry Institute have sequenced and assembled the first high-quality pikeperch (Sander lucioperca) genome, which consists of 24 chromosomes. With some 1 billion base pairs, it has about one third the size of a mammalian genome and yet contains about 22,000 genes. Nearly 40% of the genome consists of repetitive DNA sequences.

Pikeperch is considered as one of the freshwater fishes, with the highest potential for increasing diversity of aquaculture in Europe. Its faster growth compared to other Percids and its resilience and diversification potential make Sander lucioperca an attractive species for intensive rearing, as these traits promote the potential yields in commercial production.

While the global wild catches of pikeperch have halved since 2010, its aquaculture production has doubled in the same time and exceeded 900 tons a year (FAO, 2018). This illustrates the increasing importance of pikeperch for commercial aquafarming, but also reveals that pikeperch is still a niche-market species.

Despite its increasing importance for aquaculture, the pikeperch has so far lacked a well assembled and annotated genome sequence that would allow genome-based studies to improve its suitability for aquaculture. The elucidation of the genome (cf. Fig. 2) is a prerequisite for facilitating genome-wide research into pikeperch. It provides an impetus for genomic-based breeding studies to correlate phenotypic traits with genomic variation. Ultimately, this will facilitate the development of molecular bioindicators for sustainable regional fish farming in Germany.

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.

The research work was carried out within the framework of Campus bioFisch-MV and funded by the European Marine and Fisheries Fund (EMFF) and the Ministry of Agriculture and Environment of Mecklenburg-Western Pomerania (grant: MV-II.1-RN-001).

Photo FBN/Brunner: Julien Alban Nguinkal, first author of the FBN study published in the journal Genes.