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.

The aquaculture production of pikeperch has reached commercial scale in a number of European countries, but the high mortality of early life cycle stages and minor understanding of nutritional requirements are still major bottlenecks. To investigate the fate of fatty acids during early development, weaning and rearing, pikeperch larvae and juveniles from a commercial recirculating aquaculture system (RAS) were sampled over 2 months for morphometric data, as well as fatty acid composition, with a total of 6 sampling days, with four to five replicates per sampling day and between 1 and 25 pikeperch larvae per individual sample, depending on larval biomass. The biomass of sampled pikeperch larvae varied from 0.1 to 420 mg (dry mass DM), depending on the age of the larvae, and the initial length of the pikeperch larvae was about 4.5 mm. Our data confirm that, accompanied by an exponential increase in dry mass, total fatty acids (TFAs) in larval tissues increased with the beginning of exogenous feed uptake and were depleted between days 13 and 25 post hatch, most likely associated with the weaning and metamorphosis of the larvae. We conclude that all fatty acid classes may serve as metabolic fuel during metamorphosis, but the ultimate fatty acid composition is strongly impacted by the available feed. The chosen diet probably caused a lack of alpha-linolenic (18:3n-3; ALA) and docosahexaenoic acid (22:6n-3; DHA) during larval development and a shortage of vaccenic (18:1n-7), alpha-linolenic (18:3n-3; ALA) and arachidonic acid (20:4n-6; ARA) in juvenile pikeperch. This led to low DHA/EPA ratios 13 days post hatch, a high EPA/ARA ratio at days 41 and 56 post hatch and a fluctuating ratio of alpha-linolenic acid to linoleic acid (18:2n-6; LA). A temporary lack of essential fatty acids can cause dysfunctions and eventually mortalities in pikeperch larvae and juveniles. Despite high larval growth rates, the biochemical composition of the first fed Artemia and microdiets was most likely not sufficient and in need of improvement. We suggest that deficiencies must be compensated, e.g., through the substitution of the offered Artemia with more suitable live feed organisms, such as freshwater rotifers, and the enrichment of current microdiets in order to prevent high mortalities during pikeperch rearing and weaning.