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

Abstract

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.

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

“…Comparison of statistics between our chromosome-scale assembly and the first published pikeperch draft assembly (GenBank accession PRJNA561467). Genome annotation metrics were taken from Nguinkal et al (2019) 21 . Differences between the statistic results shown in this table and NCBI are due to the use of different genome annotation services.…”

“…Sequence processing and genotyping. The pikeperch draft assembly (GenBank accession: PRJNA561467) 21 was used as reference genome. This draft assembly consists of ~ 900 Mb of total sequence, comprising 1966 contigs ordered into 1313 scaffolds with N50 lengths of 3.0 Mb and 4.9 Mb, respectively.…”

“…The pikeperch draft assembly (GenBank accession: PRJNA561467) was upgraded in two steps. First, we generated a new de novo assembly with the previously released sequencing data of S. lucioperca 21 , i.e. the genomic PacBio Single-molecule real-time sequencing (SMRT) reads (Accession: SRX6760932) and Illumina paired-end data (Accession: SRX6750544) 52 was used to construct this de novo assembly.…”

Characterization of Sialic Acid-Binding Immunoglobulin-Type Lectins in Fish Reveals Teleost-Specific Structures and Expression Patterns

“…Coding sequences for rainbow trout were retrieved from the NCBI public database. To identify Siglec sequences from pikeperch or maraena whitefish, we aligned the orthologous sequences from yellow perch (Perca flavescens) or rainbow trout, Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch), respectively, with the recently published pikeperch genome [24] or our RNA-seq read collection from maraena whitefish [25] using Bowtie 2 software (v. 2.2.4; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). These alignments were then indexed and sorted with the Samtools software package (v. 16; http://www.htslib.org/), and final consensus sequences were obtained with Ugene software (v. 1.29; http://ugene.net/).…”

“…ebi.ac.uk/Tools/msa/clustalo/). The sequences of CD22, MAG and Siglec15 were derived by blasting the orthologous sequences of rainbow trout (O. mykiss; Om), coho salmon (O. kisutch; Ok), Atlantic salmon (S. salar; Ss), yellow perch (P. flavescens; Pf), and barred knifejaw (O. fasciatus; Of) against the sequence assemblies of maraena whitefish and pikeperch [24,29]. In addition, the CD22 and MAG sequences of maraena whitefish were completed by sequencing the results.…”