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

Abstract

Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch

“…The reference-guided assembly with StringTie2 yielded 79,936 contigs in total. As expected, merging all assemblies with EvidentialGene substantially reduced the contig count to a number of 56,302 contigs, which is quite consistent with the total number of proteins (N = 56,557) annotated in the pikeperch reference genome [ 13 ], indicating that our multitissue-assembly nearly spans the whole pikeperch proteome. Overall, the meta-transcriptome outperformed the separate assemblies (Trinity, rnaSPAdes and Hisat2+StringTie2) in terms of BUSCO completeness and protein functional database records.…”

“…Additionally, we generated a genome-guided assembly with StringTie2 (version 2.1.2) [ 25 ]. Briefly, the combined RNA-Seq reads of all tissues were aligned to the latest pikeperch reference genome (SLUC_FBN_1.2, GenBank accession: GCA_008315115.2) [ 13 ] using HISAT2 (version 2.2.0) [ 26 ]. Reads alignments were then assembled with StringTie2 [ 25 ] using the ‘ ’ option to obtain a non-redundant set of transcripts across all tissue samples.…”

“…The trimmed and filtered RNA-Seq reads from each sample were individually mapped to the pikeperch reference genome (SLUC_FBN_1.2) [ 13 ] using STAR (version 2.7.5a) [ 35 ], in two-pass mode. Abundance levels of transcripts were estimated using TPMCalculator [ 36 ], a one-step software to quantify mRNA expression abundance directly from RNA-Seq alignments.…”

“…In fact, more than 90% of multi-omics studies in pikeperch, as recorded by PubMed Central, 30 June 2021, have been published in the last five years (2016–2021). Notable genomics efforts include the transcriptome profiling of eggs from wild and domesticated populations along with the generation of the first transcriptomic resource for pikeperch [ 10 ], the development of transcriptome-based simple sequence repeats (SSR) markers [ 11 ], and the construction of high-density linkage maps using specific locus amplified fragment sequencing (SLAF-Seq) [ 12 ], and single-nucleotide polymorphism (SNPs) markers [ 13 ]. The recent publication of the chromosome-level reference genome (SLUC_FBN_1.2) for S. lucioperca [ 14 ] has dramatically improved the ability to investigate its complex traits with commercial relevance.…”

Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)

“…We analyzed genotype data of pikeperch families initially produced for a linkage analysis ( De los Ríos-Pérez et al, 2020 ). The production was based on F0 individuals without information about pedigree and former breeding practices.…”