Sigbjørn Lien

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

PRDM9 Alleles Guide Distinct Patterns of Recombination Localization in Atlantic Salmon

The paper shows that different PRDM9 alleles in Atlantic salmon lead to distinct recombination patterns, similar to what is seen in mammals.

Transcriptomic view of key events during early embryogenesis in the duplicated Atlantic salmon genome

This study presents a transcriptomic analysis of Atlantic salmon embryogenesis, identifying key transcriptional events and regulatory mechanisms during early development.

Salmonids reveal principles of regulatory evolution following autotetraploidization

The paper studies gene regulatory evolution in salmonids after autotetraploidization, finding that it is influenced by developmental and tissue-specific factors, with constraints at advanced embryogenesis.

A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon

The paper introduces nf-RASQUAL, a Nextflow pipeline for molQTL mapping in small datasets, applied to Atlantic salmon to identify expression and chromatin accessibility QTLs.

Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning

This paper develops a deep learning framework to predict the regulatory impact of non-coding variants in farmed animals using chromatin data, improving genomic prediction for livestock and aquaculture.

Large haplotypes linked to climate and life history variation in divergent lineages of Atlantic salmon (Salmo salar)

The paper identifies a large haplotype block in Atlantic salmon linked to climate and life history traits, showing continent-specific haplotypes and introgression patterns.

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

The paper identifies structural variants, SNPs, and indels in Atlantic salmon populations to explore their role in local adaptation.

Genome-wide reconstruction of rediploidization following autopolyploidizationacross one hundred million years of salmonid evolution

This study reconstructs genome-wide rediploidization after autopolyploidization in salmonids over 100 million years, showing two waves of rediploidization and lineage-specific ohnologue divergence.

The salmon louse genome: copepod features and parasitic adaptations.

The paper presents the genome of Lepeophtheirus salmonis, revealing copepod-specific features and parasitic adaptations, including gene expression shifts and loss of peroxisomes.

The structural variation landscape in 492 Atlantic salmon genomes

This study identifies 15,483 high-confidence structural variants in 492 Atlantic salmon genomes, revealing their role in population structure, functional impact, and domestication traits.

A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea.

This paper presents a high-quality chromosome-level genome assembly for a southern Atlantic cod population using nanopore sequencing, revealing chromosomal inversions and centromeric repetitive elements.

Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color.

The paper identifies two SNPs associated with salmon flesh color and suggests bco1l as the likely gene responsible for color variation through functional studies.

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

The paper identifies a supergene linked to migration in Atlantic cod, showing reduced genetic diversity and population collapse due to overfishing.

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

The paper compares chromosome-scale genome assemblies of African cichlids to identify structural variations and their evolutionary implications.

Development and validation of 58K SNP-array and high-density linkage map in Nile tilapia (O. niloticus)

The paper develops a 58K SNP-array and high-density linkage map for Nile tilapia to improve genomic selection and genetic progress in aquaculture.

The grayling genome reveals selection on gene expression regulation after whole genome duplication

The paper analyzes the grayling genome to study regulatory divergence of Ss4R duplicates after whole genome duplication, finding purifying selection and adaptive divergence in brain-related and immune functions.

A zinc knuckle gene on the Y chromosome (zkY) determines sex in Atlantic cod (Gadus morhua)

The paper identifies a Y-linked gene zkY in Atlantic cod that functions as a master sex-determining gene by suppressing germ cell division in males.

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

The paper examines how Pleistocene glaciations shaped genomic and karyotypic diversity in Atlantic salmon through trans-Atlantic divergence, admixture, and adaptive evolution.

Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

The paper introduces FAASG, an initiative to study salmonid genomes to understand phenotypic variation and improve aquaculture and conservation.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

The paper proposes LORe as a model explaining delayed rediploidization and its impact on salmonid evolution, showing lineage-specific ohnologue divergence and functional adaptation.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

The paper improves the Atlantic cod genome assembly using long-read sequencing and multiple assembly programs, revealing a high density of tandem repeats and heterozygous variation.

Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

The paper identifies a sex-dependent dominance locus, VGLL3, that maintains variation in age at maturity in Atlantic salmon by reducing intralocus sexual conflict.