Biology subjects

Gjuvsland, A. B.

Publications and source records attributed to Gjuvsland, A. B..

8 recordsLinked to original sources

bioRxiv2026

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

The Duroc-derived reference genome Sscrofa11.1 has provided a critical foundation for pig genomics, providing a high-quality reference genome for accurate variant detection and comparative genomics but does not capture breed-specific variation. Here, we present a near-complete, gap-free genome assembly for the Landrace pig (Landrace_v1, GCA_963921485.1), spanning all 20 chromosomes and totaling 2.6 Gb, including 176 Mb of sequence absent from Sscrofa11.1. Comparative analyses with recently published high-quality pig genomes reveal a conserved centromere organization across breeds, accompanied by substantial variation in repeat composition and length, and identify a pig specific pattern of telomere variant repeats across eight pig breeds. The improved resolution of repetitive regions in Landrace_v1 enables more complete reconstruction of complex gene families, including olfactory receptors, and uncovers structural variation at the KIT proto-oncogene receptor tyrosine kinase locus not represented in the Duroc reference. Together, these findings highlight the limitations of single-reference genomes and demonstrate the value of breed-specific assemblies for capturing genomic diversity and improving downstream analyses.

genomics↗

bioRxiv2026

Haplotype assembly without parental sequencing: Genotype-based trio-binning (GT-Trio)

Trio-binning is a robust method for haplotype-resolved assembly, providing the most accurate representation of diploid genomes including complex and haplotype-specific variation. Conventional trio-binning methods depend on parental short-read sequences to differentiate offspring reads originating from the maternal and paternal haplotypes. Here, we present a genotype-based trio-binning pipeline (GT-Trio) which reconstructs parent sequences from phased parental genotypes and uses this as an alternative source of parental information for haplotype assembly. The GT-Trio pipeline was applied to assemble the maternal and paternal haplotypes of three Norwegian Red (NR) cattle individuals, using phased parental genotypes imputed from array to sequence as input. Haplotypes assembled with GT-Trio using all sequence variants as parental input demonstrated assembly quality and phasing accuracy comparable to that achieved with conventional trio-binning. Using lower density subsets of array SNPs led to a slight reduction in accuracy of haplotype separation, accompanied by an increase in size, contiguity and completeness, suggesting a trade-off between assembly quality and phasing accuracy associated with the density of parental genotypes provided as input to the pipeline. Overall, GT-Trio provides a scalable framework for haplotype assembly without parental sequencing and will be applicable in livestock species where genotyping and imputation is performed routinely. The GT-Trio pipeline is available at https://github.com/theahettasch/GT-Trio.

genomics↗

bioRxiv2025

Haplotype-resolved genome assemblies for Norwegian Red cattle

Norwegian Red (NR) cattle are the main dairy breed in Norway, bred according to a broad breeding goal including health and fertility since the 1970s. Genomic studies on NR cattle have relied on the public Hereford reference, thus increasing the risk of missing or misrepresenting NR breed-specific variation. Moreover, the Hereford reference is a pseudohaploid assembly, representing homologous chromosomes in a collapsed manner, which results in loss of haplotype-specific alleles and misrepresentation of complex variants. To develop more refined NR specific resources, we utilised long-read sequencing (PacBio HiFi + ONT) and trio-binning to construct six new haplotype-resolved assemblies representing NR genomes. These six NR2025 assemblies show high completeness (BUSCO: 95.82-98.11%) and contiguity (N50: 73.8-88.5 Mb) and are accurately phased (hamming error rate: 0.46-2.52%). Most autosomes have been assembled into the acrocentric centromere, and mapping of bovine satellite sequences reveal distinct organisational patterns of different satellite units across this highly repetitive region. The NR2025 assemblies provide a valuable resource for identification of novel variants and haplotypes in the NR population, which will enable more accurate association studies of genotype-to-phenotype relations and genomic predictions in NR cattle, ultimately enhancing the efficacy of selection for desirable traits.

genomics↗

bioRxiv2025

Genome-wide CRISPR knockout screen reveals the landscape of essential genes across the porcine genome

1Characterization of essential genes across the genome is fundamental to understanding cellular functions at a molecular level. While significant progress has been made in characterizing essential genes in human and mouse models, relatively little is known about essential genes in the porcine genome. Pigs are an important production species and are now emerging as valuable models for studying human diseases due to their physiological similarities to humans. To map essential genes across the porcine genome, we have developed a novel porcine genome-wide CRISPR knockout screening library (pGeCKO) and applied it to two porcine cell lines, PK15 and IPEC-J2. We identified 2,245 essential genes in PK15 cells and 919 essential genes in IPEC-J2 cells, with 683 of these shared between both cell lines. Functional analyses revealed that most essential genes are involved in core cellular processes such as cell cycle regulation, DNA replication, transcription, and translation. Comparative analysis with human essential genes from the DepMap project revealed that over half of the genes are shared with humans and the rest are porcine-specific. These porcine-specific essential genes included genes in core functional pathways related to protein and RNA processing as well as many related to N-glycan biosynthesis, signal transduction, and several long-noncoding RNAs. This work provides a new resource for leveraging porcine models in disease research, enhancing our understanding of porcine genetics and its implications for human health.

genomics↗

bioRxiv2024

Individual variation in meiotic crossover positioning, rate and interference are driven by distinct genetic processes in domestic pigs.

Meiotic crossovers are essential for proper chromosome segregation, and provide an important mechanism for adaptation through linking beneficial alleles and purging deleterious mutations. However, crossovers can also break apart beneficial alleles and are themselves a source of new mutations within the genome. The rate and distribution of crossovers shows huge variation both within and between chromosomes, individuals and species, yet the molecular and evolutionary causes and consequences of this variation remain poorly understood. A key step in understanding this variation is to understand the genetic architecture of how many crossovers occur, where they occur, and how they interfere, as this allows us to identify the degree to which these factors are governed by common or distinct genetic processes. Here, we investigate individual variation in crossover count, crossover interference ({nu}), and crossover positioning measured as both intra-chromosomal allelic shuffling and distance to telomere (Mb), in a large genotyped breeding population of domestic pigs. Using measures from 82,474 gametes from 4,704 mothers and 271 fathers, we show that crossover traits are heritable within each sex (h2 = 0.03 - 0.11), with the exception of male crossover interference. Crossover count and interference have a strongly shared genetic architecture in females, mostly driven by variants at RNF212. Female crossover positioning is mediated by variants at MEI4, PRDM9, and SYCP2. We also identify tentative associations at genomic regions corresponding to CTCF and REC114/REC8/CCNB1IP1 (crossover count), and ZCWPW1 and ZCWPW2 (crossover positioning). Our results show that crossover count and crossover positioning in female pigs have the capacity to evolve somewhat independently in our dataset.

genomics↗

bioRxiv2021

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds. Author summaryAtlantic salmon aquaculture generates billions of euros annually, but faces challenges of sustainability. Salmon are carnivores by nature, and fish oil and fish meal have become scarce resources in fish feed production. Novel, sustainable feedstuffs are being trialed hand in hand with studies of the genetics of growth and feed efficiency. This calls for a mathematical-biological framework to integrate data with understanding of the effects of novel feeds on salmon physiology and its interplay with genetics. We have developed the SALARECON model of the core salmon metabolic reaction network, linking its genome to metabolic fluxes and growth. Computational analyses show good agreement with observed growth, amino acid limitations, and feed efficiencies, illustrating the potential for in silico studies of potential feed mixtures. In particular, in silico screening of possible diets will enable more efficient animal experiments with improved knowledge gain. We have adopted best practices for test-driven development, virtual experiments to assay metabolic capabilities, revision control, and FAIR data and model management. This facilitates fast, collaborative, reliable development of the model for future applications in sustainable production biology.

systems biology↗

bioRxiv2020

Control of mitochondrial superoxide production includes programmed mtDNA deletion and restoration

Deletion of mitochondrial DNA in eukaryotes is mainly attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that the regulatory circuitry underlying this editing critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. Our results may therefore be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease. One-Sentence SummaryGenetically controlled editing of mitochondrial DNA is an integral part of the yeasts defenses against oxidative damage.

cell biology↗

bioRxiv2017

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

BackgroundIt has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced transport capacity of dietary lipids. However, there has not been performed any in-depth ontological analysis of intestinal PL and LP synthesis with development of salmon. Therefore in this paper we used RNA-seq technology to test the hypothesis that the high PL requirement in salmon fry was associated with undeveloped PL synthesis and LP formation pathways in intestine. There was a special focus on the understanding homologous genes, especially from salmonid-specific fourth vertebrate whole-genome duplication (Ss4R), contribution to salmonid specific features of regulation of PL metabolic pathways. The study was performed in stomach, pyloric caeca and hindgut at 0.16g (1 day before first-feeding), 2.5g and 10g of salmon.\n\nResultsIn general, we found an up-regulation of de-novo phosphatidylcholine (PtdCho) synthesis, phosphatidylethanolamine (PtdEtn) and LP formation pathways in pyloric caeca of salmon between 0.16g and 10g. Thirteen genes in these pathways were highly (q<0.05) up-regulated in 2.5g salmon compared to 0.16g, while only five more significant (q<0.05) genes were found when the fish grew up to 10g. Different homologous genes were found dominating in stomach, pyloric caeca and hindgut. However, the expression of dominating genes in PL and LP synthesis pathways was much higher in pyloric caeca than stomach and hindgut. Salmon-specific homologous (Ss4R) genes had similar expression during development, while other homologs had more diverged expression.\n\nConclusionsAn increasing capacity for PL synthesis and LP formation was confirmed in pyloric caeca. The up-regulation of the de-novo PtdCho pathway confirms that the salmon fry have increasing requirement for dietary PtdCho compared to adult. The similar expressions between Ss4R homologous genes suggest that the functional divergence of these genes was incomplete compared to homologs derived from other whole genome duplication. The results of the present study have provided new information on the molecular mechanisms of phospholipid synthesis and lipoprotein formation in fish.

molecular biology↗