Biology subjects

Kent, M. P.

Publications and source records attributed to Kent, M. P..

13 recordsLinked to original sources

bioRxiv2026

PRDM9 Alleles Guide Distinct Patterns of Recombination Localization in Atlantic Salmon

Meiotic recombination in many vertebrate lineages is directed to genomic regions by the DNA-binding protein PRDM9. To date, PRDM9 research has focused primarily on mammals, and its role in recombination localization has only recently been established in salmonids. PRDM9 binding specificity is determined by a tandemly repeated zinc-finger array that exhibits extensive allelic diversity within and between species. However, the extent to which PRDM9 variation shapes recombination landscapes in salmonids remains poorly understood. Here, we performed large-scale genotyping of PRDM9 in an aquaculture population of Atlantic salmon (Salmo salar) using long-read sequencing. By integrating PRDM9 genotypes with pedigree information and genome-wide recombination data, we generated PRDM9-specific linkage maps and sets of inferred crossover events. We show that the presence of specific PRDM9 alleles is associated with differences in recombination localization and identify patterns consistent with dominance interactions between alleles. Using population-averaged recombination rate estimates, we further link a previously described sequence motif enriched in European recombination hotspots to the presence of a common PRDM9 zinc-finger array allele (RPT6a). Together, our results demonstrate functional differences between PRDM9 alleles which contribute to divergence in recombination landscapes in Atlantic salmon, paralleling patterns observed in mammals. The broad geographic distribution of Atlantic salmon, combined with extensive pedigree data generated through aquaculture, highlights its potential as a powerful model for studying PRDM9 function and evolution beyond mammals.

genetics↗

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↗

bioRxiv2022

Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large SNP array and low coverage whole genome re-sequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with large-effect loci (vgll3, six6) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified largely non-repeated sweep signatures and sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of repeated genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.

evolutionary biology↗

bioRxiv2022

The gastric mucosa of Atlantic salmon (Salmo salar) is abundant in highly active chitinases

The Atlantic salmon (Salmo salar) genome contains 10 chitinase encoding genes, but little is known about the function of these chitinases. We show that the protein products of three genes, the family 18 glycoside hydrolase (GH18) chitinases Chia.3, Chia.4, and Chia.7 are secreted in the stomach mucosa and are amongst the most abundant proteins in this matrix. Chia.3 and Chia.4, sharing 95% sequence identity, were not possible to separate by standard chromatographic methods and were thus purified as a chitinase pair. Biochemical analysis revealed chitinolytic activity towards {beta}-chitin for up to 24 hours at pH 2-6. Further in vitro analysis showed that this chitinase pair efficiently degraded various chitin-containing substrates to chitobiose (GlcNAc2) suggesting that Atlantic salmon has the potential to utilize novel chitin-containing feed sources.

biochemistry↗

bioRxiv2022

The effect of dietary chitin on Atlantic salmon (Salmo salar) chitinase activity, gene expression, and microbial composition

BackgroundChitin is a common component in the natural diet of many fish, and a range of chitinases with the potential to down chitin have been identified. Yet whether chitin is metabolized in fish is still unclear. Here we used a combination of chitinase activity assay, transcriptomics, and 16S rRNA bacterial analysis to assess the effect of chitin supplementation on Atlantic salmon gene expression and microbial community. ResultsAtlantic salmon express multiple genes associated with chitin metabolism, and we show that the expression and activity of Atlantic salmon chitinases are not affected by the addition of dietary chitin. We do, however, demonstrate an association between gut microbial composition, chitinase activity in the gut, and host chitinase expression. ConclusionThe findings presented here support the idea that chitin metabolism genes are linked to the maintenance of a chitin-based barrier in the teleost gut. These results contribute to a greater understanding of chitin metabolism in fish.

genetics↗

bioRxiv2022

Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)

BackgroundChitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "non-chitinous" organisms, despite having highly conserved chitin metabolism associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet little is still known about the genes and proteins responsible for these dynamic processes. Here we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin-metabolism in teleosts, with a particular focus on Atlantic salmon. ResultsReconstruction of gene family phylogenies provide evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin-metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). These transcription factors are also potential regulators of multiple glycosyltransferases being co-expressed with the chitin remodeling genes. ConclusionThe findings presented here add support to the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.

genetics↗

bioRxiv2021

Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods

Resolving the genetic architecture of fitness-related traits is key to understanding the evolution and maintenance of fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to further characterize known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci (on chromosomes ssa06, ssa09, ssa21, and ssa25) out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at each of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of Atlantic salmon maturation includes multiple loci with simple, non-clustered alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.

evolutionary biology↗

bioRxiv2020

Insertion of an endogenous Jaagsiekte Sheep Retrovirus element into the BCO2 - gene abolish its function and leads to yellow discoloration of adipose tissue in Norwegian Splaesau (Ovis aries).

BackgroundThe accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. However, not all sheep breeds suffering from yellow fat have this nonsense mutation, meaning that other functional mechanisms must exist. We investigated one such breed, the Norwegian spaelsau. ResultsIn spaelsau we detected an aberration in BCO2 mRNA. Nanopore sequencing of genomic DNA revealed the insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene. Close examination of its cDNA revealed that the BCO2 genes first exon was spliced together with enJSRV-sequence immediately downstream of a potential - AG splice acceptor site at enJSRV position 415. The hybrid protein product consists of 29 amino acids coded by the BCO2 exon 1, followed by 29 amino acids arbitrary coded for by the enJSRV-sequence, before a translation stop codon is reached. ConclusionsConsidering that the functional BCO2 protein consists of 575 amino acids, it is unlikely that the 58 amino acid BCO2/enJSRV hybrid protein can display any enzymatic function. The existence of this novel BCO2 allele represents an alternative functional mechanism accounting for BCO2 inactivation and is a perfect example of the potential benefits for searching for structural variants using long-read sequencing data.

genomics↗

bioRxiv2020

The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

genomics↗

bioRxiv2018

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

Intraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

genomics↗

bioRxiv2018

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

The genetic mechanisms determining sex in teleost fishes are highly variable, ranging from a single gene to complex patterns of polygenic regulation. The master sex determining gene has only been identified in very few species and there is no information about the gene in the superorder Paracanthopterygii that includes the codfishes, toadfishes and anglerfishes. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene named zkY for zinc knuckle on the Y chromosome. A diagnostic PCR test of phenotypically sexed males and females of Atlantic cod confirmed the sex-specific nature of the Y-sequence. We searched for autosomal gene copies of zkY and identified twelve highly similar genes, of which eight (zk1-zk8) code for proteins containing the zinc knuckle motif. 3D structure modelling suggests that the amino acid changes observed in six of the eight copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific gene zkY was expressed at high levels in the developing larvae before the onset of sex differentiation. We propose that cod zkY functions as the master masculinization gene by coding for a suppressor of germ cell division in males. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that this novel sex determining mechanism emerged in codfishes more than 7.5 million years ago.\n\nAuthor SummaryStudying the diverse sex determining genes in teleost fish may contribute to increase our understanding of sex chromosome evolution in vertebrates. To date, no sex determinant is known for the superorder Paracanthopterygii, comprising about 1340 species, including the commercially important Atlantic cod. In this study we characterize a Y-specific region of 9 kb on linkage group 11 containing a single gene named zkY for zinc knuckle on the Y chromosome. The gene is transcribed at high levels in larvae before commencement of sex differentiation and encodes a novel zinc knuckle protein that putatively binds RNA target sequences. We propose that cod zkY suppresses germ cell proliferation in the developing males by interacting with the germ-cell specific RNA regulatory network.

genetics↗