Biology subjects

Wargelius, A.

Publications and source records attributed to Wargelius, A..

7 recordsLinked to original sources

bioRxiv2026

Vgll3a promotes sexual maturation in male and female Atlantic salmon

The age at which Atlantic salmon reaches sexual maturity shows a strong hereditary component associated with the vgll3a locus. The role of Vgll3 in maturation has remained unknown in vertebrates until recently, when it has been linked to pleiotropic roles in killifish, both delaying male maturation and affecting lifespan by protecting against cancer. As Atlantic salmon has two vgll3 paralogs, where only vgll3a has been associated with sexual maturation, it may provide a suitable model for studying the maturation-specific function of vgll3, as the other paralog may buffer for pleiotropic roles of vgll3. To address this, we used CRISPR/Cas9 to generate fish highly mutated in the vgll3a gene. We monitored their maturation and crossed highly mutated crispants to generate two year-classes of complete loss-of-function. All groups were reared under environmental conditions triggering early maturation in one-year-old males. We found a clear difference in the proportion of sexually maturing or mature fish between the different genotypes: in all experiments significantly fewer vgll3a-/- males entered puberty and reached final maturation compared to vgll3a+/- and vgll3a+/+ males. Furthermore, loss of vgll3a resulted in lower frequencies of maturation also in females. We conclude that Vgll3a stimulates maturation and that its complete removal significantly reduced maturation rates in both sexes in Atlantic salmon. Our findings also identify vgll3a as the causative gene in the locus associated with age at sexual maturity. Together, our findings support a new role for Vgll3 in initiating puberty in vertebrates and identifying salmon as a promising model for functional studies regarding the timing of sexual maturation.

genomics↗

bioRxiv2022

Molecular mechanisms involved in Atlantic halibut (Hippoglossus hippoglossus) egg quality: impairments at transcription and protein folding levels induce inefficient protein and energy homeostasis during early development

BackgroundReproductive success and normal development in all animals are dependent on egg quality and developmental competence of the produced embryo. This study employed tandem mass tags labeling based liquid chromatography tandem mass spectrometry for egg proteomic profiling to investigate differences in the global proteome of good versus poor quality Atlantic halibut eggs at 1-cell stage post fertilization. ResultsA total of 115 proteins were found to be differentially abundant between good and poor quality eggs. Frequency distribution of these proteins revealed higher protein folding activity in good quality eggs in comparison to higher transcription and protein degradation activities in poor quality eggs (p < 0.05). Poor quality halibut eggs were significantly enriched with additional proteins related to mitochondrial structure and biogenesis (p < 0.05). The differential abundance of a selection of proteins was first confirmed at gene expression level using a transcriptomic approach followed by a targeted proteomic approach (parallel reaction monitoring based mass spectrometry) in biological samples obtained from two consecutive reproductive seasons. The findings of global proteome profiling, together with the validation of differential abundance of targeted proteins and their related genes, suggest impairments in protein and energy homeostasis which might be related to unfolded protein response and mitochondrial stress in poor quality eggs. Additional transmission electron microscopy studies were taken to assess potential differences in abundance and morphological integrity of mitochondria between good and poor quality eggs. Observations reveal poor quality eggs to contain significantly higher number of mitochondria with higher number of cristae. These mitochondria, however, are significantly smaller and have a more irregular shape than those found in high-quality eggs. Therewithal difference in mtDNA levels represented by mt-nd5 and mt-atp6 genomic DNA abundance in this study, were found to be not statistically significant (p > 0.05) between good and bad quality eggs at both 1 hpf and 24 hpf stages. ConclusionOverall evidence from this study indicate that poor quality eggs undergo impairments at both transcription and translation level leading to endoplasmic reticulum and mitochondrial deficiencies. Additional research may be required to expediate the details and the potential of these impairments occurring in different species. Nonetheless, this study will pave the way for future research and will help in acceleration of recent advances in the field of embryonic developmental competence of living organisms.

molecular biology↗

bioRxiv2021

A refinement to gene editing in Atlantic salmon using asymmetrical oligonucleotide donors

Selective breeding programs in aquaculture are limited by the heritability of the trait and long generation time in most fish species. New breeding technology (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) have the potential to expedite genetic improvement in aquaculture, but the method requires optimization. Here we show that asymmetrical oligonucleotide (ODN) donors induce highly efficient and precise edits in individual Atlantic salmon founder animals. We performed single nucleotide replacement (SNR) in dnd with up to 59.2% efficiency, and inserted FLAG elements into slc45a2 and dnd, with up to 36.7 % and 32.7% efficiency, respectively. We found HDR efficiency to be dependent on template concentration, but a trade-off with respect to toxicity was observed. Using this NBT in salmon we demonstrate that precise modification of the genome can be achieved in a single generation, allowing efficient introgression of favorable alleles and bypassing challenges associated with traditional selective breeding.

molecular biology↗

bioRxiv2020

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies are now enabling precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software designed to specifically search for sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analyzed a published dataset of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyze new RAD-Seq datasets from 15 fish species spanning multiple systematic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in non-model species and outperforms the commonly used RAD-Seq analysis software STACKS. RADSex in speed, resource usage, ease of application, and visualization options. Furthermore, our analysis of new datasets from 15 species provides new insights on sex determination in fish.

bioinformatics↗

bioRxiv2020

Sex determining gene transposition as an evolutionary platform for chromosome turnover

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are the best studied family of fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of transposition, suggesting a recent and non-random sex chromosome turnover in this species. We hypothesized the existence of an autosomic pseudocopy of sdY that is transmitted in accordance with Mendelian inheritance. To test this we developed a qPCR methodology to detect the number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomic copies in addition to the Y-specific copy present in males. Copy number frequencies were consistent with Mendelian inheritance. Pseudocopy loci were mapped to different chromosomes evidencing non-random transitions of the sex determining gene in Atlantic salmon and the existence of functional constraints for chromosome turnover.

genetics↗

bioRxiv2020

Targeted mutagenesis of {triangleup}5 and {triangleup}6 fatty acyl desaturases induce multiplex-mutagenesis and lipogenesis in Atlantic salmon (Salmo salar)

With declining wild fish populations, farmed Atlantic salmon (Salmo salar) has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA) including 20:5n-3 and 22:6n-3. However, the introduction of plant-based oil in fish diets has reduced the content of these beneficial LC-HUFA. The capability of biosynthesis of LC-HUFAs depends on fatty acids supplied in diets and the genetic potential residing in the fish. Key proteins involved in LC-HUFA synthesis in salmon include fatty acid desaturases 2 (Fads2). In a recent study we used CRISPR/Cas9 to generate two F0 mutant strains of salmon, 1){Delta} 6abc/5Mt with mutations in{Delta} 5fads2, {Delta}6fads2-a, {Delta}6fads2-b and {Delta}6fads2-c genes, and 2){Delta} 6bcMt with mutations in{Delta} 6fads2-b and {Delta}6fads2-c genes. The CRISPR mutated salmon (crispants) had reduced levels of LC-HUFA and expression of targeted fads2 genes. In present study we apply whole transcriptome analysis on these fads2 crispants. Our purpose is to evaluate the genetic mosaicism in fads2 crispants and the effect these mutations had on other lipid metabolism pathways in fish. Both{Delta} 6abc/5Mt and{Delta} 6bcMt crispants demonstrated high percentage of indels within all intended target genes, though different indel types and percentage were observed between individuals. Skipping of a CRISPR-targeted exon was observed in{Delta} 6fads2-a gene of{Delta} 6abc/5Mt salmon. The{Delta} 6abc/5Mt fish also displayed several disruptive indels which resulted in over 100 differentially expressed genes (DEGs) enriched in lipid metabolism pathways in liver. This includes up-regulation of srebp1 genes as well as genes involved in fatty acid de-novo synthesis, fatty acid {beta}-oxidation and lipogenesis. Both elovl5 and elovl2 genes were not changed, suggesting that the genes were not targeted by Srebp1. The mutation of{Delta} 6bcMt surprisingly resulted in over 3000 DEGs which were enriched in factors encoding genes involved in mRNA regulation and stability.

molecular biology↗

bioRxiv2016

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

We describe an emerging initiative - the Functional Analysis of All Salmonid Genomes (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, through to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

genomics↗