Biology subjects

Dondrup, M.

Publications and source records attributed to Dondrup, M..

5 recordsLinked to original sources

bioRxiv2026

A relic at risk: Genomic evidence for an early-diverging domesticated lineage in Norwegian farmhouse yeast

The use of Saccharomyces cerevisiae to ferment alcoholic beverages is an ancient tradition, with genetic evidence indicating origins in Neolithic Asia, although the domestication process of the species is not fully understood. Kveik is a group of traditional yeasts used in farmhouse brewing in western Norway preserved through generations of rural brewing practice. While recent studies have highlighted the distinctiveness of kveik, its precise phylogenetic position, genetic diversity, and domestication history remain unclear. We performed whole-genome sequencing on 64 isolates from 25 traditional brewing cultures from Western Norway selected using cultural heritage criteria, and generated telomere-to-telomere (T2T) assemblies for selected strains. Phylogenomic and population genetic analyses reveal that kveik strains form a paraphyletic and early diverging group with respect to other domesticated S. cerevisiae strains. Most strains exhibit low diversity among isolates from the same brewing culture, strong geographic clustering, and little evidence of gene-flow or admixture. Mitochondrial genomes and Ty1 retrotransposon profiles corroborate this distinct lineage history. We further show that previously reported signals of gene flow between kveik and Asian fermentation strains are likely artifacts caused by population structure and selection. Divergence time estimates suggest that the common ancestor of beer, kveik, and other liquid-phase fermenting strains originated from ancestral populations 4,000 to 8,000 years ago. Our genomic resource sheds light on yeast evolution and domestication. Kveik likely comprises some of the oldest domesticated lineages in continuous use until today, connecting intangible cultural heritage to an early genetic origin. Significance statementYeast has been used to brew beer and ferment food for thousands of years, but we still do not fully understand how and where the different domesticated strains we are using today arose. We sequenced the largest collection of Norwegian farmhouse yeasts (kveik) to date, from cultures used by rural traditional brewers for generations. Our genetic analyses show that kveik forms a distinct and early branch among European brewing yeasts. This shows that historical traditions have created unique local types of yeast and helps us better understand and preserve the diversity of domesticated yeasts.

genomics↗

bioRxiv2023

Traditional Norwegian Kveik Yeast: An Ancient Sister Group to Domesticated Saccharomyces cerevisiae

Kveik is the common name of yeast that has been used in traditional farmhouse brewing of western Norway for generations. Its fast fermentation, increased flocculation, temperature tolerance, and rich flavor profile have led to growing interest in recent years. Previous genetic analyses have shown that kveik forms a distinct group within the Saccharomyces cerevisiae tree and placed its origins within the Beer I clade of industrial brewing yeasts, although with signs of mixed ancestry. In this study, we revisited the phylogenetic position of kveik within the S. cerevisiae tree. We searched for traditional farm breweries in western Norway and collected ten samples of potential kveik yeast. Using Illumina whole genome shotgun sequencing, we reconstructed the phylogenetic tree of kveik based on de novo genome assemblies and variant calls of our new kveik samples, along with published wild and domesticated S. cerevisiae strains. We calibrated and used sequential computational experiments at different thresholds to determine the most probable phylogenetic position of kveik yeast. Previously sequenced kveik genotypes form a clade with our new samples clustering partially by place of origin. Our results indicate that kveik is indeed a compact clade within S. cerevisiae with significantly reduced polymorphism compared to common brewing yeasts and wild strains. Contrary to what was previously thought, our analyses support a more ancient divergence of kveik and place it closer to the root of the S. cerevisiae tree. In conclusion, our genetic analyses suggest that kveik is a unique and ancient yeast group, distinct from other domesticated S. cerevisiae strains. Considering a possible far east origin of kveik yeast, the apparent endemism to western Norway remains as a big paradox These findings have important implications for the understanding of yeast domestication and the use of kveik in modern brewing practices.

genomics↗

bioRxiv2021

Gene co-expression network analysis facilitates identification of novel important genes for the moulting process of the salmon louse (Lepeophtheirus salmonis)

BackgroundThe salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. MethodsThree weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. ResultsEight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation. ConclusionsWe propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

bioinformatics↗

bioRxiv2021

The salmon louse genome: copepod features and parasitic adaptations.

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assembly containing {approx}60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics validated annotation and revealed a marked shift in gene expression after host attachment, including downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of peroxisomes, numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

genomics↗

bioRxiv2019

Host gill attachment enables blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae, and alters parasite development and transcriptome

Blood-feeding is a common strategy among parasitizing arthropods, including the ectoparasitic salmon louse (Lepeophtheirus salmonis), feeding off its salmon hosts skin and blood. Blood is rich in nutrients, among these iron and heme. These are essential molecules for the louse, yet their oxidative properties render them toxic to cells if not handled properly. Blood-feeding might therefore alter parasite gene expression. We infected Atlantic salmon with salmon louse copepodids and sampled the lice in two different experiments at day 10 and 18 post infestation. Parasite development and presence of host blood in their intestines were determined. We find that lice start feeding on blood when becoming mobile preadults if sitting on the fish body, however they may initiate in blood-feeding at the chalimus I stage if attached to gills. Lice attached to gills develop at a slower rate. Lice of similar instar age from gills versus lice from skin epidermis were analyzed for gene expression by RNA-sequencing in samples taken at day 10 for both experiments and at day 18 for one of the experiments. By differential expression analysis, we found 355 transcripts elevated in lice sampled from gills and 202 transcripts elevated in lice sampled from skin consistent in all experiments. Genes annotated with "peptidase activity" are among the ones elevated in lice sampled from gills, while in the other group genes annotated with "phosphorylation" and "phosphatase" is pervasive. Transcripts elevated in lice sampled from gills are often genes relatively highly expressed in the louse intestine compared with other tissues, while this was not the case for transcripts found elevated in lice sampled from skin. In both groups, more than half the transcripts are from genes higher expressed after attachment. In conclusion, blood-feeding results in an alteration in gene expression, and a premature onset of blood-feeding likely causes the parasite to develop at a slower pace.

bioinformatics↗