Snorre Hagen
Head of Department/Head of Research
Abstract
Accurate species identification is essential for conserving and managing plants that provide important ecosystem services and have ethnobotanical value. The Greyia tree genus ( G. sutherlandii , G. radlkoferi and G. flanaganii ) is endemic to South Africa and Eswatini, and certain genotypes have medicinal value for treating skin hyper‐pigmentation. However, distinguishing among species is difficult because of overlapping phenotypes and the limited resolution of standard DNA barcodes. To overcome these limitations, a robust molecular identification assay was developed using a two‐phase strategy. First, de novo SNP discovery using 3RAD sequencing identified 47,726 genome‐wide SNPs from two to three plants sampled from each species' core geographic range: G. radlkoferi in northern Limpopo, G. sutherlandii in eastern KwaZulu‐Natal, and G. flanaganii in the south‐eastern Eastern Cape. Principal component analysis and coancestry matrices revealed three discrete genetic clusters, supporting the recognition of the three species. Selecting a set of 200 SNPs with intermediate Fst values (0.2–0.5) resulted in optimal separation of the three clusters. This led to the final selection of a 23‐SNP panel that included five informative barcoding loci (ITS, trnL‐F , matK ). Second, the 23 SNPs were converted into allele‐specific fluorescent PCR assays (SNP Type) for genotyping on the BioMark HD platform. The panel was validated using genomic DNA from 17 individuals from the 3RAD population groups and successfully differentiated all three species. It was then applied to 73 trees sampled across a 1000‐km transect from the Eastern Cape to Limpopo. Genetic clustering (PCA, UPGMA and ADMIXTURE) assigned each tree to one of three species‐level groups matching their expected ranges. In a practical case study, the assay also identified the species origin of 33 Greyia trees of unknown provenance from production orchards. This study provides an efficient SNP‐based tool for accurate species identification, supporting conservation planning and the sustainable management of Greyia populations.
Authors
Michael Dondrup Atle Ove Martinussen Lisa Karine Haugland Jonas Brandenburg Oya Inanli Abdelhameed Elameen David William Peter Dolan Sushma Nagaraja Grellscheid Snorre Hagen Hannes Schroeder Tor Myking Hans Geir EikenAbstract
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 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.
Authors
Nina Johansen Hans Geir Eiken Simeon Rossmann May Bente Brurberg Monica Skogen Marta Bosque Fajardo Borghild Glorvigen Toril Eklo Finn-Arne Haugen Snorre Hagen Erik LysøeAbstract
Several aphid species pose serious treats to potato crops by causing direct damage to the plants and/or indirectly by transmitting viruses. Different morphological forms and phenotypic plasticity among aphids complicates taxonomy and identification and thus makes targeted pest management in potatoes challenging. To obtain an overview of aphids frequenting potato fields in Norway, we investigated seasonal and annual changes in aphid populations in five potato fields (58–64 °N) over a three-year period (2016–2018), using yellow pan traps. In total 2218 of the 6136 collected aphids were identified by traditional barcoding, meaning sequencing a ~ 650 fragment of the mitochondrial COI gene. This revealed 137 different species, of which 111 were identified at the species level. The remaining were identified only to the genus level, indicating potential novel species. The southernmost sampling location yielded the highest number of species and individual counts, although no clear correlations to climate factors (temperature/precipitation) was observed. Of the 111 species identified, at least 39 are potential vectors of potato virus Y (PVY) and nine species may also transmit potato virus A (PVA). Knowledge on virus vector and non-vector aphid abundance and phenology have the potential to improve pest management of potato cultivation.
