NGI offers spatial transcriptomics through the 10X Genomics Visium method, a technique recently nominated as Method of the Year by Nature Methods. The technology combines histology with unbiased transcriptomics in a spatial context.
The Illumina NovaSeq 6000 system is the largest of the Illumina sequencing instruments, able to run two flow cells independently of each other and generate massive sequencing depth at competitive prices.
NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.
Would you like to work in a field with rapid development in technologies and applications? We are now recruiting a new member to join our team of project coordinators at NGI Uppsala (the SNP&SEQ Technology platform)
Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds.
P Halvarsson, J Höglund
Parasit Vectors, 14 (1) 1756-3305 (2021)
A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.
A total of 158 fecal samples were collected (n = 35 in 2007 and n = 123 in 2013-2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 × 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.
Nematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1008 sequences per sample. In total, 16 operational taxonomical units (OTU), all with ≥ 98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which ten are commonly associated with sheep. Multiple species were identified in all pre-anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.
Our findings provide evidence that nemabiome analysis combined with diversity index analysis provides an objective methodology in the study of the efficacy of anthelmintic treatment as both high and low abundant species were detected.
Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.
JP Dumanski, J Halvardson, H Davies, E Rychlicka-Buniowska, J Mattisson, BT Moghadam, N Nagy, K Węglarczyk, K Bukowska-Strakova, M Danielsson, P Olszewski, A Piotrowski, E Oerton, A Ambicka, M Przewoźnik, Ł Bełch, T Grodzicki, PL Chłosta, S Imreh, V Giedraitis, L Kilander, J Nordlund, A Ameur, U Gyllensten, Å Johansson, A Józkowicz, M Siedlar, A Klich-Rączka, J Jaszczyński, S Enroth, J Baran, M Ingelsson, JRB Perry, J Ryś, LA Forsberg
NGI CollaborationCell. Mol. Life Sci., 78 (8) 1420-9071 (2021)
Epidemiological investigations show that mosaic loss of chromosome Y (LOY) in leukocytes is associated with earlier mortality and morbidity from many diseases in men. LOY is the most common acquired mutation and is associated with aberrant clonal expansion of cells, yet it remains unclear whether this mosaicism exerts a direct physiological effect. We studied DNA and RNA from leukocytes in sorted- and single-cells in vivo and in vitro. DNA analyses of sorted cells showed that men diagnosed with Alzheimer's disease was primarily affected with LOY in NK cells whereas prostate cancer patients more frequently displayed LOY in CD4 + T cells and granulocytes. Moreover, bulk and single-cell RNA sequencing in leukocytes allowed scoring of LOY from mRNA data and confirmed considerable variation in the rate of LOY across individuals and cell types. LOY-associated transcriptional effect (LATE) was observed in ~ 500 autosomal genes showing dysregulation in leukocytes with LOY. The fraction of LATE genes within specific cell types was substantially larger than the fraction of LATE genes shared between different subsets of leukocytes, suggesting that LOY might have pleiotropic effects. LATE genes are involved in immune functions but also encode proteins with roles in other diverse biological processes. Our findings highlight a surprisingly broad role for chromosome Y, challenging the view of it as a "genetic wasteland", and support the hypothesis that altered immune function in leukocytes could be a mechanism linking LOY to increased risk for disease.
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.
B von der Heyde, A Emmanouilidou, E Mazzaferro, S Vicenzi, I Höijer, T Klingström, S Jumaa, O Dethlefsen, H Snieder, E de Geus, A Ameur, E Ingelsson, A Allalou, HL Brooke, M den Hoed
NGI CollaborationSci Rep, 10 (1) 2045-2322 (2020)
A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 µM ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).
Halophytophthora fluviatilis Pathogenicity and Distribution along a Mediterranean-Subalpine Gradient.
M Caballol, D Štraus, H Macia, X Ramis, MÁ Redondo, J Oliva
JoF, 7 (2) 2309-608X (2021)
Halophytophthora species have been traditionally regarded as brackish water oomycetes; however, recent reports in inland freshwater call for a better understanding of their ecology and possible pathogenicity. We studied the distribution of Halophytophthora fluviatilis in 117 forest streams by metabarcoding river filtrates taken in spring and autumn and by direct isolation from floating leaves. Pathogenicity on six Fagaceae species and Alnus glutinosa was assessed by stem inoculations. The distribution of H. fluviatilis was correlated with high mean annual temperatures (>93.5% of reports in Ta > 12.2 °C) and low precipitation records. H. fluviatilis was therefore widely distributed in forest streams in a warm-dry climate, but it was mostly absent in subalpine streams. H. fluviatilis was primarily detected in autumn with few findings in spring (28.4% vs. 2.7% of streams). H. fluviatilis was able to cause small lesions on some tree species such as Quercus pubescens, Q. suber and A. glutinosa. Our findings suggest that H. fluviatilis may be adapted to warm and dry conditions, and that it does not pose a significant threat to the most common Mediterranean broadleaved trees.
Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs.
M Wille, JJ Wensman, S Larsson, R van Damme, AK Theelke, J Hayer, M Malmberg
Infection, Genetics and Evolution, 82 1567-7257 (2020)
Canine respiratory coronavirus (CRCoV) has been identified as a causative agent of canine infectious respiratory disease, an upper respiratory infection affecting dogs. The epidemiology is currently opaque, with an unclear understanding of global prevalence, pathology, and genetic characteristics. In this study, Swedish privately-owned dogs with characteristic signs of canine infectious respiratory disease (n = 88) were screened for CRCoV and 13 positive samples (14.7%, 8.4-23.7% [95% confidence interval (CI)]) were further sequenced. Sequenced Swedish CRCoV isolates were highly similar despite being detected in dogs living in geographically distant locations and sampled across 3 years (2013-2015). This is due to a single introduction into Swedish dogs in approximately 2010, as inferred by time structured phylogeny. Unlike other CRCoVs, there was no evidence of recombination in Swedish CRCoV viruses, further supporting a single introduction. Finally, there were low levels of polymorphisms, in the spike genes. Overall, we demonstrate that there is little diversity of CRCoV which is endemic in Swedish dogs.
Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic-based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus 18 integrated into the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18-chr8 integrations at base-pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions.
Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes.
AM Ilumäe, H Post, R Flores, M Karmin, H Sahakyan, M Mondal, F Montinaro, L Saag, C Bormans, LF Sanchez, A Ameur, U Gyllensten, M Kals, R Mägi, L Pagani, DM Behar, S Rootsi, R Villems
NGI CollaborationEur. J. Hum. Genet., 1476-5438 (2021)
The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.
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