NGI is one of the largest technical platforms at SciLifeLab. We provide access to technology for sequencing, genotyping and associated bioinformatics support to researchers based in Sweden.
We're thrilled to announce that we have now transitioned to exclusively using the data delivery system Data Delivery System (DDS) for all our data deliveries. DDS will now be our default system, streamlining our processes and enhancing our service.
We are seeking a skilled Bioinformatician to join our production team at the National Genomics Infrastructure (NGI), one of Europe’s largest sequencing facilities, located at SciLifeLab in Solna. The successful applicant will be employed by Karolinska Institutet.
NGI is proud to collaborate with the National Bioinformatics Infrastructure Sweden (NBIS) on a series of talks that we call “Lite”. You can either choose to pronounce the word like “light” in English or “lite” på Svenska.
Want to stay in touch? Join our newsletter!
All the latest updates from NGI direct to your inbox!
Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.
Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness.
The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.
Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.
WH Lewis, AE Lind, KM Sendra, H Onsbring, TA Williams, GF Esteban, RP Hirt, TJG Ettema, TM Embley
Mol. Biol. Evol., 37 (2) 1537-1719 (2020)
Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.
Methylation of lysine 36 on histone H3 is required to control transposon activities in somatic cells.
H Lindehell, YB Schwartz, J Larsson
Life Sci. Alliance, 6 (8) 2575-1077 (2023)
Transposable elements constitute a substantial portion of most eukaryotic genomes and their activity can lead to developmental and neuronal defects. In the germline, transposon activity is antagonized by the PIWI-interacting RNA pathway tasked with repression of transposon transcription and degrading transcripts that have already been produced. However, most of the genes required for transposon control are not expressed outside the germline, prompting the question: what causes deleterious transposons activity in the soma and how is it managed? Here, we show that disruptions of the Histone 3 lysine 36 methylation machinery led to increased transposon transcription in Drosophila melanogaster brains and that there is division of labour for the repression of transposable elements between the different methyltransferases Set2, NSD, and Ash1. Furthermore, we show that disruption of methylation leads to somatic activation of key genes in the PIWI-interacting RNA pathway and the preferential production of RNA from dual-strand piRNA clusters.
Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.
S Ny, L Sandegren, M Salemi, CG Giske
Sci Rep, 9 (1) 2045-2322 (2019)
Clonal lineages of ESBL (Extended-Spectrum β-Lactamase)-producing E. coli belonging to sequence type 131 (ST131) have disseminated globally during the last 30 years, leading to an increased prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in clinical isolates of E. coli. We aimed to study if Swedish ESBL-producing ST131 isolates originated from single or multiple introductions to the population by assessing the amount of genetic variation, on chromosomal and plasmid level, between Swedish and international E. coli ST131. Bayesian inference of Swedish E. coli ST131 isolates (n = 29), sequenced using PacBio RSII, together with an international ST131 dataset showed that the Swedish isolates were part of the international ST131 A, C1 and C2 clades. Highly conserved plasmids were identified in three clusters although they were separated by several years, which indicates a strong co-evolution between some ST131 lineages and specific plasmids. In conclusion, the tight clonal relationship observed within the ST131 clades, together with highly conserved plasmids, challenges investigation of strain transmission events. A combination of few SNPs on a genome-wide scale and an epidemiological temporospatial link, are needed to track the spread of the ST131 subclones.
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
LE Hernandez-Castro, M Paterno, AG Villacís, B Andersson, JA Costales, M De Noia, S Ocaña-Mayorga, CA Yumiseva, MJ Grijalva, MS Llewellyn
PLoS Negl Trop Dis, 11 (7) 1935-2735 (2017)
Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses.
The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area.
Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.
Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.
J Hill, M Lillie, ME Pettersson, C Rubin, BR Grant, PR Grant, L Andersson, P Jern
Nat Commun, 13 (1) 2041-1723 (2022)
Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.
Z Wang, A Emmerich, NJ Pillon, T Moore, D Hemerich, MC Cornelis, E Mazzaferro, S Broos, TS Ahluwalia, TM Bartz, AR Bentley, LF Bielak, M Chong, AY Chu, D Berry, R Dorajoo, ND Dueker, E Kasbohm, B Feenstra, MF Feitosa, C Gieger, M Graff, LM Hall, T Haller, FP Hartwig, DA Hillis, V Huikari, N Heard-Costa, C Holzapfel, AU Jackson, Å Johansson, AM Jørgensen, MA Kaakinen, R Karlsson, KF Kerr, B Kim, CM Koolhaas, Z Kutalik, V Lagou, PA Lind, M Lorentzon, L Lyytikäinen, M Mangino, C Metzendorf, KR Monroe, A Pacolet, L Pérusse, R Pool, RC Richmond, NV Rivera, S Robiou-du-Pont, KE Schraut, C Schulz, HM Stringham, T Tanaka, A Teumer, C Turman, PJ van der Most, M Vanmunster, FJA van Rooij, JV van Vliet-Ostaptchouk, X Zhang, J Zhao, W Zhao, Z Balkhiyarova, MN Balslev-Harder, SE Baumeister, J Beilby, J Blangero, DI Boomsma, S Brage, PS Braund, JA Brody, M Bruinenberg, U Ekelund, C Liu, JW Cole, FS Collins, LA Cupples, T Esko, S Enroth, JD Faul, L Fernandez-Rhodes, AE Fohner, OH Franco, TE Galesloot, SD Gordon, N Grarup, CA Hartman, G Heiss, J Hui, T Illig, R Jago, A James, PK Joshi, T Jung, M Kähönen, TO Kilpeläinen, W Koh, I Kolcic, PP Kraft, J Kuusisto, LJ Launer, A Li, A Linneberg, J Luan, PM Vidal, SE Medland, Y Milaneschi, A Moscati, B Musk, CP Nelson, IM Nolte, NL Pedersen, A Peters, PA Peyser, C Power, OT Raitakari, M Reedik, AP Reiner, PM Ridker, I Rudan, K Ryan, MA Sarzynski, LJ Scott, RA Scott, S Sidney, K Siggeirsdottir, AV Smith, JA Smith, E Sonestedt, M Strøm, ES Tai, KK Teo, B Thorand, A Tönjes, A Tremblay, AG Uitterlinden, J Vangipurapu, N van Schoor, U Völker, G Willemsen, K Williams, Q Wong, H Xu, KL Young, JM Yuan, MC Zillikens, AB Zonderman, A Ameur, S Bandinelli, JC Bis, M Boehnke, C Bouchard, DI Chasman, GD Smith, EJC de Geus, L Deldicque, M Dörr, MK Evans, L Ferrucci, M Fornage, C Fox, T Garland, V Gudnason, U Gyllensten, T Hansen, C Hayward, BL Horta, E Hyppönen, M Jarvelin, WC Johnson, SLR Kardia, LA Kiemeney, M Laakso, C Langenberg, T Lehtimäki, LL Marchand, Lifelines Cohort Study, PKE Magnusson, NG Martin, M Melbye, A Metspalu, D Meyre, KE North, C Ohlsson, AJ Oldehinkel, M Orho-Melander, G Pare, T Park, O Pedersen, BWJH Penninx, TH Pers, O Polasek, I Prokopenko, CN Rotimi, NJ Samani, X Sim, H Snieder, TIA Sørensen, TD Spector, NJ Timpson, RM van Dam, N van der Velde, CM van Duijn, P Vollenweider, H Völzke, T Voortman, G Waeber, NJ Wareham, DR Weir, H Wichmann, JF Wilson, AL Hevener, A Krook, JR Zierath, MAI Thomis, RJF Loos, Md Hoed
Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associate with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), leisure screen time (LST) and/or sedentary behavior at work. Loci associated with LST are enriched for genes whose expression in skeletal muscle is altered by resistance training. A missense variant in ACTN3 makes the alpha-actinin-3 filaments more flexible, resulting in lower maximal force in isolated type IIA muscle fibers, and possibly protection from exercise-induced muscle damage. Finally, Mendelian randomization analyses show that beneficial effects of lower LST and higher MVPA on several risk factors and diseases are mediated or confounded by body mass index (BMI). Our results provide insights into physical activity mechanisms and its role in disease prevention.
Last Updated: 25th February 2024
This website uses cookies to improve your experience. AcceptRead More
Privacy & Cookies Policy
Privacy Overview
This website uses cookies to improve your experience while you navigate through the website. Out of these, the cookies that are categorized as necessary are stored on your browser as they are essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may affect your browsing experience.
Necessary cookies are absolutely essential for the website to function properly. This category only includes cookies that ensures basic functionalities and security features of the website. These cookies do not store any personal information.
Any cookies that may not be particularly necessary for the website to function and is used specifically to collect user personal data via analytics, ads, other embedded contents are termed as non-necessary cookies. It is mandatory to procure user consent prior to running these cookies on your website.