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  • 1.
    Engel, Philipp
    et al.
    Univ Lausanne, Dept Fundamental Microbiol, Lausanne, Switzerland..
    Kwong, Waldan K.
    Yale Univ, Ecol & Evolutionary Biol, New Haven, CT USA.;Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA..
    McFrederick, Quinn
    Univ Calif Riverside, Dept Entomol, Riverside, CA 92521 USA..
    Anderson, Kirk E.
    USDA, Carl Hayden Bee Res Ctr, Tucson, AZ USA..
    Barribeau, Seth Michael
    E Carolina Univ, Dept Biol, Greenville, NC USA..
    Chandler, James Angus
    Calif Acad Sci, Dept Microbiol, San Francisco, CA 94118 USA.;Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA..
    Cornman, R. Scott
    US Geol Survey, Ft Collins Sci Ctr, Ft Collins, CO USA..
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Linkopings Univ Victoria Westling, BILS, Linkoping, Sweden..
    de Miranda, Joachim R.
    Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden..
    Doublet, Vincent
    Univ Halle Wittenberg, Inst Biol, D-06108 Halle, Germany.;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany..
    Emery, Olivier
    Univ Lausanne, Dept Fundamental Microbiol, Lausanne, Switzerland..
    Evans, Jay D.
    ARS, USDA, Bee Res Lab, Beltsville, MD USA..
    Farinelli, Laurent
    Fasteris SA, Plan Les Ouates, Switzerland..
    Flenniken, Michelle L.
    Montana State Univ, Dept Plant Sci & Plant Pathol, Bozeman, MT 59717 USA..
    Granberg, Fredrik
    BVF, SLU, Uppsala, Sweden..
    Grasis, Juris A.
    San Diego State Univ, Dept Biol, North Life Sci, San Diego, CA 92182 USA..
    Gauthier, Laurent
    Univ Lausanne, Dept Fundamental Microbiol, Lausanne, Switzerland.;Yale Univ, Ecol & Evolutionary Biol, New Haven, CT USA..
    Hayer, Juliette
    SLU, Inst Husdjursgenet, Uppsala, Sweden..
    Koch, Hauke
    Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA.;Royal Bot Gardens, Richmond, Surrey, England..
    Kocher, Sarah
    Harvard Univ, Dept Organism & Evolutionary Biol, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Martinson, Vincent G.
    Univ Rochester, Dept Biol, Rochester, NY 14627 USA..
    Moran, Nancy
    Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA..
    Munoz-Torres, Monica
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Genom & Syst Biol Div, Berkeley, CA 94720 USA..
    Newton, Irene
    Indiana Univ, Dept Biol, Bloomington, IN USA..
    Paxton, Robert J.
    Univ Halle Wittenberg, Inst Biol, D-06108 Halle, Germany.;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany..
    Powell, Eli
    Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA..
    Sadd, Ben M.
    Illinois State Univ, Sch Biol Sci, Normal, IL 61761 USA..
    Schmid-Hempel, Paul
    ETHZ Inst Integrat Biol, Zurich, Switzerland..
    Schmid-Hempel, Regula
    ETHZ Inst Integrat Biol, Zurich, Switzerland..
    Song, Se Jin
    Univ Colorado, Boulder, CO 80309 USA..
    Schwarz, Ryan S.
    ARS, USDA, Bee Res Lab, Beltsville, MD USA..
    vanengelsdorp, Dennis
    Univ Maryland, Dept Entomol, College Pk, MD 20742 USA..
    Dainat, Benjamin
    Univ Lausanne, Dept Fundamental Microbiol, Lausanne, Switzerland.;Swiss Bee Resegman Ctr, Bern, Switzerland.;Apiservice, Bee Hlth Extens Serv, Bern, Switzerland.;Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA..
    The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions2016Inngår i: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 7, nr 2, artikkel-id e02164Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the micro biome. The bee micro biome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee micro biome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

  • 2.
    Glemin, Sylvain
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Univ Rennes, CNRS, UMR 6553, ECOBIO Ecosyst Biodiversite Evolut, F-35042 Rennes, France.
    Scornavacca, Celine
    Univ Montpellier, Inst Sci Evolut, CNRS, IRD,EPHE CC 064, Pl Eugene Bataillon, F-34095 Montpellier 05, France.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Burgarella, Concetta
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France;CIRAD, UMR AGAP, F-34398 Montpellier, France.
    Viader, Veronique
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Ardisson, Morgane
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Sarah, Gautier
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France;INRA, South Green Bioinformat Platform, BIOVERS, CIRAD,IRD,Montpellier SupAgro, Montpellier, France.
    Santoni, Sylvain
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    David, Jacques
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Ranwez, Vincent
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Pervasive hybridizations in the history of wheat relatives2019Inngår i: Science Advances, E-ISSN 2375-2548, Vol. 5, nr 5, artikkel-id eaav9188Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought-Aegilops mutica, an overlooked wild species-instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

  • 3.
    Martínez Barrio, Álvaro
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lamichhaney, Sangeet
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Fan, Guangyi
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; BGI-Shenzhen, Shenzen, China; 5 College of Physics, Qingdao University, Qingdao, China .
    Rafati, Nima
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Pettersson, Mats
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Zhang, He
    BGI-Shenzhen, Shenzen, China; College of Physics, Qingdao University, Qingdao, China.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ekman, Diana
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Höppner, Marc P.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Martin, Marcel
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Nystedt, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Liu, Xin
    BGI-Shenzhen, Shenzen, China.
    Chen, Wenbin
    BGI-Shenzhen, Shenzhen, China.
    Liang, Xinming
    BGI-Shenzhen, Shenzhen, China.
    Shi, Chengcheng
    BGI-Shenzhen, Shenzhen, China.
    Fu, Yuanyuan
    BGI-Shenzhen, Shenzhen, China.
    Ma, Kailong
    BGI-Shenzhen, Shenzhen, China.
    Zhan, Xiao
    BGI-Shenzhen, Shenzhen, China.
    Feng, Chungang
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Gustafson, Ulla
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    Rubin, Carl-Johan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sällman Almén, Markus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Blass, Martina
    Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden.
    Casini, Michele
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research.
    Folkvord, Arild
    Department of Biology, University of Bergen, Bergen, Norway; Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway; Institute of Marine Research, Bergen, Norway .
    Laikre, Linda
    Department of Zoology, Stockholm University.
    Ryman, Nils
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Lee, Simon Ming-Yuen Lee
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao.
    Xu, Xun
    BGI-Shenzhen, Shenzhen, China.
    Andersson, Leif
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States.
    The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing2016Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 5, artikkel-id e12081Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

  • 4.
    Moreno, Antonio D.
    et al.
    Chalmers Univ Technol, Dept Biol & Biol Engn, Ind Biotechnol, Gothenburg, Sweden;CIEMAT, Dept Energy, Biofuels Unit, Madrid, Spain.
    Tellgren-Roth, Christian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Soler, Lucile
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Olsson, Lisbeth
    Chalmers Univ Technol, Dept Biol & Biol Engn, Ind Biotechnol, Gothenburg, Sweden.
    Geijer, Cecilia
    Chalmers Univ Technol, Dept Biol & Biol Engn, Ind Biotechnol, Gothenburg, Sweden.
    Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 47152017Inngår i: MICROBIOLOGY RESOURCE ANNOUNCEMENTS, ISSN 2576-098X, Vol. 5, nr 14, artikkel-id e00138-17Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sustainable biofuel production from lignocellulosic materials requires efficient and complete use of all abundant sugars in the biomass, including xylose. Here, we report on the de novo genome assemblies of two strains of the xylose-fermenting yeast Candida intermedia: CBS 141442 and PYCC 4715.

  • 5.
    Nielsen, Jens Christian
    et al.
    Chalmers, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden..
    Grijseels, Sietske
    Tech Univ Denmark, Dept Biotechnol & Biomed, DK-2800 Lyngby, Denmark..
    Prigent, Sylvain
    Chalmers, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden..
    Ji, Boyang
    Chalmers, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden..
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Nielsen, Kristian Fog
    Tech Univ Denmark, Dept Biotechnol & Biomed, DK-2800 Lyngby, Denmark..
    Frisvad, Jens Christian
    Tech Univ Denmark, Dept Biotechnol & Biomed, DK-2800 Lyngby, Denmark..
    Workman, Mhairi
    Tech Univ Denmark, Dept Biotechnol & Biomed, DK-2800 Lyngby, Denmark..
    Nielsen, Jens
    Chalmers, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden.;Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2800 Lyngby, Denmark..
    Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species2017Inngår i: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, nr 6, artikkel-id 17044Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.

  • 6.
    Sayadi, Ahmed
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Martínez Barrio, Álvaro
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Immonen, Elina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Berger, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Tellgren-Roth, Christian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Nystedt, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Arnqvist, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Uppsala Univ, Dept Ecol & Genet, Anim Ecol, Uppsala, Sweden.
    The genomic footprint of sexual conflict2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 12, s. 1725-1730Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic 'tug-of-war' between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.

  • 7.
    Tiukova, Ievgeniia A.
    et al.
    Swedish Univ Agr Sci, Dept Biol & Biol Engn Syst & Synthet Biol, SE-41296 Gothenburg, Sweden;Swedish Univ Agr Sci, Dept Mol Sci, Box 7015, SE-75007 Uppsala, Sweden.
    Jiang, Huifeng
    Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Hoeppner, Marc P.
    Uppsala Univ, Dept Med Biochem & Microbiol, Box 582, S-75237 Uppsala, Sweden;NBIS, S-75237 Uppsala, Sweden;Christian Albrechts Univ Kiel, Inst Clin Mol Biol, D-24118 Kiel, Germany.
    Lantz, Henrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Piskur, Jure
    Lund Univ, Dept Biol, S-22362 Lund, Sweden.
    Sandgren, Mats
    Swedish Univ Agr Sci, Dept Mol Sci, Box 7015, SE-75007 Uppsala, Sweden.
    Nielsen, Jens
    Swedish Univ Agr Sci, Dept Biol & Biol Engn Syst & Synthet Biol, SE-41296 Gothenburg, Sweden.
    Gu, Zhenglong
    Cornell Univ, Div Nutr Sci, Ithaca, NY 14853 USA.
    Passoth, Volkmar
    Swedish Univ Agr Sci, Dept Mol Sci, Box 7015, SE-75007 Uppsala, Sweden.
    Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 75402019Inngår i: MICROORGANISMS, ISSN 2076-2607, Vol. 7, nr 11, artikkel-id 489Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

  • 8.
    Tiukova, Ievgeniia A.
    et al.
    Chalmers Univ Technol, Dept Biol & Biol Engn, Syst & Synthet Biol, Gothenburg, Sweden;Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden.
    Pettersson, Mats
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Höppner, Marc P.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. NBIS, Uppsala, Sweden;Christian Albrechts Univ Kiel, Inst Clin Mol Biol, Kiel, Germany;Royal Inst Technol KTH, Sci Life Lab, Div Gene Technol, Sch Biotechnol, Solna, Sweden.
    Olsen, Remi-Andre
    Kaller, Max
    Royal Inst Technol, Biotechnol & Hlth, Sch Engn Sci Chem, SciLifeLab, Stockholm, Sweden;Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden.
    Nielsen, Jens
    Chalmers Univ Technol, Dept Biol & Biol Engn, Syst & Synthet Biol, Gothenburg, Sweden.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. NBIS, Uppsala, Sweden.
    Lantz, Henrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. NBIS, Uppsala, Sweden.
    Söderberg, Jonas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Passoth, Volkmar
    Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden.
    Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis2019Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, nr 5, artikkel-id e0215077Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

  • 9.
    Zamani, Neda
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sundström, Görel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Meadows, Jennifer R. S.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Höppner, Marc P.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Lantz, Henrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Haas, Brian J.
    Grabherr, Manfred G.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    A universal genomic coordinate translator for comparative genomics2014Inngår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 15, s. 227-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N-2 with the number of available genomes, N. Results: Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Conclusions: Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.

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