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Gutiérrez-Valencia J, Zervakis PI, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Pettersson OV, Arroyo J, Slotte T. Genetic causes and genomic consequences of breakdown of distyly in Linum trigynum. Mol Biol Evol 2024:msae087. [PMID: 38709782 DOI: 10.1093/molbev/msae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility (SI). Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male SI and/or anther height could underlie homostyly and self-compatibility (SC) in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Panagiotis-Ioannis Zervakis
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Olga Vinnere Pettersson
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U. The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes. Front Genet 2023; 14:1244493. [PMID: 37829276 PMCID: PMC10565955 DOI: 10.3389/fgene.2023.1244493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group's main clades and whose origin has been dated more than 400 million years ago. Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades. Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system. Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Julia Heintz
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
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Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan W, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience 2022; 11:6659719. [PMID: 35946988 PMCID: PMC9364683 DOI: 10.1093/gigascience/giac068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. RESULTS We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. CONCLUSION We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
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Affiliation(s)
| | | | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Iliana Bista
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | | | | | | | - Karen Oliver
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michelle Smith
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Anne Kraus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Stephen Mac
- Arima Genomics, Inc., San Diego, CA 92121, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Tanya Lama
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Samara Brown
- The Rockefeller University, New York, NY 10065, USA
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Olivier Fedrigo
- Correspondence address. Olivier Fedrigo, Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA. E-mail:
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Moškrič A, Marinč A, Ferk P, Leskošek B, Mosbech MB, Bunikis I, Pettersson OV, Soler L, Prešern J. The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies. Insects 2022; 13:insects13050403. [PMID: 35621738 PMCID: PMC9146700 DOI: 10.3390/insects13050403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry. Abstract The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.
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Affiliation(s)
- Ajda Moškrič
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
- Correspondence:
| | - Andraž Marinč
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
| | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Mai-Britt Mosbech
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, 751 24 Uppsala, Sweden;
| | - Janez Prešern
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
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5
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Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, Richards S. Standards recommendations for the Earth BioGenome Project. Proc Natl Acad Sci U S A 2022; 119:e2115639118. [PMID: 35042802 PMCID: PMC8795494 DOI: 10.1073/pnas.2115639118] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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Affiliation(s)
- Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Paul Flicek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 751 23 Uppsala, Sweden
| | | | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - William J Baker
- Department of Accelerated Taxonomy, Royal Botanic Gardens, Kew, Surrey TW9 3AE, United Kingdom
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark L Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Tomas Marques Bonet
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas-Universitat Pompeau Fabra, Parc de Rechercha Biomédica Barcelona 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Geonòmica - Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20560-0105
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | - Robert P Davey
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | | | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Neil Hall
- Genome British Columbia, Vancouver, BC V5Z 0C4, Canada
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, Center for Functional Genomics of Microbes, University of Greifswald 17489 Greifswald, Germany
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Erich D Jarvis
- Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863
| | - Rebecca N Johnson
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20560-0105
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Xin Liu
- China National GeneBank, Shenzhen 518120, China
| | - Jose Victor Lopez
- Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, FL 33004
| | - Eugene W Myers
- Department of Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894
| | - Monica F Poelchau
- National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD 20705
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894
| | | | - Sunil Kumar Sahu
- China National GeneBank, Shenzhen 518120, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Nicholas A Salmon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894
| | - Sibo Wang
- China National GeneBank, Shenzhen 518120, China
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, Computational Biology Core, University of Connecticut, Storrs, CT 06269
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 1165 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences 650223 Kunming, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen 266555 Qingdao, China
| | - Harris A Lewin
- University of California Davis Genome Center, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616;
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6
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Wallberg A, Bunikis I, Pettersson OV, Mosbech MB, Childers AK, Evans JD, Mikheyev AS, Robertson HM, Robinson GE, Webster MT. A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics 2019; 20:275. [PMID: 30961563 PMCID: PMC6454739 DOI: 10.1186/s12864-019-5642-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mai-Britt Mosbech
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna K Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA.,USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Hugh M Robertson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Dominguez Del Angel V, Hjerde E, Sterck L, Capella-Gutierrez S, Notredame C, Vinnere Pettersson O, Amselem J, Bouri L, Bocs S, Klopp C, Gibrat JF, Vlasova A, Leskosek BL, Soler L, Binzer-Panchal M, Lantz H. Ten steps to get started in Genome Assembly and Annotation. F1000Res 2018; 7. [PMID: 29568489 PMCID: PMC5850084 DOI: 10.12688/f1000research.13598.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).
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Affiliation(s)
| | - Erik Hjerde
- Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, 9019, Norway
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, Ghent University - VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Salvadors Capella-Gutierrez
- Spanish National Bioinformatics Institute (INB), Barcelona, Spain.,Barcelona Supercomputing Center (BSC), Centro Nacional de Supercomputación, Barcelona, Spain
| | - Cederic Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-752 37 , Sweden
| | - Joelle Amselem
- URGI, INRA, Université Paris-Saclay, Versailles, 78026, France
| | - Laurent Bouri
- Institut Français de Bioinformatique, UMS3601-CNRS, Université Paris-Saclay, Orsay, 91403, France
| | - Stephanie Bocs
- CIRAD, UMR AGAP, Montpellier, 34398, France.,AGAP, Cirad, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France.,South Green Bioinformatics Platform, Montpellier, France
| | | | - Jean-Francois Gibrat
- Institut Français de Bioinformatique, UMS3601-CNRS, Université Paris-Saclay, Orsay, 91403, France.,Unité de recherche , INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anna Vlasova
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Brane L Leskosek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, University of Ljubljana, Ljubljana, Slovenia
| | - Lucile Soler
- IMBIM/NBIS/SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Henrik Lantz
- IMBIM/NBIS/SciLifeLab, Uppsala University, Uppsala, Sweden
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Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F. De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping. Gigascience 2015; 4:56. [PMID: 26617983 PMCID: PMC4661999 DOI: 10.1186/s13742-015-0094-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome. METHODS In this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work. RESULTS We obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.
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Affiliation(s)
- Remi-Andre Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden
| | - Ievgeniia Tiukova
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden
| | - Kicki Holmberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Britta Lötstedt
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden
| | - Volkmar Passoth
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden
| | - Max Käller
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
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Pitt JI, Lantz H, Pettersson OV, Leong SLL. Xerochrysium gen. nov. and Bettsia, genera encompassing xerophilic species of Chrysosporium. IMA Fungus 2013; 4:229-41. [PMID: 24563835 PMCID: PMC3905941 DOI: 10.5598/imafungus.2013.04.02.08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022] Open
Abstract
On the basis of a study of ITS sequences, Vidal et al. (Rev. Iber. Micol. 17: 22, 2000) recommended that the genus Chrysosporium be restricted to species belonging to Onygenales. Using nrLSU genes, we studied the majority of clades examined by Vidal et al. and showed that currently accepted species in Chrysosporium phylogenetically belong in six clades in three orders. Surprisingly, the xerophilic species of Chrysosporium, long thought to be a single grouping away from the majority of Chrysosporium species, occupy two clades, one in Leotiales, the other in Eurotiales. Species accepted in Leotiales are related to the sexual genus Bettsia. One is the type species B. alvei, and related asexual strains classified as C. farinicola, the second is C. fastidium transferred to Bettsia as B. fastidia. Species in the Eurotiales are transferred to Xerochrysium gen. nov., where the accepted species are X. xerophilum and X. dermatitidis, the correct name for C. inops on transfer to Xerochrysium. All accepted species are extreme xerophiles, found in dried and concentrated foods.
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Affiliation(s)
- John I. Pitt
- CSIRO Animal, Food and Health Sciences, P.O. Box 52, North Ryde, NSW 1670, Australia
| | - Henrik Lantz
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Dept of Microbiology, Box 7025, Uppsala 75007, Sweden
- Uppsala University, Department of Medical Biochemistry and Microbiology, Box 582, 75123 Uppsala
| | - Olga Vinnere Pettersson
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Dept of Microbiology, Box 7025, Uppsala 75007, Sweden
- Uppsala University, Immunology, Genetics and Pathology, Rudbecklaboratoriet, 75185 Uppsala
| | - Su-lin L. Leong
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Dept of Microbiology, Box 7025, Uppsala 75007, Sweden
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Tiukova IA, Petterson ME, Tellgren-Roth C, Bunikis I, Eberhard T, Pettersson OV, Passoth V. Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation. PLoS One 2013; 8:e58455. [PMID: 23516483 PMCID: PMC3596373 DOI: 10.1371/journal.pone.0058455] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/04/2013] [Indexed: 11/29/2022] Open
Abstract
Dekkera bruxellensis can outcompete Saccharomyces cerevisiae in environments with low sugar concentrations. It is usually regarded as a spoilage yeast but has lately been identified as an alternative ethanol production organism. In this study, global gene expression in the industrial isolate D. bruxellensis CBS 11270 under oxygen and glucose limitation was investigated by whole transcriptome sequencing using the AB SOLiD technology. Among other observations, we noted expression of respiratory complex I NADH-ubiquinone reductase although D. bruxellensis is a Crabtree positive yeast. The observed higher expression of NADH-generating enzymes compared to NAD+-generating enzymes might be the reason for the previously observed NADH imbalance and resulting Custer effect in D. bruxellensis. Low expression of genes involved in glycerol production is probably the molecular basis for high efficiency of D. bruxellensis metabolism under nutrient limitation. No D. bruxellensis homologs to the genes involved in the final reactions of glycerol biosynthesis were detected. A high number of expressed sugar transporter genes is consistent with the hypothesis that the competitiveness of D. bruxellensis is due to a higher affinity for the limiting substrate.
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Affiliation(s)
- Ievgeniia A. Tiukova
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala Biocenter, Uppsala, Sweden
| | - Mats E. Petterson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala Biocenter, Uppsala, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
| | - Thomas Eberhard
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala Biocenter, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
| | - Volkmar Passoth
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala Biocenter, Uppsala, Sweden
- * E-mail:
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Pettersson OV, Leong SLL, Lantz H, Rice T, Dijksterhuis J, Houbraken J, Samson RA, Schnürer J. Phylogeny and intraspecific variation of the extreme xerophile, Xeromyces bisporus. Fungal Biol 2011; 115:1100-11. [PMID: 22036289 DOI: 10.1016/j.funbio.2011.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 06/07/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
Abstract
The filamentous ascomycete Xeromyces bisporus is an extreme xerophile able to grow down to a water activity of 0.62. We have inferred the phylogenetic position of Xeromyces in relation to other xerophilic and xerotolerant fungi in the order Eurotiales. Using nrDNA and betatubulin sequences, we show that it is more closely related to the xerophilic foodborne species of the genus Chrysosporium, than to the genus Monascus. The taxonomy of X. bisporus and Monascus is discussed. Based on physiological, morphological, and phylogenetic distinctiveness, we suggest that Xeromyces should be retained as a separate genus.
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Affiliation(s)
- Olga Vinnere Pettersson
- Department of Microbiology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7025, SE-75007 Uppsala, Sweden.
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Leong SLL, Pettersson OV, Rice T, Hocking AD, Schnürer J. The extreme xerophilic mould Xeromyces bisporus — Growth and competition at various water activities. Int J Food Microbiol 2011; 145:57-63. [DOI: 10.1016/j.ijfoodmicro.2010.11.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 11/11/2010] [Accepted: 11/14/2010] [Indexed: 11/15/2022]
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Berglund EC, Ehrenborg C, Vinnere Pettersson O, Granberg F, Näslund K, Holmberg M, Andersson SGE. Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents. BMC Genomics 2010; 11:152. [PMID: 20202191 PMCID: PMC2847970 DOI: 10.1186/1471-2164-11-152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 03/04/2010] [Indexed: 01/02/2023] Open
Abstract
Background Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed. Results To study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid. Conclusion Our study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.
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Affiliation(s)
- Eva C Berglund
- Department of Moleculcar Evolution, Norbyvägen 18C, S-75236 Uppsala, Sweden
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Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, Eriksson AS, Näslund K, Holmberg M, Lindroos H, Andersson SGE. Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PLoS Genet 2009; 5:e1000546. [PMID: 19578403 PMCID: PMC2697382 DOI: 10.1371/journal.pgen.1000546] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 06/01/2009] [Indexed: 11/20/2022] Open
Abstract
The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella. Emerging infectious diseases represent an increasing human health problem with many examples of disease outbreaks caused by transmissions from animals to humans, such as, most recently, the bird flu virus. Genes involved in virulence and antibiotic resistance are often carried by mobile elements like plasmids and viruses, which mediate transfer between cells at an amazing speed. Rodents represent a major carrier of infectious agents, and it is therefore particularly important to study the gene transfer processes in bacteria that use rodents as their natural host reservoir. We have studied the genome of a bacterium that is naturally adapted to mice and identified many more putative host-interaction genes than were observed in previously recognized human pathogens. Furthermore, most of these genes are located in a segment of about 25% of the genome, which was massively amplified and packaged into viral particles. This is the first demonstration of targeted packaging of a portion of the bacterial chromosome into viral particles, and we propose that this is a novel strategy for increased exchange of genes involved in the infectious process.
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Affiliation(s)
- Eva C. Berglund
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - A. Carolin Frank
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexandra Calteau
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fredrik Granberg
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ann-Sofie Eriksson
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Kristina Näslund
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Martin Holmberg
- Department of Medical Sciences, Section for Infectious Diseases, Uppsala University Hospital, Uppsala, Sweden
| | - Hillevi Lindroos
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Siv G. E. Andersson
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
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