1
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Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. Plant Cell 2024; 36:812-828. [PMID: 38231860 PMCID: PMC10980355 DOI: 10.1093/plcell/koae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/19/2024]
Abstract
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.
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Affiliation(s)
- Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
- VIB Single Cell Core Facility, Ghent 9052, Belgium
| | - Dongbo Shi
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manuel Neumann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yuji Ke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Fabio Gomez-Cano
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Olivier C Martin
- Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette 91192, France
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael T Raissig
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gergo Palfalvi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marc Libault
- Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65201, USA
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
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2
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Grujčić V, Saarenpää S, Sundh J, Sennblad B, Norgren B, Latz M, Giacomello S, Foster RA, Andersson AF. Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. PLoS One 2024; 19:e0296672. [PMID: 38241213 PMCID: PMC10798536 DOI: 10.1371/journal.pone.0296672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/13/2023] [Indexed: 01/21/2024] Open
Abstract
Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.
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Affiliation(s)
- Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Sweden
| | - Bengt Sennblad
- Science for Life Laboratory, Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Benjamin Norgren
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Meike Latz
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rachel A. Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Anders F. Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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3
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Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Lundberg DS, Weigel D, Giacomello S. Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nat Biotechnol 2023:10.1038/s41587-023-01979-2. [PMID: 37985875 DOI: 10.1038/s41587-023-01979-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/06/2023] [Indexed: 11/22/2023]
Abstract
The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks and spatial patterns. Existing technology does not allow the simultaneous investigation of spatial interactions between a host and the multitude of its colonizing microorganisms, which limits our understanding of host-microorganism interactions within a plant or animal tissue. Here we present spatial metatranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and find tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intrakingdom spatial interactions among microorganisms, as well as the host response to microbial hotspots. SmT provides an approach for answering fundamental questions on host-microbiome interplay.
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Affiliation(s)
- Sami Saarenpää
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Or Shalev
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Systems Biology of Microbial Communities, University of Tübingen, Tübingen, Germany
| | - Haim Ashkenazy
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vanessa Carlos
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Derek Severi Lundberg
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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4
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Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Rezene S, Gupta S, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S. Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections. Genome Biol 2023; 24:237. [PMID: 37858234 PMCID: PMC10588020 DOI: 10.1186/s13059-023-03080-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Enikő Lázár
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Jian Wu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Tibor Várkonyi
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Tibor Glasz
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | | | - Sefanit Rezene
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Soham Gupta
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Olaf Bergmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
- Universitätsmedizin Göttingen, Institute of Pharmacology and Toxicology, Göttingen, Germany
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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5
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Sounart H, Voronin D, Masarapu Y, Chung M, Saarenpää S, Ghedin E, Giacomello S. Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale. Nat Commun 2023; 14:6500. [PMID: 37838705 PMCID: PMC10576761 DOI: 10.1038/s41467-023-42237-y] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 10/03/2023] [Indexed: 10/16/2023] Open
Abstract
Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Denis Voronin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sami Saarenpää
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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6
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Manzano A, Weging S, Bezdan D, Borg J, Cahill T, Carnero-Diaz E, Cope H, Deane CS, Etheridge T, Giacomello S, Hardiman G, Leys N, Madrigal P, Mastroleo F, Medina FJ, Mieczkowski J, Fernandez-Rojo MA, Siew K, Szewczyk NJ, Walsh SB, da Silveira WA, Herranz R. Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research. iScience 2023; 26:107289. [PMID: 37636054 PMCID: PMC10448007 DOI: 10.1016/j.isci.2023.107289] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Following on from the NASA twins' study, there has been a tremendous interest in the use of omics techniques in spaceflight. Individual space agencies, NASA's GeneLab, JAXA's ibSLS, and the ESA-funded Space Omics Topical Team and the International Standards for Space Omics Processing (ISSOP) groups have established several initiatives to support this growth. Here, we present recommendations from the Space Omics Topical Team to promote standard application of space omics in Europe. We focus on four main themes: i) continued participation in and coordination with international omics endeavors, ii) strengthening of the European space omics infrastructure including workforce and facilities, iii) capitalizing on the emerging opportunities in the commercial space sector, and iv) capitalizing on the emerging opportunities in human subjects research.
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Affiliation(s)
- Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | | | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- Yuri GmbH, Meckenbeuren, Germany
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, 2080 Msida MSD, Malta
| | - Thomas Cahill
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast BT7 1NN, UK
| | - Eugénie Carnero-Diaz
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Sorbonne Université, CNRS, EPHE, UA, 75005 Paris, France
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Colleen S. Deane
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Timothy Etheridge
- Department of Sport and Health Science, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK
| | - Stefania Giacomello
- Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Gary Hardiman
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast BT7 1NN, UK
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Felice Mastroleo
- Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - F. Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Jakub Mieczkowski
- 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Manuel A. Fernandez-Rojo
- Hepatic Regenerative Medicine Lab, Madrid Institute for Advanced Studies in Food, 28049 Madrid, Spain
| | - Keith Siew
- University College London, London NW3 2PF, UK
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Ohio Musculoskeletal and Neurological Institute, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | | | - Willian A. da Silveira
- Department of Biological Sciences, School of Health, Science and Wellbeing, Staffordshire University, Stoke-on-Trent ST4 2DF, UK
- International Space University, 67400 Illkirch-Graffenstaden, France
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
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7
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Sylvén C, Wärdell E, Månsson-Broberg A, Cingolani E, Ampatzis K, Larsson L, Björklund Å, Giacomello S. High cardiomyocyte diversity in human early prenatal heart development. iScience 2022; 26:105857. [PMID: 36624836 PMCID: PMC9823232 DOI: 10.1016/j.isci.2022.105857] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/19/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Cardiomyocytes play key roles during cardiogenesis, but have poorly understood features, especially in prenatal stages. Here, we characterized human prenatal cardiomyocytes, 6.5-7 weeks post-conception, by integrating single-cell RNA sequencing, spatial transcriptomics, and ligand-receptor interaction information. Using a computational workflow developed to dissect cell type heterogeneity, localize cell types, and explore their molecular interactions, we identified eight types of developing cardiomyocyte, more than double compared to the ones identified in the Human Developmental Cell Atlas. These have high variability in cell cycle activity, mitochondrial content, and connexin gene expression, and are differentially distributed in the ventricles, including outflow tract, and atria, including sinoatrial node. Moreover, cardiomyocyte ligand-receptor crosstalk is mainly with non-cardiomyocyte cell types, encompassing cardiogenesis-related pathways. Thus, early prenatal human cardiomyocytes are highly heterogeneous and develop unique location-dependent properties, with complex ligand-receptor crosstalk. Further elucidation of their developmental dynamics may give rise to new therapies.
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Affiliation(s)
- Christer Sylvén
- Department of Medicine, Karolinska Institute, Huddinge, Sweden,Corresponding author
| | - Eva Wärdell
- Department of Medicine, Karolinska Institute, Huddinge, Sweden
| | | | | | | | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden,Corresponding author
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8
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Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. Cell Rep Methods 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
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Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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9
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Herranz R, da Silveira W, Bezdan D, Giacomello S, Szewczyk N. Building the Space Omics Topical Team to boost European space researchers’ role in the international consortia redefining spaceflight-generated datasets. iScience 2022; 25:104868. [PMID: 36060057 PMCID: PMC9436748 DOI: 10.1016/j.isci.2022.104868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In a broadening and more competitive space exploration landscape, playing at scale is necessary to obtain results. European researchers share their lessons learned on growing a research program where omics techniques can feed new knowledge, both fundamental and practical, for space exploration. Sending people to new space destinations will require interdisciplinary research centered around omics and personalized medicine, with added constraints of low-gravity and high-radiation environments.
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10
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Cope H, Willis CR, MacKay MJ, Rutter LA, Toh LS, Williams PM, Herranz R, Borg J, Bezdan D, Giacomello S, Muratani M, Mason CE, Etheridge T, Szewczyk NJ. Routine omics collection is a golden opportunity for European human research in space and analog environments. Patterns 2022; 3:100550. [PMID: 36277820 PMCID: PMC9583032 DOI: 10.1016/j.patter.2022.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Niu S, Li J, Bo W, Yang W, Zuccolo A, Giacomello S, Chen X, Han F, Yang J, Song Y, Nie Y, Zhou B, Wang P, Zuo Q, Zhang H, Ma J, Wang J, Wang L, Zhu Q, Zhao H, Liu Z, Zhang X, Liu T, Pei S, Li Z, Hu Y, Yang Y, Li W, Zan Y, Zhou L, Lin J, Yuan T, Li W, Li Y, Wei H, Wu HX. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 2021; 185:204-217.e14. [PMID: 34965378 DOI: 10.1016/j.cell.2021.12.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [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: 07/27/2021] [Revised: 10/23/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022]
Abstract
Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.
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Affiliation(s)
- Shihui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China.
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Wenhao Bo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Stefania Giacomello
- SciLife Lab, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Stockholm, Sweden
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Fangxu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Junhe Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yitong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yumeng Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Biao Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Peiyi Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Quan Zuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Hui Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Jingjing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Jun Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Lvji Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Qianya Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Huanhuan Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Zhanmin Liu
- Qigou State-owned Forest Farm, Pingquan, Hebei Province 067509, P. R. China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Yao Hu
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Yehui Yang
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Wenzhao Li
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Yanjun Zan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden
| | - Linghua Zhou
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Tongqi Yuan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China; College of Material Science and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - Harry X Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China; Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden; CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT 2601, Australia.
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12
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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13
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Alm Rosenblad M, Abramova A, Lind U, Ólason P, Giacomello S, Nystedt B, Blomberg A. Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions. Mar Biotechnol (NY) 2021; 23:402-416. [PMID: 33931810 PMCID: PMC8270832 DOI: 10.1007/s10126-021-10033-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/05/2021] [Indexed: 05/11/2023]
Abstract
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
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Affiliation(s)
- Magnus Alm Rosenblad
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Anna Abramova
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Ulrika Lind
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Páll Ólason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Anders Blomberg
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden.
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14
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Giacomello S. A new era for plant science: spatial single-cell transcriptomics. Curr Opin Plant Biol 2021; 60:102041. [PMID: 33915520 DOI: 10.1016/j.pbi.2021.102041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/04/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
To achieve a complete understanding of how organisms function, there is a need to study their fundamental unit, the cell, in its spatial context. In recent years, we have seen fast-paced technological progress to study the transcriptional content of single cells and their spatial relationships. This review highlights modern advancements in single-cell RNA-sequencing, provides an overview of the technologies that led the plant field toward spatial transcriptomics, and describes the available spatial transcriptomics approaches providing examples of their application to plant tissues. In addition, it discusses the integration of these methods to study plant tissues. Taken together, we propose a central role of spatial transcriptomics approaches in plant science.
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Affiliation(s)
- Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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15
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Madrigal P, Gabel A, Villacampa A, Manzano A, Deane CS, Bezdan D, Carnero-Diaz E, Medina FJ, Hardiman G, Grosse I, Szewczyk N, Weging S, Giacomello S, Harridge SDR, Morris-Paterson T, Cahill T, da Silveira WA, Herranz R. Revamping Space-omics in Europe. Cell Syst 2020; 11:555-556. [PMID: 33242401 DOI: 10.1016/j.cels.2020.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, UK
| | | | - Alicia Villacampa
- Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), Madrid E28040, Spain
| | - Aránzazu Manzano
- Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), Madrid E28040, Spain
| | - Colleen S Deane
- Department of Sport and Health Science, College of Life and Environmental Sciences, University of Exeter, Exeter, UK; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | | | - Eugénie Carnero-Diaz
- Institut Systématique, Evolution, Biodiversité (ISYEB), Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, Paris, France
| | - F Javier Medina
- Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), Madrid E28040, Spain
| | - Gary Hardiman
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Belfast, Northern Ireland, UK
| | - Ivo Grosse
- University of Halle, Halle (Saale), Germany
| | - Nathaniel Szewczyk
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, University of Nottingham, School of Medicine. Royal Derby Hospital Centre, Derby, UK
| | | | | | - Stephen D R Harridge
- Centre for Human & Applied Physiological Sciences (CHAPS) Faculty of Life Sciences & Medicine, King's College London, Shepherd's House, Guy's Campus, London, UK
| | - Tessa Morris-Paterson
- Centre for Human & Applied Physiological Sciences (CHAPS) Faculty of Life Sciences & Medicine, King's College London, Shepherd's House, Guy's Campus, London, UK
| | - Thomas Cahill
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Belfast, Northern Ireland, UK
| | - Willian A da Silveira
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Belfast, Northern Ireland, UK
| | - Raúl Herranz
- Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), Madrid E28040, Spain.
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16
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Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M. A New Era for Space Life Science: International Standards for Space Omics Processing. Patterns (N Y) 2020; 1:100148. [PMID: 33336201 PMCID: PMC7733874 DOI: 10.1016/j.patter.2020.100148] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance standard guidelines between space biologists at a global level. Here we introduce our consortium and share past lessons learned and future challenges related to spaceflight omics.
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Affiliation(s)
- Lindsay Rutter
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Henry Cope
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Kathleen M. Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mariano I. Gabitto
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Samrawit Gebre
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Stefan J. Green
- Genome Research Core, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sigrid S. Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Nathaniel J. Szewczyk
- Ohio Musculoskeletal and Neurological Institute (OMNI), Ohio University, Athens, OH 45701, USA
| | - Deanne M. Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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17
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Klimovich A, Giacomello S, Björklund Å, Faure L, Kaucka M, Giez C, Murillo-Rincon AP, Matt AS, Willoweit-Ohl D, Crupi G, de Anda J, Wong GCL, D'Amato M, Adameyko I, Bosch TCG. Prototypical pacemaker neurons interact with the resident microbiota. Proc Natl Acad Sci U S A 2020; 117:17854-17863. [PMID: 32647059 PMCID: PMC7395494 DOI: 10.1073/pnas.1920469117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 02/08/2023] Open
Abstract
Pacemaker neurons exert control over neuronal circuit function by their intrinsic ability to generate rhythmic bursts of action potential. Recent work has identified rhythmic gut contractions in human, mice, and hydra to be dependent on both neurons and the resident microbiota. However, little is known about the evolutionary origin of these neurons and their interaction with microbes. In this study, we identified and functionally characterized prototypical ANO/SCN/TRPM ion channel-expressing pacemaker cells in the basal metazoan Hydra by using a combination of single-cell transcriptomics, immunochemistry, and functional experiments. Unexpectedly, these prototypical pacemaker neurons express a rich set of immune-related genes mediating their interaction with the microbial environment. Furthermore, functional experiments gave a strong support to a model of the evolutionary emergence of pacemaker cells as neurons using components of innate immunity to interact with the microbial environment and ion channels to generate rhythmic contractions.
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Affiliation(s)
- Alexander Klimovich
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany;
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Infrastructure of Sweden, Science for Life Laboratory, Stockholm University, 17121 Solna, Sweden
- Department of Gene Technology, Science for Life Laboratory, Kungligia Tekniska Högskolan Royal Institute of Technology, 17121 Solna, Sweden
| | - Åsa Björklund
- Department of Cell and Molecular Biology, National Infrastructure of Sweden, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Louis Faure
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
| | - Marketa Kaucka
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, SH 24306 Plön, Germany
| | - Christoph Giez
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Andrea P Murillo-Rincon
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Ann-Sophie Matt
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Doris Willoweit-Ohl
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Gabriele Crupi
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany
| | - Jaime de Anda
- Department of Bioengineering, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
- Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
| | - Gerard C L Wong
- Department of Bioengineering, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
- Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Igor Adameyko
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Thomas C G Bosch
- Department of Cell and Developmental Biology, Zoological Institute, University of Kiel, D-24118 Kiel, Germany;
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18
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Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell 2020; 179:1647-1660.e19. [PMID: 31835037 DOI: 10.1016/j.cell.2019.11.025] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [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: 06/28/2018] [Revised: 09/06/2019] [Accepted: 11/14/2019] [Indexed: 10/25/2022]
Abstract
The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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Affiliation(s)
- Michaela Asp
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoyan Qian
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Eva Wärdell
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joaquin Custodio
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Salmén
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Cecilia Österholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Elisabet Åkesson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Olaf Bergmann
- Center for Regenerative Therapies Dresden, TU-Dresden, Dresden, Germany; Karolinska Institutet, Cell and Molecular Biology, Stockholm, Sweden
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christer Sylvén
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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19
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Berglund E, Saarenpää S, Jemt A, Gruselius J, Larsson L, Bergenstråhle L, Lundeberg J, Giacomello S. Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues. BMC Genomics 2020; 21:298. [PMID: 32293264 PMCID: PMC7158132 DOI: 10.1186/s12864-020-6631-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/20/2019] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets. RESULTS We have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples. CONCLUSIONS The new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.
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Affiliation(s)
- Emelie Berglund
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Sami Saarenpää
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Anders Jemt
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joel Gruselius
- Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
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20
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Cossu RM, Casola C, Giacomello S, Vidalis A, Scofield DG, Zuccolo A. LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biol Evol 2018; 9:3449-3462. [PMID: 29228262 PMCID: PMC5751070 DOI: 10.1093/gbe/evx260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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] [Accepted: 12/07/2017] [Indexed: 12/29/2022] Open
Abstract
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
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Affiliation(s)
- Rosa Maria Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Istituto di Genomica Applicata, Udine, Italy
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21
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Giacomello S, Lundeberg J. Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays. Nat Protoc 2018; 13:2425-2446. [DOI: 10.1038/s41596-018-0046-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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Marques S, van Bruggen D, Vanichkina DP, Floriddia EM, Munguba H, Väremo L, Giacomello S, Falcão AM, Meijer M, Björklund ÅK, Hjerling-Leffler J, Taft RJ, Castelo-Branco G. Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development. Dev Cell 2018; 46:504-517.e7. [PMID: 30078729 PMCID: PMC6104814 DOI: 10.1016/j.devcel.2018.07.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [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: 09/05/2017] [Revised: 05/23/2018] [Accepted: 07/03/2018] [Indexed: 01/31/2023]
Abstract
Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryogenesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different oligodendrocyte (OL) states at adult stages. Here, we present bulk and single-cell transcriptomics resources providing insights on how transitions between these states occur. We found that post-natal OPCs from brain and spinal cord present similar transcriptional signatures. Moreover, post-natal OPC progeny of E13.5 Pdgfra+ cells present electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves, indicating that Pdgfra+ pre-OPCs rewire their transcriptional network during development. Single-cell RNA-seq and lineage tracing indicates that a subset of E13.5 Pdgfra+ cells originates cells of the pericyte lineage. Thus, our results indicate that embryonic Pdgfra+ cells in the CNS give rise to distinct post-natal cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions. OPCs arising from different parts of the CNS are highly similar to one another Pre-OPCs converge into similar transcriptional and electrophysiological OPC states E13.5 Pdgfra+ cells give rise mainly to OPCs in the post-natal CNS E13.5 Pdgfra+ cells also give rise to cells of the pericyte lineage
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Affiliation(s)
- Sueli Marques
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - David van Bruggen
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Darya Pavlovna Vanichkina
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW 2050, Australia; Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4067, Australia
| | - Elisa Mariagrazia Floriddia
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Hermany Munguba
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Leif Väremo
- Science for Life Laboratory, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Göteborg 412 96, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Åsa Kristina Björklund
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ryan James Taft
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4067, Australia; Illumina, Inc., San Diego, CA 92122, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, Stockholm 17177, Sweden.
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23
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Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. Spatially resolved transcriptome profiling in model plant species. Nat Plants 2017; 3:17061. [PMID: 28481330 DOI: 10.1038/nplants.2017.61] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/31/2017] [Indexed: 05/08/2023]
Abstract
Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.
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Affiliation(s)
- Stefania Giacomello
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17165 Solna, Sweden
| | - Fredrik Salmén
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
| | - Barbara K Terebieniec
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Sanja Vickovic
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
| | | | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17165 Solna, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, 17121 Solna, Sweden
| | - Johan Reimegård
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75237 Uppsala, Sweden
| | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 11421 Stockholm, Sweden
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 11421 Stockholm, Sweden
- ARC Centre of Excellence in Plant and Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, Adelaide, South Australia 5064, Australia
| | - Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institute, 17165 Solna, Sweden
| | - Jens F Sundström
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Joakim Lundeberg
- Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden
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24
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Bersani C, Huss M, Giacomello S, Xu LD, Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui WO, Wiman KG. Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. Oncotarget 2016; 7:1895-911. [PMID: 26672765 PMCID: PMC4811505 DOI: 10.18632/oncotarget.6557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 06/24/2015] [Accepted: 11/15/2015] [Indexed: 02/06/2023] Open
Abstract
RNA-binding proteins (RBPs) play important roles in the regulation of gene expression through a variety of post-transcriptional mechanisms. The p53-induced RBP Wig-1 (Zmat3) binds RNA through its zinc finger domains and enhances stability of p53 and N-Myc mRNAs and decreases stability of FAS mRNA. To identify novel Wig-1-bound RNAs, we performed RNA-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) in HCT116 and Saos-2 cells. We identified 286 Wig-1-bound mRNAs common between the two cell lines. Sequence analysis revealed that AU-rich elements (AREs) are highly enriched in the 3′UTR of these Wig-1-bound mRNAs. Network enrichment analysis showed that Wig-1 preferentially binds mRNAs involved in cell cycle regulation. Moreover, we identified a 2D Wig-1 binding motif in HIF1A mRNA. Our findings confirm that Wig-1 is an ARE-BP that regulates cell cycle-related processes and provide a novel view of how Wig-1 may bind mRNA through a putative structural motif. We also significantly extend the repertoire of Wig-1 target mRNAs. Since Wig-1 is a transcriptional target of the tumor suppressor p53, these results have implications for our understanding of p53-dependent stress responses and tumor suppression.
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Affiliation(s)
- Cinzia Bersani
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Mikael Huss
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Li-Di Xu
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Julie Bianchi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Sofi Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Fredrik Jerhammar
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumour and Cell biology, Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Klas G Wiman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
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25
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Lindholm ME, Giacomello S, Werne Solnestam B, Fischer H, Huss M, Kjellqvist S, Sundberg CJ. The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts. PLoS Genet 2016; 12:e1006294. [PMID: 27657503 PMCID: PMC5033478 DOI: 10.1371/journal.pgen.1006294] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/10/2016] [Indexed: 01/02/2023] Open
Abstract
Regularly performed endurance training has many beneficial effects on health and skeletal muscle function, and can be used to prevent and treat common diseases e.g. cardiovascular disease, type II diabetes and obesity. The molecular adaptation mechanisms regulating these effects are incompletely understood. To date, global transcriptome changes in skeletal muscles have been studied at the gene level only. Therefore, global isoform expression changes following exercise training in humans are unknown. Also, the effects of repeated interventions on transcriptional memory or training response have not been studied before. In this study, 23 individuals trained one leg for three months. Nine months later, 12 of the same subjects trained both legs in a second training period. Skeletal muscle biopsies were obtained from both legs before and after both training periods. RNA sequencing analysis of all 119 skeletal muscle biopsies showed that training altered the expression of 3,404 gene isoforms, mainly associated with oxidative ATP production. Fifty-four genes had isoforms that changed in opposite directions. Training altered expression of 34 novel transcripts, all with protein-coding potential. After nine months of detraining, no training-induced transcriptome differences were detected between the previously trained and untrained legs. Although there were several differences in the physiological and transcriptional responses to repeated training, no coherent evidence of an endurance training induced transcriptional skeletal muscle memory was found. This human lifestyle intervention induced differential expression of thousands of isoforms and several transcripts from unannotated regions of the genome. It is likely that the observed isoform expression changes reflect adaptational mechanisms and processes that provide the functional and health benefits of regular physical activity. Skeletal muscle is the most abundant tissue of the healthy human body. It is also highly adaptable to different environmental stimuli, e.g. regular exercise. Exercise training improves overall health and muscle function, and can be used to prevent and treat several common diseases e.g. cardiovascular disease and type II diabetes. Therefore, it is of great importance to understand the molecular mechanisms behind adaptation processes in human skeletal muscle. In this study, we show that different expression variants from the same gene can be regulated in different directions with training, implicating alternative protein functions from one single gene. Such findings are emblematic of the complex mechanisms regulating the effects of training. We also find that training changes the activity of functionally unknown parts of the genome, with the potential for new proteins involved in the health-enhancing effects of exercise. Additionally, our results challenge the belief of a skeletal muscle memory, where previous training can affect the response to a subsequent training period. Overall, we provide understanding of the skeletal muscle biology and novel insights into the mechanisms behind the massive benefits of regular exercise on the human skeletal muscle transcriptome, inspiring further studies for deeper investigation.
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Affiliation(s)
- Maléne E Lindholm
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MEL); (CJS)
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Beata Werne Solnestam
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Helene Fischer
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Huss
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Sanela Kjellqvist
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MEL); (CJS)
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Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, Le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, Morgante M. Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation. Mol Biol Evol 2016; 33:2706-19. [PMID: 27499133 PMCID: PMC5026262 DOI: 10.1093/molbev/msw161] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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] [Indexed: 12/23/2022] Open
Abstract
Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species. With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species. Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes. Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.
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Affiliation(s)
- Sara Pinosio
- Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy
| | - Stefania Giacomello
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | | | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Veronique Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France
| | | | - Giusi Zaina
- Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | | | | | - Fabio Marroni
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
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27
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Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 2016; 353:78-82. [DOI: 10.1126/science.aaf2403] [Citation(s) in RCA: 1166] [Impact Index Per Article: 145.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/31/2016] [Indexed: 12/27/2022]
Abstract
Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call “spatial transcriptomics,” that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.
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28
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Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guérin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour 2016; 16:1023-36. [PMID: 26929265 DOI: 10.1111/1755-0998.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
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Affiliation(s)
| | - G Zaina
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - V Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Giacomello
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Segura
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Scalabrin
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Guérin
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - E De Paoli
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - C Aluome
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.,INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Viger
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - F Cattonaro
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - A Payne
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | | | | | - A Berard
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France
| | - M R Allwright
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - M Villar
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - G Taylor
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - C Bastien
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Morgante
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.,IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
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29
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Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 2014; 15:819. [PMID: 25261295 PMCID: PMC4192438 DOI: 10.1186/1471-2164-15-819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/22/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes. RESULTS The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations. CONCLUSIONS We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.
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Affiliation(s)
- Alexey Kutsenko
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Thomas Svensson
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Björn Nystedt
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE 752 37 Uppsala, Sweden
| | - Joakim Lundeberg
- />Science for Life Laboratory, KTH, Royal Institute of Technology, Science for Life Laboratory, SE 171 65 Solna, Sweden
| | - Petra Björk
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Erik Sonnhammer
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Stefania Giacomello
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Neus Visa
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Lars Wieslander
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
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