1
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Isaacson JR, Berg MD, Yeung W, Villén J, Brandl CJ, Moehring AJ. Impact of tRNA-induced proline-to-serine mistranslation on the transcriptome of Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593249. [PMID: 38766246 PMCID: PMC11100759 DOI: 10.1101/2024.05.08.593249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Mistranslation is the misincorporation of an amino acid into a polypeptide. Mistranslation has diverse effects on multicellular eukaryotes and is implicated in several human diseases. In Drosophila melanogaster, a serine transfer RNA (tRNA) that misincorporates serine at proline codons (P→S) affects male and female flies differently. The mechanisms behind this discrepancy are currently unknown. Here, we compare the transcriptional response of male and female flies to P→S mistranslation to identify genes and cellular processes that underlie sex-specific differences. Both males and females downregulate genes associated with various metabolic processes in response to P→S mistranslation. Males downregulate genes associated with extracellular matrix organization and response to negative stimuli such as wounding, whereas females downregulate aerobic respiration and ATP synthesis genes. Both sexes upregulate genes associated with gametogenesis, but females also upregulate cell cycle and DNA repair genes. These observed differences in the transcriptional response of male and female flies to P→S mistranslation have important implications for the sex-specific impact of mistranslation on disease and tRNA therapeutics.
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Affiliation(s)
| | - Matthew D. Berg
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195
| | - William Yeung
- Department of Biology, Western University, N6A 5B7, London, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195
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2
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Perna S, Tang W, Blimbaum S, Li A, Zhou L. Shared Transcriptomic Signatures of Inflammaging Among Diverse Strains of Drosophila melanogaster. RESEARCH SQUARE 2024:rs.3.rs-4146509. [PMID: 38645033 PMCID: PMC11030547 DOI: 10.21203/rs.3.rs-4146509/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background A prominent hallmark of aging is inflammaging-the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes-or any others-can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear. Methods and Results We compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especially SPH93. We further showed that machine learning models can be used to predict the "inflammatory age" of the fruit y. Conclusion A core group of genes may serve as markers for studying inflammaging in Drosophila. RNA-Seq profiles, in combination with machine-learning models, can be applied to measure the acceleration or deceleration of inflammaging.
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Steinmetz EL, Noh S, Klöppel C, Fuhr MF, Bach N, Raffael ME, Hildebrandt K, Wittling F, Jann D, Walldorf U. Generation of Mutants from the 57B Region of Drosophila melanogaster. Genes (Basel) 2023; 14:2047. [PMID: 38002990 PMCID: PMC10671637 DOI: 10.3390/genes14112047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The 57B region of Drosophila melanogaster includes a cluster of the three homeobox genes orthopedia (otp), Drosophila Retinal homeobox (DRx), and homeobrain (hbn). In an attempt to isolate mutants for these genes, we performed an EMS mutagenesis and isolated lethal mutants from the 57B region, among them mutants for otp, DRx, and hbn. With the help of two newly generated deletions from the 57B region, we mapped additional mutants to specific chromosomal intervals and identified several of these mutants from the 57B region molecularly. In addition, we generated mutants for CG15651 and RIC-3 by gene targeting and mutants for the genes CG9344, CG15649, CG15650, and ND-B14.7 using the CRISPR/Cas9 system. We determined the lethality period during development for most isolated mutants. In total, we analysed alleles from nine different genes from the 57B region of Drosophila, which could now be used to further explore the functions of the corresponding genes in the future.
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Affiliation(s)
- Eva Louise Steinmetz
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Zoology & Physiology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building B2.1, D-66123 Saarbrücken, Germany
| | - Sandra Noh
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Christine Klöppel
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Martin F. Fuhr
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Nicole Bach
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Mona Evelyn Raffael
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Kirsten Hildebrandt
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Fabienne Wittling
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Doris Jann
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Medical Biochemistry & Molecular Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 45.2, D-66421 Homburg, Germany
| | - Uwe Walldorf
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
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4
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Chaturvedi A, Li X, Dhandapani V, Marshall H, Kissane S, Cuenca-Cambronero M, Asole G, Calvet F, Ruiz-Romero M, Marangio P, Guigó R, Rago D, Mirbahai L, Eastwood N, Colbourne J, Zhou J, Mallon E, Orsini L. The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome. Nucleic Acids Res 2023; 51:9785-9803. [PMID: 37638757 PMCID: PMC10570034 DOI: 10.1093/nar/gkad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
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Affiliation(s)
- Anurag Chaturvedi
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Cuenca-Cambronero
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain
| | - Giovanni Asole
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Paolo Marangio
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Daria Rago
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Niamh Eastwood
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn Mallon
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- The Alan Turing Institute, British Library, London NW1 2DB, UK
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5
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Taniguchi T, Okuno M, Shinoda T, Kobayashi F, Takahashi K, Yuasa H, Nakamura Y, Tanaka H, Kajitani R, Itoh T. GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level. DNA Res 2023; 30:dsad017. [PMID: 37478310 PMCID: PMC10439787 DOI: 10.1093/dnares/dsad017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023] Open
Abstract
The prediction of gene structure within the genome sequence is the starting point of genome analysis, and its accuracy has a significant impact on the quality of subsequent analyses. Gene structure prediction is roughly divided into RNA-Seq-based methods, ab initio-based methods, homology-based methods, and the integration of individual prediction methods. Integrated methods are mainstream in recent genome projects because they improve prediction accuracy by combining or taking the best individual prediction findings; however, adequate prediction accuracy for eukaryotic species has not yet been achieved. Therefore, we developed an integrated tool, GINGER, that solves various issues related to gene structure prediction in higher eukaryotes. By handling artefacts in alignments of RNA and protein sequences, reconstructing gene structures via dynamic programming with appropriately weighted and scored exon/intron/intergenic regions, and applying different prediction processes and filtering criteria to multi-exon and single-exon genes, we achieved a significant improvement in accuracy compared to the existing integration methods. The feature of GINGER is its high prediction accuracy at the gene and exon levels, which is pronounced for species with more complex gene architectures. GINGER is implemented using Nextflow, which allows for the efficient and effective use of computing resources.
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Affiliation(s)
- Takeaki Taniguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Takahiro Shinoda
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Fumiya Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Hideaki Yuasa
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yuta Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
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6
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Tang HW, Spirohn K, Hu Y, Hao T, Kovács IA, Gao Y, Binari R, Yang-Zhou D, Wan KH, Bader JS, Balcha D, Bian W, Booth BW, Coté AG, de Rouck S, Desbuleux A, Goh KY, Kim DK, Knapp JJ, Lee WX, Lemmens I, Li C, Li M, Li R, Lim HJ, Liu Y, Luck K, Markey D, Pollis C, Rangarajan S, Rodiger J, Schlabach S, Shen Y, Sheykhkarimli D, TeeKing B, Roth FP, Tavernier J, Calderwood MA, Hill DE, Celniker SE, Vidal M, Perrimon N, Mohr SE. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nat Commun 2023; 14:2162. [PMID: 37061542 PMCID: PMC10105736 DOI: 10.1038/s41467-023-37876-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 04/17/2023] Open
Abstract
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
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Affiliation(s)
- Hong-Wen Tang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Kerstin Spirohn
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Tong Hao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - István A Kovács
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Physics and Astronomy, Northwestern University, 633 Clark Street, Evanston, IL, 60208, USA
- Northwestern Institute on Complex Systems, Chambers Hall, Northwestern University, 600 Foster St, Evanston, IL, 60208, USA
| | - Yue Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Donghui Yang-Zhou
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kenneth H Wan
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
- High-Throughput Biology Center, Institute of Basic Biological Sciences, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21205, USA
| | - Dawit Balcha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Wenting Bian
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Benjamin W Booth
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Atina G Coté
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Steffi de Rouck
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Alice Desbuleux
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Jennifer J Knapp
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Irma Lemmens
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Cathleen Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Mian Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Roujia Li
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Katja Luck
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dylan Markey
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Carl Pollis
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sudharshan Rangarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Sadie Schlabach
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yun Shen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dayag Sheykhkarimli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Bridget TeeKing
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Frederick P Roth
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
- Department of Computer Science, University of Toronto, 40 St George St, Toronto, ON, M5S 2E4, Canada
| | - Jan Tavernier
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Michael A Calderwood
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - David E Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
| | - Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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7
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Trajković J, Makevic V, Pesic M, Pavković-Lučić S, Milojevic S, Cvjetkovic S, Hagerman R, Budimirovic DB, Protic D. Drosophila melanogaster as a Model to Study Fragile X-Associated Disorders. Genes (Basel) 2022; 14:genes14010087. [PMID: 36672829 PMCID: PMC9859539 DOI: 10.3390/genes14010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Fragile X syndrome (FXS) is a global neurodevelopmental disorder caused by the expansion of CGG trinucleotide repeats (≥200) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. FXS is the hallmark of Fragile X-associated disorders (FXD) and the most common monogenic cause of inherited intellectual disability and autism spectrum disorder. There are several animal models used to study FXS. In the FXS model of Drosophila, the only ortholog of FMR1, dfmr1, is mutated so that its protein is missing. This model has several relevant phenotypes, including defects in the circadian output pathway, sleep problems, memory deficits in the conditioned courtship and olfactory conditioning paradigms, deficits in social interaction, and deficits in neuronal development. In addition to FXS, a model of another FXD, Fragile X-associated tremor/ataxia syndrome (FXTAS), has also been established in Drosophila. This review summarizes many years of research on FXD in Drosophila models.
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Affiliation(s)
- Jelena Trajković
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Vedrana Makevic
- Department of Pathophysiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Milica Pesic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Sara Milojevic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Smiljana Cvjetkovic
- Department of Humanities, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Randi Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50th Street, Sacramento, CA 95817, USA
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA 95817, USA
| | - Dejan B. Budimirovic
- Department of Psychiatry, Fragile X Clinic, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences-Child Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dragana Protic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence:
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8
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In vitro production of infectious Plasmodium falciparum sporozoites. Nature 2022; 612:534-539. [PMID: 36477528 DOI: 10.1038/s41586-022-05466-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
An effective vaccine is needed for the prevention and elimination of malaria. The only immunogens that have been shown to have a protective efficacy of more than 90% against human malaria are Plasmodium falciparum (Pf) sporozoites (PfSPZ) manufactured in mosquitoes (mPfSPZ)1-7. The ability to produce PfSPZ in vitro (iPfSPZ) without mosquitoes would substantially enhance the production of PfSPZ vaccines and mosquito-stage malaria research, but this ability is lacking. Here we report the production of hundreds of millions of iPfSPZ. iPfSPZ invaded human hepatocytes in culture and developed to mature liver-stage schizonts expressing P. falciparum merozoite surface protein 1 (PfMSP1) in numbers comparable to mPfSPZ. When injected into FRGhuHep mice containing humanized livers, iPfSPZ invaded the human hepatocytes and developed to PfMSP1-expressing late liver stage parasites at 45% the quantity of cryopreserved mPfSPZ. Human blood from FRGhuHep mice infected with iPfSPZ produced asexual and sexual erythrocytic-stage parasites in culture, and gametocytes developed to PfSPZ when fed to mosquitoes, completing the P. falciparum life cycle from infectious gametocyte to infectious gametocyte without mosquitoes or primates.
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9
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Huda A, Omelchenko AA, Vaden TJ, Castaneda AN, Ni L. Responses of different Drosophila species to temperature changes. J Exp Biol 2022; 225:275567. [PMID: 35481475 DOI: 10.1242/jeb.243708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022]
Abstract
Temperature is a critical environmental variable that affects the distribution, survival, and reproduction of most animals. Although temperature receptors have been identified in many animals, how these receptors respond to temperature is still unclear. Here, we describe an automated tracking method for studying the thermotactic behaviors of Drosophila larvae and adults. We build optimal experimental setups to capture behavioral recordings and analyze them using free software, Fiji and TrackMate, which do not require programming knowledge. Then, the adult thermotactic two-choice assay is applied to examine the movement and temperature preferences of nine Drosophila species. The ability or inclination to move varies among these species and at different temperatures. Distinct species prefer various ranges of temperatures. Wild-type D. melanogaster flies avoid the warmer temperature in the warm avoidance assay and the cooler temperature in the cool avoidance assay. Conversely, D. bipectinata and D. yakuba do not avoid warm or cool temperatures in the respective assays, and D. biarmipes and D. mojavensis do not avoid the warm temperature in the warm avoidance assay. These results demonstrate that Drosophila species have different mobilities and temperature preferences, which will benefit further research in exploring molecular mechanisms of temperature responsiveness.
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Affiliation(s)
- Ainul Huda
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Alisa A Omelchenko
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Thomas J Vaden
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Allison N Castaneda
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Lina Ni
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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10
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Ho CH, Paolantoni C, Bawankar P, Tang Z, Brown S, Roignant J, Treisman JE. An exon junction complex-independent function of Barentsz in neuromuscular synapse growth. EMBO Rep 2022; 23:e53231. [PMID: 34726300 PMCID: PMC8728599 DOI: 10.15252/embr.202153231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
The exon junction complex controls the translation, degradation, and localization of spliced mRNAs, and three of its core subunits also play a role in splicing. Here, we show that a fourth subunit, Barentsz, has distinct functions within and separate from the exon junction complex in Drosophila neuromuscular development. The distribution of mitochondria in larval muscles requires Barentsz as well as other exon junction complex subunits and is not rescued by a Barentsz transgene in which residues required for binding to the core subunit eIF4AIII are mutated. In contrast, interactions with the exon junction complex are not required for Barentsz to promote the growth of neuromuscular synapses. We find that the Activin ligand Dawdle shows reduced expression in barentsz mutants and acts downstream of Barentsz to control synapse growth. Both barentsz and dawdle are required in motor neurons, muscles, and glia for normal synapse growth, and exogenous Dawdle can rescue synapse growth in the absence of barentsz. These results identify a biological function for Barentsz that is independent of the exon junction complex.
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Affiliation(s)
- Cheuk Hei Ho
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Praveen Bawankar
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Zuojian Tang
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
Computational Biology at Ridgefield US, Global Computational Biology and Digital ScienceBoehringer IngelheimRidgefieldCTUSA
| | - Stuart Brown
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
ExxonMobil Corporate Strategic ResearchAnnandaleNJUSA
| | - Jean‐Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Jessica E Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
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11
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Diagnostic Yield of Targeted Hearing Loss Gene Panel Sequencing in a Large German Cohort With a Balanced Age Distribution from a Single Diagnostic Center: An Eight-year Study. Ear Hear 2021; 43:1049-1066. [PMID: 34753855 PMCID: PMC9007094 DOI: 10.1097/aud.0000000000001159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objectives: Hereditary hearing loss exhibits high degrees of genetic and clinical heterogeneity. To elucidate the population-specific and age-related genetic and clinical spectra of hereditary hearing loss, we investigated the sequencing data of causally associated hearing loss genes in a large cohort of hearing-impaired probands with a balanced age distribution from a single center in Southwest Germany. Design: Genetic testing was applied to 305 hearing-impaired probands/families with a suspected genetic hearing loss etiology and a balanced age distribution over a period of 8 years (2011–2018). These individuals were representative of the regional population according to age and sex distributions. The genetic testing workflow consisted of single-gene screening (n = 21) and custom-designed hearing loss gene panel sequencing (n = 284) targeting known nonsyndromic and syndromic hearing loss genes in a diagnostic setup. Retrospective reanalysis of sequencing data was conducted by applying the current American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. Results: A genetic diagnosis was established for 75 (25%) of the probands that involved 75 causal variants in 35 genes, including 16 novel causal variants and 9 medically significant variant reclassifications. Nearly half of the solved cases (47%; n = 35) were related to variants in the five most frequently affected genes: GJB2 (25%), MYO15A, WFS1, SLC26A4, and COL11A1 (all 5%). Nearly one-quarter of the cases (23%; n = 17) were associated with variants in seven additional genes (TMPRSS3, COL4A3, LOXHD1, EDNRB, MYO6, TECTA, and USH2A). The remaining one-third of single cases (33%; n = 25) were linked to variants in 25 distinct genes. Diagnostic rates and gene distribution were highly dependent on phenotypic characteristics. A positive family history of autosomal-recessive inheritance in combination with early onset and higher grades of hearing loss significantly increased the solve rate up to 60%, while late onset and lower grades of hearing loss yielded significantly fewer diagnoses. Regarding genetic diagnoses, autosomal-dominant genes accounted for 37%, autosomal-recessive genes for 60%, and X-linked genes for 3% of the solved cases. Syndromic/nonsyndromic hearing loss mimic genes were affected in 27% of the genetic diagnoses. Conclusions: The genetic epidemiology of the largest German cohort subjected to comprehensive targeted sequencing for hereditary hearing loss to date revealed broad causal gene and variant spectra in this population. Targeted hearing loss gene panel analysis proved to be an effective tool for ensuring an appropriate diagnostic yield in a routine clinical setting including the identification of novel variants and medically significant reclassifications. Solve rates were highly sensitive to phenotypic characteristics. The unique population-adapted and balanced age distribution of the cohort favoring late hearing loss onset uncovered a markedly large contribution of autosomal-dominant genes to the diagnoses which may be a representative for other age balanced cohorts in other populations.
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12
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Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila. Genome Res 2021; 31:2069-2079. [PMID: 34675069 PMCID: PMC8559708 DOI: 10.1101/gr.275503.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022]
Abstract
Dosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda, in which both the neo-Y and the neo-X are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that emerged independently in D. albomicans and D. americana and reanalyzed neo-sex chromosome evolution in D. miranda. Comparative genomic and transcriptomic analyses revealed that the pseudogenization rate on the neo-X is also accelerated in D. albomicans and D. americana although to a lesser extent than in D. miranda. In males, neo-X-linked genes whose neo-Y-linked homologs are pseudogenized tended to be up-regulated more than those whose neo-Y-linked homologs remain functional. Moreover, genes under strong functional constraint and genes highly expressed in the testis tended to remain functional on the neo-X and neo-Y, respectively. Focusing on the D. miranda and D. albomicans neo-sex chromosomes that emerged independently from the same autosome, we further found that the same genes tend to become pseudogenized in parallel on the neo-Y. These genes include Idgf6 and JhI-26, which may be unnecessary or even harmful in males. Our results indicate that neo-sex chromosomes in Drosophila share a common evolutionary trajectory after their emergence, which may prevent sex chromosomes from being an evolutionary dead end.
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Jang S, Lee J, Mathews J, Ruess H, Williford AO, Rangan P, Betrán E, Buszczak M. The Drosophila ribosome protein S5 paralog RpS5b promotes germ cell and follicle cell differentiation during oogenesis. Development 2021; 148:272089. [PMID: 34495316 DOI: 10.1242/dev.199511] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/01/2021] [Indexed: 01/15/2023]
Abstract
Emerging evidence suggests that ribosome heterogeneity may have important functional consequences in the translation of specific mRNAs within different cell types and under various conditions. Ribosome heterogeneity comes in many forms, including post-translational modification of ribosome proteins (RPs), absence of specific RPs and inclusion of different RP paralogs. The Drosophila genome encodes two RpS5 paralogs: RpS5a and RpS5b. While RpS5a is ubiquitously expressed, RpS5b exhibits enriched expression in the reproductive system. Deletion of RpS5b results in female sterility marked by developmental arrest of egg chambers at stages 7-8, disruption of vitellogenesis and posterior follicle cell (PFC) hyperplasia. While transgenic rescue experiments suggest functional redundancy between RpS5a and RpS5b, molecular, biochemical and ribo-seq experiments indicate that RpS5b mutants display increased rRNA transcription and RP production, accompanied by increased protein synthesis. Loss of RpS5b results in microtubule-based defects and in mislocalization of Delta and Mindbomb1, leading to failure of Notch pathway activation in PFCs. Together, our results indicate that germ cell-specific expression of RpS5b promotes proper egg chamber development by ensuring the homeostasis of functional ribosomes.
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Affiliation(s)
- Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeon Lee
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy Mathews
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Holly Ruess
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anna O Williford
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Prashanth Rangan
- RNA Institute, Department of Biological Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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14
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Ullastres A, Merenciano M, González J. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biol 2021; 22:265. [PMID: 34521452 PMCID: PMC8439047 DOI: 10.1186/s13059-021-02471-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02471-3.
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Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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15
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Whole Genome Sequences of 23 Species from the Drosophila montium Species Group (Diptera: Drosophilidae): A Resource for Testing Evolutionary Hypotheses. G3-GENES GENOMES GENETICS 2020; 10:1443-1455. [PMID: 32220952 PMCID: PMC7202002 DOI: 10.1534/g3.119.400959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is well-positioned for clade genomics. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the montium group and D. melanogaster is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the montium group range from 155 Mb to 223 Mb (mean = 196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min = 18 kb, max = 390 kb, mean = 74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5-15%. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96% of known single-copy Dipteran genes (BUSCOs, n = 2,799). Similarly, by aligning our assemblies to the D. melanogaster genome and remapping coordinates for a large set of transcriptional enhancers (n = 3,457), we showed that each montium assembly contains orthologs for at least 91% of D. melanogaster enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous Drosophila assemblies. The alignment of our own D. serrata assembly to a previously published PacBio D. serrata assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis-regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.
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16
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Liu G, Xuan N, Rajashekar B, Arnaud P, Offmann B, Picimbon JF. Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions. Genes (Basel) 2020; 11:genes11040413. [PMID: 32290210 PMCID: PMC7230875 DOI: 10.3390/genes11040413] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/29/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
In this review we present the developmental, histological, evolutionary and functional properties of insect chemosensory proteins (CSPs) in insect species. CSPs are small globular proteins folded like a prism and notoriously known for their complex and arguably obscure function(s), particularly in pheromone olfaction. Here, we focus on direct functional consequences on protein function depending on duplication, expression and RNA editing. The result of our analysis is important for understanding the significance of RNA-editing on functionality of CSP genes, particularly in the brain tissue.
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Affiliation(s)
- Guoxia Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (G.L.); (N.X.)
| | - Ning Xuan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (G.L.); (N.X.)
| | - Balaji Rajashekar
- Institute of Computer Science, University of Tartu, Tartu 50090, Estonia;
| | - Philippe Arnaud
- Protein Engineering and Functionality Unit, University of Nantes, 44322 Nantes, France; (P.A.); (B.O.)
| | - Bernard Offmann
- Protein Engineering and Functionality Unit, University of Nantes, 44322 Nantes, France; (P.A.); (B.O.)
| | - Jean-François Picimbon
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (G.L.); (N.X.)
- School of Bioengineering, Qilu University of Technology, Jinan 250353, China
- Correspondence: ; Tel.: +86-531-89631190
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17
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Paula DP, Menger J, Andow DA, Koch RL. Diverse patterns of constitutive and inducible overexpression of detoxifying enzyme genes among resistant Aphis glycines populations. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:100-114. [PMID: 32284115 DOI: 10.1016/j.pestbp.2019.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 06/11/2023]
Abstract
Understanding the mechanisms of pyrethroid resistance is essential to the effective management of pesticide resistance in Aphis glycines Matsumura (Hemiptera: Aphididae). We mined putative detoxifying enzyme genes in the draft genome sequence of A. glycines for cytochrome oxidase P450 (CYP), glutathione-S-transferase (GST) and esterases (E4 and carboxylesterases-CES). Aphids from clonal populations resistant to pyrethroids from three sites in Minnesota, USA, were screened against a diagnostic LC99 concentration of either λ-cyhalothrin or bifenthrin and detoxifying enzyme genes expression in survivors was analyzed by qPCR. Their expression profiles were compared relative to a susceptible clonal population. We found 61 CYP (40 full-length), seven GST (all full-length), seven E4 (five full-length) and three CES (two full-length) genes, including 24 possible pseudogenes. The detoxifying enzymes had different expression profiles across resistant aphid populations, possibly reflecting differences in the genetic background and pyrethroid selection pressures as the number of constitutively overexpressed detoxifying enzyme genes was correlated with the level of resistance. Our findings will strengthen the understanding of the pyrethroid resistance mechanisms in A. glycines.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF 70770-917, Brazil.
| | - James Menger
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - David A Andow
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - Robert L Koch
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
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18
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Fabrizio JJ, Rollins J, Bazinet CW, Wegener S, Koziy I, Daniel R, Lombardo V, Pryce D, Bharrat K, Innabi E, Villanobos M, Mendoza G, Ferrara E, Rodway S, Vicioso M, Siracusa V, Dailey E, Pronovost J, Innabi S, Patel V, DeSouza N, Quaranto D, Niknejad A. Tubulin-binding cofactor E-like (TBCEL), the protein product of the mulet gene, is required in the germline for the regulation of inter-flagellar microtubule dynamics during spermatid individualization. Biol Open 2020; 9:bio049080. [PMID: 32033965 PMCID: PMC7055396 DOI: 10.1242/bio.049080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/22/2020] [Indexed: 11/14/2022] Open
Abstract
Individual sperm cells are resolved from a syncytium during late step of spermiogenesis known as individualization, which is accomplished by an Individualization Complex (IC) composed of 64 investment cones. mulet encodes Tubulin-binding cofactor E-like (TBCEL), suggesting a role for microtubule dynamics in individualization. Indeed, a population of ∼100 cytoplasmic microtubules fails to disappear in mulet mutant testes during spermatogenesis. This persistence, detected using epi-fluorescence and electron microscopy, suggests that removal of these microtubules by TBCEL is a prerequisite for individualization. Immunofluorescence reveals TBCEL expression in elongated spermatid cysts. In addition, testes from mulet mutant males were rescued to wild type using tubulin-Gal4 to drive TBCEL expression, indicating that the mutant phenotype is caused by the lack of TBCEL. Finally, RNAi driven by bam-GAL4 successfully phenocopied mulet, confirming that mulet is required in the germline for individualization. We propose a model in which the cytoplasmic microtubules serve as alternate tracks for investment cones in mulet mutant testes.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- James J Fabrizio
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Janet Rollins
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | | | - Stephanie Wegener
- Leibniz Institute for Neurobiology Magdeburg, Department Genetics of Learning and Memory, 39118 Magdeburg, Germany
| | - Iryna Koziy
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Rachel Daniel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vincent Lombardo
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Dwaine Pryce
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Kavita Bharrat
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elissa Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Marielle Villanobos
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Gabriela Mendoza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elisa Ferrara
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Stephanie Rodway
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Matthew Vicioso
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Victoria Siracusa
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Erin Dailey
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Justin Pronovost
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Simon Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vrutant Patel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Nicole DeSouza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Danielle Quaranto
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Amir Niknejad
- Department of Mathematics, College of Mt St Vincent, Bronx, NY 10471, USA
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19
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Liu J, Wu H, Yi J, Zhang G. Two gustatory receptors are necessary for sensing sucrose in an egg parasitoid, Trichogramma chilonis. CHEMOECOLOGY 2020. [DOI: 10.1007/s00049-020-00301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
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Affiliation(s)
- F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - X Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - C Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Y Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Z Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - J R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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21
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Brenner D, Yilmaz R, Müller K, Grehl T, Petri S, Meyer T, Grosskreutz J, Weydt P, Ruf W, Neuwirth C, Weber M, Pinto S, Claeys KG, Schrank B, Jordan B, Knehr A, Günther K, Hübers A, Zeller D, Kubisch C, Jablonka S, Sendtner M, Klopstock T, de Carvalho M, Sperfeld A, Borck G, Volk AE, Dorst J, Weis J, Otto M, Schuster J, Del Tredici K, Braak H, Danzer KM, Freischmidt A, Meitinger T, Strom TM, Ludolph AC, Andersen PM, Weishaupt JH. Hot-spot KIF5A mutations cause familial ALS. Brain 2019; 141:688-697. [PMID: 29342275 PMCID: PMC5837483 DOI: 10.1093/brain/awx370] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022] Open
Abstract
Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis. Using whole exome sequencing followed by rare variant analysis of 426 patients with familial amyotrophic lateral sclerosis and 6137 control subjects, we detected an enrichment of KIF5A splice-site mutations in amyotrophic lateral sclerosis (2/426 compared to 0/6137 in controls; P = 4.2 × 10−3), both located in a hot-spot in the C-terminus of the protein and predicted to affect splicing exon 27. We additionally show co-segregation with amyotrophic lateral sclerosis of two canonical splice-site mutations in two families. Investigation of lymphoblast cell lines from patients with KIF5A splice-site mutations revealed the loss of mutant RNA expression and suggested haploinsufficiency as the most probable underlying molecular mechanism. Furthermore, mRNA sequencing of a rare non-synonymous missense mutation (predicting p.Arg1007Gly) located in the C-terminus of the protein shortly upstream of the splice donor of exon 27 revealed defective KIF5A pre-mRNA splicing in respective patient-derived cell lines owing to abrogation of the donor site. Finally, the non-synonymous single nucleotide variant rs113247976 (minor allele frequency = 1.00% in controls, n = 6137), also located in the C-terminal region [p.(Pro986Leu) in exon 26], was significantly enriched in familial amyotrophic lateral sclerosis patients (minor allele frequency = 3.40%; P = 1.28 × 10−7). Our study demonstrates that mutations located specifically in a C-terminal hotspot of KIF5A can cause a classical amyotrophic lateral sclerosis phenotype, and underline the involvement of intracellular transport processes in amyotrophic lateral sclerosis pathogenesis.
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Affiliation(s)
| | | | | | - Torsten Grehl
- Department of Neurology, Alfried Krupp Hospital, Essen, Germany
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Thomas Meyer
- Charité University Hospital, Humboldt-University, Berlin, Germany
| | | | - Patrick Weydt
- Neurology Department, Ulm University, Ulm, Germany.,Department for Neurodegenerative Disorders and Gerontopsychiatry, Bonn University, Bonn, Germany
| | - Wolfgang Ruf
- Neurology Department, Ulm University, Ulm, Germany
| | - Christoph Neuwirth
- Kantonsspital St. Gallen, ALS Outpatient Clinic, St. Gallen, Switzerland
| | - Markus Weber
- Kantonsspital St. Gallen, ALS Outpatient Clinic, St. Gallen, Switzerland
| | - Susana Pinto
- Department of Neurosciences and Mental Health, Hospital de Santa Maria-CHLN, Lisbon, Portugal.,Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - Kristl G Claeys
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany.,Department of Neurology, RWTH Aachen University Hospital, Aachen, Germany.,Department of Neurology, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, Experimental Neurology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Berthold Schrank
- Department of Neurology, DKD HELIOS Klinik Wiesbaden, Wiesbaden, Germany
| | - Berit Jordan
- Department of Neurology Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Antje Knehr
- Neurology Department, Ulm University, Ulm, Germany
| | | | | | - Daniel Zeller
- Department of Neurology, University of Würzburg, Würzburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, Ulm University, Ulm, Germany.,Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, Germany
| | - Thomas Klopstock
- Department of Neurology with Friedrich-Baur-Institute, University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Mamede de Carvalho
- Department of Neurosciences and Mental Health, Hospital de Santa Maria-CHLN, Lisbon, Portugal.,Instituto de Medicina Molecular and Institute of Physiology, Faculty of Medicine, University of Lisbon, Portugal
| | - Anne Sperfeld
- Department of Neurology Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Alexander E Volk
- Institute of Human Genetics, Ulm University, Ulm, Germany.,Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Markus Otto
- Neurology Department, Ulm University, Ulm, Germany
| | | | | | - Heiko Braak
- Neurology Department, Ulm University, Ulm, Germany
| | | | | | - Thomas Meitinger
- SyNergy, Munich Cluster for Systems Neurology, Ludwig Maximilians Universität München, Germany.,Institute of Human Genetics, Technische Universität München, München, Germany
| | - Tim M Strom
- SyNergy, Munich Cluster for Systems Neurology, Ludwig Maximilians Universität München, Germany.,Institute of Human Genetics, Technische Universität München, München, Germany
| | | | - Peter M Andersen
- Neurology Department, Ulm University, Ulm, Germany.,Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
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22
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Korhonen PK, Hall RS, Young ND, Gasser RB. Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data. Gigascience 2019; 8:giz014. [PMID: 30821816 PMCID: PMC6451199 DOI: 10.1093/gigascience/giz014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/03/2018] [Accepted: 01/25/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. FINDINGS We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. CONCLUSIONS This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.
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Affiliation(s)
- Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross S Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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23
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Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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24
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Miao H, Sun P, Liu J, Wang J, Xu B, Jin Z. Overexpression of a Novel ROP Gene from the Banana ( MaROP5g) Confers Increased Salt Stress Tolerance. Int J Mol Sci 2018; 19:ijms19103108. [PMID: 30314273 PMCID: PMC6213407 DOI: 10.3390/ijms19103108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022] Open
Abstract
Rho-like GTPases from plants (ROPs) are plant-specific molecular switches that are crucial for plant survival when subjected to abiotic stress. We identified and characterized 17 novel ROP proteins from Musa acuminata (MaROPs) using genomic techniques. The identified MaROPs fell into three of the four previously described ROP groups (Groups II⁻IV), with MaROPs in each group having similar genetic structures and conserved motifs. Our transcriptomic analysis showed that the two banana genotypes tested, Fen Jiao and BaXi Jiao, had similar responses to abiotic stress: Six genes (MaROP-3b, -5a, -5c, -5f, -5g, and -6) were highly expressed in response to cold, salt, and drought stress conditions in both genotypes. Of these, MaROP5g was most highly expressed in response to salt stress. Co-localization experiments showed that the MaROP5g protein was localized at the plasma membrane. When subjected to salt stress, transgenic Arabidopsis thaliana overexpressing MaROP5g had longer primary roots and increased survival rates compared to wild-type A. thaliana. The increased salt tolerance conferred by MaROP5g might be related to reduced membrane injury and the increased cytosolic K⁺/Na⁺ ratio and Ca2+ concentration in the transgenic plants as compared to wild-type. The increased expression of salt overly sensitive (SOS)-pathway genes and calcium-signaling pathway genes in MaROP5g-overexpressing A. thaliana reflected the enhanced tolerance to salt stress by the transgenic lines in comparison to wild-type. Collectively, our results suggested that abiotic stress tolerance in banana plants might be regulated by multiple MaROPs, and that MaROP5g might enhance salt tolerance by increasing root length, improving membrane injury and ion distribution.
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Affiliation(s)
- Hongxia Miao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Peiguang Sun
- Key Laboratory of Genetic Improvement of Bananas, Hainan Province, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 570102, China.
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Jingyi Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
- Key Laboratory of Genetic Improvement of Bananas, Hainan Province, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 570102, China.
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25
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An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons. Genes (Basel) 2018; 9:genes9070356. [PMID: 30018239 PMCID: PMC6071210 DOI: 10.3390/genes9070356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing is a commonly-used mechanism of diversifying gene products. Mutually exclusive exons (MXE) represent a particular type of alternative splicing, in which one and only one exon from an array is included in the mature RNA. A number of genes with MXE do so by using a mechanism that depends on RNA structure. Transcripts of these genes contain multiple sites called selector sequences that are all complementary to a regulatory element called the docking site; only one of the competing base pairings can form at a time, which exposes one exon from the cluster to the spliceosome. MXE tend to have similar lengths and sequence content and are believed to originate through tandem genomic duplications. Here, we report that pre-mRNAs of this class of exons have an increased capacity to fold into competing secondary structures. We propose an evolutionary mechanism for the generation of such structures via duplications that affect not only exons, but also their adjacent introns with stem-loop structures. If one of the two arms of a stem-loop is duplicated, it will generate two selector sequences that compete for the same docking site, a pattern that is associated with MXE splicing. A similar partial duplication of two independent stem-loops produces a pattern that is consistent with the so-called bidirectional pairing model. These models explain why tandem exon duplications frequently result in mutually exclusive splicing.
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26
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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27
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Tvedte ES, Forbes AA, Logsdon JM. Retention of Core Meiotic Genes Across Diverse Hymenoptera. J Hered 2018; 108:791-806. [PMID: 28992199 DOI: 10.1093/jhered/esx062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.
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Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA 52242
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28
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Morrison CA, Chen H, Cook T, Brown S, Treisman JE. Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye. PLoS Genet 2018; 14:e1007173. [PMID: 29324767 PMCID: PMC5783423 DOI: 10.1371/journal.pgen.1007173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/24/2018] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye.
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Affiliation(s)
- Carolyn A. Morrison
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Hao Chen
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Tiffany Cook
- Center of Molecular Medicine and Genomics and Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Stuart Brown
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Jessica E. Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
- * E-mail:
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29
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Yablonovitch AL, Fu J, Li K, Mahato S, Kang L, Rashkovetsky E, Korol AB, Tang H, Michalak P, Zelhof AC, Nevo E, Li JB. Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates. Nat Commun 2017; 8:1570. [PMID: 29146998 PMCID: PMC5691062 DOI: 10.1038/s41467-017-01658-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/05/2017] [Indexed: 12/30/2022] Open
Abstract
Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from 'Evolution Canyon' in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels. We also demonstrate that while temperature affects editing levels at more sites than genetic differences, genetically regulated sites tend to be less affected by temperature. This work shows the extent to which gene expression and RNA editing differ between flies from different microclimates, and provides insights into the regulation responsible for these differences.
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Affiliation(s)
- Arielle L Yablonovitch
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Jeremy Fu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kexin Li
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Simpla Mahato
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
| | | | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24060, USA
| | - Andrew C Zelhof
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Biophysics Program, Stanford University, Stanford, CA, 94305, USA.
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30
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Castillejo-López C, Cai X, Fahmy K, Baumgartner S. Drosophila exoribonuclease nibbler is a tumor suppressor, acts within the RNA i machinery and is not enriched in the nuage during early oogenesis. Hereditas 2017; 155:12. [PMID: 28974923 PMCID: PMC5622571 DOI: 10.1186/s41065-017-0047-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023] Open
Abstract
Background micro RNAs (miRNAs) are important regulators of many biological pathways. A plethora of steps are required to form, from a precursor, the mature miRNA that eventually acts on its target RNA to repress its expression or to inhibit translation. Recently, Drosophila nibbler (nbr) has been shown to be an important player in the maturation process of miRNA and piRNA. Nbr is an exoribonuclease which helps to shape the 3′ end of miRNAs by trimming the 3′ overhang to a final length. Results In contrast to previous reports on the localization of Nbr, we report that 1) Nbr is expressed only during a short time of oogenesis and appears ubiquitously localized within oocytes, and that 2) Nbr was is not enriched in the nuage where it was shown to be involved in piwi-mediated mechanisms. To date, there is little information available on the function of nbr for cellular and developmental processes. Due to the fact that nbr mutants are viable with minor deleterious effects, we used the GAL4/UAS over-expression system to define novel functions of nbr. We disclose hitherto unknown functions of nbr 1) as a tumor suppressor and 2) as a suppressor of RNAi. Finally, we confirm that nbr is a suppressor of transposon activity. Conclusions Our data suggest that nbr exerts much more widespread functions than previously reported from trimming 3′ ends of miRNAs only.
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Affiliation(s)
- Casimiro Castillejo-López
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden.,Present address: Department of Molecular Epidemiology, Uppsala University, 75185 Uppsala, Sweden
| | - Xiaoli Cai
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden
| | - Khalid Fahmy
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden.,Present address: Department of Genetics, Ain Shams University, Cairo, Egypt
| | - Stefan Baumgartner
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden
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Silencing of Repetitive DNA Is Controlled by a Member of an Unusual Caenorhabditis elegans Gene Family. Genetics 2017; 207:529-545. [PMID: 28801529 DOI: 10.1534/genetics.117.300134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/10/2017] [Indexed: 01/08/2023] Open
Abstract
Repetitive DNA sequences are subject to gene silencing in various animal species. Under specific circumstances repetitive DNA sequences can escape such silencing. For example, exogenously added, extrachromosomal DNA sequences that are stably inherited in multicopy repetitive arrays in the nematode Caenorhabditis elegans are frequently silenced in the germline, whereas such silencing often does not occur in the soma. This indicates that somatic cells might utilize factors that prevent repetitive DNA silencing. Indeed, such "antisilencing" factors have been revealed through genetic screens that identified mutant loci in which repetitive transgenic arrays are aberrantly silenced in the soma. We describe here a novel locus, pals-22 (for protein containing ALS2CR12 signature), required to prevent silencing of repetitive transgenes in neurons and other somatic tissue types. pals-22 deficiency also severely impacts animal vigor and confers phenotypes reminiscent of accelerated aging. We find that pals-22 is a member of a large family of divergent genes (39 members), defined by homology to the ALS2CR12 protein family. While gene family members are highly divergent, they show striking patterns of chromosomal clustering. The family expansion appears C. elegans-specific and has not occurred to the same extent in other nematode species for which genome sequences are available. The transgene-silencing phenotype observed upon loss of PALS-22 protein depends on the biogenesis of small RNAs. We speculate that the pals gene family may be part of a species-specific cellular defense mechanism.
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32
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Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw163. [PMID: 28077566 PMCID: PMC5225397 DOI: 10.1093/database/baw163] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
Abstract
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC—a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases. Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w
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Affiliation(s)
- Qingyu Chen
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
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33
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Abstract
Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly's tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism's natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.
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34
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Rius N, Guillén Y, Delprat A, Kapusta A, Feschotte C, Ruiz A. Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. BMC Genomics 2016; 17:344. [PMID: 27164953 PMCID: PMC4862133 DOI: 10.1186/s12864-016-2648-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis. Results We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes. Conclusions TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2648-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nuria Rius
- Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | - Yolanda Guillén
- Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alejandra Delprat
- Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alfredo Ruiz
- Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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35
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Huang L, Xiao X, Li S, Jia X, Wang P, Sun W, Xu Y, Xin W, Guo X, Zhang Q. Molecular genetics of cone-rod dystrophy in Chinese patients: New data from 61 probands and mutation overview of 163 probands. Exp Eye Res 2016; 146:252-258. [DOI: 10.1016/j.exer.2016.03.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/27/2015] [Accepted: 03/14/2016] [Indexed: 01/17/2023]
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36
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Gurdziel K, Lorberbaum DS, Udager AM, Song JY, Richards N, Parker DS, Johnson LA, Allen BL, Barolo S, Gumucio DL. Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density. PLoS One 2015; 10:e0145225. [PMID: 26710299 PMCID: PMC4692483 DOI: 10.1371/journal.pone.0145225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/01/2015] [Indexed: 01/20/2023] Open
Abstract
The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci.
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Affiliation(s)
- Katherine Gurdziel
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- Department of Computational Medicine and Bioinformatics, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - David S. Lorberbaum
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- Cellular and Molecular Biology Program, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Aaron M. Udager
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jane Y. Song
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- Cellular and Molecular Biology Program, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Neil Richards
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - David S. Parker
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lisa A. Johnson
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Benjamin L. Allen
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- * E-mail: (DLG); (SB); (BLA)
| | - Scott Barolo
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- * E-mail: (DLG); (SB); (BLA)
| | - Deborah L. Gumucio
- Department of Cell and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, United States of America
- * E-mail: (DLG); (SB); (BLA)
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37
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Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing. Genet Med 2015; 18:823-32. [PMID: 26681312 PMCID: PMC4985612 DOI: 10.1038/gim.2015.166] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022] Open
Abstract
Purpose: Germ-line testing for panels of cancer genes using next-generation sequencing is becoming more common in clinical care. We report our experience as a clinical laboratory testing both well-established, high-risk cancer genes (e.g., BRCA1/2, MLH1, MSH2) as well as more recently identified cancer genes (e.g., PALB2, BRIP1), many of which have increased but less well-defined penetrance. Genet Med18 8, 823–832. Methods: Clinical genetic testing was performed on over 10,000 consecutive cases referred for evaluation of germ-line cancer genes, and results were analyzed for frequency of pathogenic or likely pathogenic variants, and were stratified by testing panel, gene, and clinical history. Genet Med18 8, 823–832. Results: Overall, a molecular diagnosis was made in 9.0% of patients tested, with the highest yield in the Lynch syndrome/colorectal cancer panel. In patients with breast, ovarian, or colon/stomach cancer, positive yields were 9.7, 13.4, and 14.8%, respectively. Approximately half of the pathogenic variants identified in patients with breast or ovarian cancer were in genes other than BRCA1/2. Genet Med18 8, 823–832. Conclusion: The high frequency of positive results in a wide range of cancer genes, including those of high penetrance and with clinical care guidelines, underscores both the genetic heterogeneity of hereditary cancer and the usefulness of multigene panels over genetic tests of one or two genes. Genet Med18 8, 823–832.
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Aflitos SA, Severing E, Sanchez-Perez G, Peters S, de Jong H, de Ridder D. Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. BMC Bioinformatics 2015; 16:352. [PMID: 26525298 PMCID: PMC4630969 DOI: 10.1186/s12859-015-0806-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/29/2015] [Indexed: 12/05/2022] Open
Abstract
Background Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. Results We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100 % identification accuracy at supra-species level and 78 % accuracy at the species level. Conclusion CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design). Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0806-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saulo Alves Aflitos
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. .,Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
| | - Edouard Severing
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
| | - Gabino Sanchez-Perez
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. .,Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
| | - Sander Peters
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
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39
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Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle. G3-GENES GENOMES GENETICS 2015; 5:2843-56. [PMID: 26497146 PMCID: PMC4683655 DOI: 10.1534/g3.115.021931] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Symbiotic interactions between microbes and their multicellular hosts have manifold biological consequences. To better understand how bacteria maintain symbiotic associations with animal hosts, we analyzed genome-wide gene expression for the endosymbiotic α-proteobacteria Wolbachia pipientis across the entire life cycle of Drosophila melanogaster. We found that the majority of Wolbachia genes are expressed stably across the D. melanogaster life cycle, but that 7.8% of Wolbachia genes exhibit robust stage- or sex-specific expression differences when studied in the whole-organism context. Differentially-expressed Wolbachia genes are typically up-regulated after Drosophila embryogenesis and include many bacterial membrane, secretion system, and ankyrin repeat-containing proteins. Sex-biased genes are often organized as small operons of uncharacterized genes and are mainly up-regulated in adult Drosophila males in an age-dependent manner. We also systematically investigated expression levels of previously-reported candidate genes thought to be involved in host-microbe interaction, including those in the WO-A and WO-B prophages and in the Octomom region, which has been implicated in regulating bacterial titer and pathogenicity. Our work provides comprehensive insight into the developmental dynamics of gene expression for a widespread endosymbiont in its natural host context, and shows that public gene expression data harbor rich resources to probe the functional basis of the Wolbachia-Drosophila symbiosis and annotate the transcriptional outputs of the Wolbachia genome.
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40
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Hasanagic M, van Meel E, Luan S, Aurora R, Kornfeld S, Eissenberg JC. The lysosomal enzyme receptor protein (LERP) is not essential, but is implicated in lysosomal function in Drosophila melanogaster. Biol Open 2015; 4:1316-25. [PMID: 26405051 PMCID: PMC4610224 DOI: 10.1242/bio.013334] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/20/2015] [Indexed: 12/12/2022] Open
Abstract
The lysosomal enzyme receptor protein (LERP) of Drosophila melanogaster is the ortholog of the mammalian cation-independent mannose 6-phosphate (Man 6-P) receptor, which mediates trafficking of newly synthesized lysosomal acid hydrolases to lysosomes. However, flies lack the enzymes necessary to make the Man 6-P mark, and the amino acids implicated in Man 6-P binding by the mammalian receptor are not conserved in LERP. Thus, the function of LERP in sorting of lysosomal enzymes to lysosomes in Drosophila is unclear. Here, we analyze the consequence of LERP depletion in S2 cells and intact flies. RNAi-mediated knockdown of LERP in S2 cells had little or no effect on the cellular content or secretion of several lysosomal hydrolases. We generated a novel Lerp null mutation, Lerp(F6), which abolishes LERP protein expression. Lerp mutants have normal viability and fertility and display no overt phenotypes other than reduced body weight. Lerp mutant flies exhibit a 30-40% decrease in the level of several lysosomal hydrolases, and are hypersensitive to dietary chloroquine and starvation, consistent with impaired lysosome function. Loss of LERP also enhances an eye phenotype associated with defective autophagy. Our findings implicate Lerp in lysosome function and autophagy.
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Affiliation(s)
- Medina Hasanagic
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Eline van Meel
- Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shan Luan
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Rajeev Aurora
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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41
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Abstract
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.
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42
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Carl SH, Russell S. Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. BMC Genomics 2015; 16:292. [PMID: 25887553 PMCID: PMC4419465 DOI: 10.1186/s12864-015-1495-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/27/2015] [Indexed: 01/08/2023] Open
Abstract
Background Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. Results We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. Conclusion We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1495-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah H Carl
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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43
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Evolution of herbivory in Drosophilidae linked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet. Proc Natl Acad Sci U S A 2015; 112:3026-31. [PMID: 25624509 DOI: 10.1073/pnas.1424656112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Herbivory is a key innovation in insects, yet has only evolved in one-third of living orders. The evolution of herbivory likely involves major behavioral changes mediated by remodeling of canonical chemosensory modules. Herbivorous flies in the genus Scaptomyza (Drosophilidae) are compelling species in which to study the genomic architecture linked to the transition to herbivory because they recently evolved from microbe-feeding ancestors and are closely related to Drosophila melanogaster. We found that Scaptomyza flava, a leaf-mining specialist on plants in the family (Brassicaceae), was not attracted to yeast volatiles in a four-field olfactometer assay, whereas D. melanogaster was strongly attracted to these volatiles. Yeast-associated volatiles, especially short-chain aliphatic esters, elicited strong antennal responses in D. melanogaster, but weak antennal responses in electroantennographic recordings from S. flava. We sequenced the genome of S. flava and characterized this species' odorant receptor repertoire. Orthologs of odorant receptors, which detect yeast volatiles in D. melanogaster and mediate critical host-choice behavior, were deleted or pseudogenized in the genome of S. flava. These genes were lost step-wise during the evolution of Scaptomyza. Additionally, Scaptomyza has experienced gene duplication and likely positive selection in paralogs of Or67b in D. melanogaster. Olfactory sensory neurons expressing Or67b are sensitive to green-leaf volatiles. Major trophic shifts in insects are associated with chemoreceptor gene loss as recently evolved ecologies shape sensory repertoires.
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44
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Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 2015; 25:445-58. [PMID: 25589440 PMCID: PMC4352887 DOI: 10.1101/gr.185579.114] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Drosophila melanogaster plays an important role in molecular,
genetic, and genomic studies of heredity, development, metabolism, behavior, and
human disease. The initial reference genome sequence reported more than a decade ago
had a profound impact on progress in Drosophila research, and
improving the accuracy and completeness of this sequence continues to be important to
further progress. We previously described improvement of the 117-Mb sequence in the
euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a
whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here,
we report an improved reference sequence of the single-copy and middle-repetitive
regions of the genome, produced using cytogenetic mapping to mitotic and polytene
chromosomes, clone-based finishing and BAC fingerprint verification, ordering of
scaffolds by alignment to cDNA sequences, incorporation of other map and sequence
data, and validation by whole-genome optical restriction mapping. These data
substantially improve the accuracy and completeness of the reference sequence and the
order and orientation of sequence scaffolds into chromosome arm assemblies.
Representation of the Y chromosome and other heterochromatic regions
is particularly improved. The new 143.9-Mb reference sequence, designated Release 6,
effectively exhausts clone-based technologies for mapping and sequencing. Highly
repeat-rich regions, including large satellite blocks and functional elements such as
the ribosomal RNA genes and the centromeres, are largely inaccessible to current
sequencing and assembly methods and remain poorly represented. Further significant
improvements will require sequencing technologies that do not depend on molecular
cloning and that produce very long reads.
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Affiliation(s)
- Roger A Hoskins
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
| | - Joseph W Carlson
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H Wan
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Soo Park
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ivonne Mendez
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel E Galle
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Benjamin W Booth
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Barret D Pfeiffer
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Reed A George
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Robert Svirskas
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Jacqueline Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Maria Carmela Accardo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Elisabetta Damia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - María Méndez-Lago
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Beatriz de Pablos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Olga V Demakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - A Bernardo Carvalho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, CEP 21944-970, Rio de Janeiro, Brazil
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Gerald M Rubin
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Gary H Karpen
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Susan E Celniker
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
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45
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Figueiredo MLA, Kim M, Philip P, Allgardsson A, Stenberg P, Larsson J. Non-coding roX RNAs prevent the binding of the MSL-complex to heterochromatic regions. PLoS Genet 2014; 10:e1004865. [PMID: 25501352 PMCID: PMC4263465 DOI: 10.1371/journal.pgen.1004865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/30/2014] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs contribute to dosage compensation in both mammals and Drosophila by inducing changes in the chromatin structure of the X-chromosome. In Drosophila melanogaster, roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increasing its transcriptional output. Studies on polytene chromosomes have demonstrated that when both roX1 and roX2 are absent, the MSL-complex becomes less abundant on the male X-chromosome and is relocated to the chromocenter and the 4th chromosome. Here we address the role of roX RNAs in MSL-complex targeting and the evolution of dosage compensation in Drosophila. We performed ChIP-seq experiments which showed that MSL-complex recruitment to high affinity sites (HAS) on the X-chromosome is independent of roX and that the HAS sequence motif is conserved in D. simulans. Additionally, a complete and enzymatically active MSL-complex is recruited to six specific genes on the 4th chromosome. Interestingly, our sequence analysis showed that in the absence of roX RNAs, the MSL-complex has an affinity for regions enriched in Hoppel transposable elements and repeats in general. We hypothesize that roX mutants reveal the ancient targeting of the MSL-complex and propose that the role of roX RNAs is to prevent the binding of the MSL-complex to heterochromatin. In both fruit flies and humans, males and females have different sets of sex chromosomes. This generates differences in gene dosage that must be compensated for by adjusting the transcriptional output of most genes located on the X-chromosome. The specific recognition and targeting of the X-chromosome is essential for such dosage compensation. In fruit flies, dosage compensation is mediated by the male-specific lethal (MSL) complex, which upregulates gene transcription on the male X-chromosome. The MSL-complex consists of five proteins and two non-coding RNAs, roX1 and roX2. While non-coding RNAs are known to be critical for dosage compensation in both flies and mammals, their precise functions remain elusive. Here we present a study on the targeting and function of the MSL-complex in the absence of roX RNAs. The results obtained suggest that the dosage compensating MSL-complex has an intrinsic tendency to target repeat-rich regions and that the function of roX RNAs is to prevent its binding to such targets. Our findings reveal an ancient targeting and regulatory function of the MSL-complex that has been adapted for use in dosage compensation and modified by the rapidly evolving noncoding roX RNAs.
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Affiliation(s)
| | - Maria Kim
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Philge Philip
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | | | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Jan Larsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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46
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Lowe N, Rees JS, Roote J, Ryder E, Armean IM, Johnson G, Drummond E, Spriggs H, Drummond J, Magbanua JP, Naylor H, Sanson B, Bastock R, Huelsmann S, Trovisco V, Landgraf M, Knowles-Barley S, Armstrong JD, White-Cooper H, Hansen C, Phillips RG, Lilley KS, Russell S, St Johnston D. Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Development 2014; 141:3994-4005. [PMID: 25294943 PMCID: PMC4197710 DOI: 10.1242/dev.111054] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures.
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Affiliation(s)
- Nick Lowe
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Johanna S Rees
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - John Roote
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ed Ryder
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Irina M Armean
- The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Glynnis Johnson
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Emma Drummond
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Helen Spriggs
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jenny Drummond
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jose P Magbanua
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Huw Naylor
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Bénédicte Sanson
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Rebecca Bastock
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sven Huelsmann
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Vitor Trovisco
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Matthias Landgraf
- The Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Seymour Knowles-Barley
- Institute for Adaptive and Neural Computation, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - J Douglas Armstrong
- Institute for Adaptive and Neural Computation, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - Helen White-Cooper
- Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Celia Hansen
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Roger G Phillips
- Centre for Advanced Microscopy, University of Sussex, School of Life Sciences, John Maynard Smith Building, Falmer, Brighton and Hove BN1 9QG, UK
| | | | - Kathryn S Lilley
- The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Steven Russell
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Daniel St Johnston
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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47
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Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DEA, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data 2014; 1:140045. [PMID: 25977796 PMCID: PMC4365909 DOI: 10.1038/sdata.2014.45] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/03/2014] [Indexed: 12/22/2022] Open
Abstract
Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.
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Affiliation(s)
- Kristi E Kim
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Paul Peluso
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Primo Babayan
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - P. Jane Yeadon
- Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, South Australia 5001, Australia
| | - Charles Yu
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - William W Fisher
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Chen-Shan Chin
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Nicole A Rapicavoli
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - David R Rank
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Joachim Li
- Department of Microbiology and Immunology, UCSF, San Francisco, California 94158, USA
| | - David E. A Catcheside
- Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, South Australia 5001, Australia
| | - Susan E Celniker
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Adam M Phillippy
- National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jane M Landolin
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
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48
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dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM. FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res 2014; 43:D690-7. [PMID: 25398896 PMCID: PMC4383921 DOI: 10.1093/nar/gku1099] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.
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Affiliation(s)
- Gilberto dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Andrew J Schroeder
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - David B Emmert
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - William M Gelbart
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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49
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Zhu CT, Chang C, Reenan RA, Helfand SL. Indy gene variation in natural populations confers fitness advantage and life span extension through transposon insertion. Aging (Albany NY) 2014; 6:58-69. [PMID: 24519859 PMCID: PMC3927810 DOI: 10.18632/aging.100634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Natural selection acts to maximize reproductive fitness. However, antagonism between life span and reproductive success frequently poses a dilemma pitting the cost of fecundity against longevity. Here, we show that natural populations of Drosophila melanogaster harbor a Hoppel transposon insertion variant in the longevity gene Indy (I'm not dead yet), which confers both increased reproduction and longevity through metabolic changes. Heterozygosity for this natural long-lived variant has been maintained in isolates despite long-term inbreeding under laboratory conditions and advantageously confers increased fecundity. DNA sequences of variant chromosome isolates show evidence of selective sweep acting on the advantageous allele, suggesting that natural selection acts to maintain this variant. The transposon insertion also regulates Indy expression level, which has experimentally been shown to affect life span and fecundity. Thus, in the wild, evolution reaffirms that the mechanism of heterozygote advantage has acted upon the Indy gene to assure increased reproductive fitness and, coincidentally, longer life span through regulatory transposon mutagenesis.
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Affiliation(s)
- Chen-Tseh Zhu
- Department of Molecular Biology, Cell Biology and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912
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50
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McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One 2014; 9:e106689. [PMID: 25188499 PMCID: PMC4154752 DOI: 10.1371/journal.pone.0106689] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 07/24/2014] [Indexed: 11/18/2022] Open
Abstract
High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or complex genomic arrangements. While TEs strongly affect genome function and evolution, most current de novo assembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly-parallel library preparation and local assembly of short read data and which achieve lengths of 1.5–18.5 Kbp with an extremely low error rate (0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organism Drosophila melanogaster (reference genome strain y; cn, bw, sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long-reads, offer a powerful approach to improve de novo assemblies of whole genomes.
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Affiliation(s)
- Rajiv C. McCoy
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Ryan W. Taylor
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael Kertesz
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Dmitry Pushkarev
- Department of Physics, Stanford University, Stanford, California, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Anna-Sophie Fiston-Lavier
- Department of Biology, Stanford University, Stanford, California, United States of America
- Institut des Sciences de l'Evolution-Montpellier, Montpellier, France
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