5
|
Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Bonn S, Kollmar M. The landscape of human mutually exclusive splicing. Mol Syst Biol 2017; 13:959. [PMID: 29242366 PMCID: PMC5740500 DOI: 10.15252/msb.20177728] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.
Collapse
Affiliation(s)
- Klas Hatje
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Raza-Ur Rahman
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ramon O Vidal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science Georg-August-University, Göttingen, Germany
| | - Björn Hammesfahr
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vikas Bansal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ashish Rajput
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Michel Edwar Mickael
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ting Sun
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany .,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
6
|
Reinert K, Dadi TH, Ehrhardt M, Hauswedell H, Mehringer S, Rahn R, Kim J, Pockrandt C, Winkler J, Siragusa E, Urgese G, Weese D. The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. J Biotechnol 2017; 261:157-168. [PMID: 28888961 DOI: 10.1016/j.jbiotec.2017.07.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. We previously addressed this by introducing the SeqAn library of efficient data types and algorithms in 2008 (Döring et al., 2008). RESULTS The SeqAn library has matured considerably since its first publication 9 years ago. In this article we review its status as an established resource for programmers in the field of sequence analysis and its contributions to many analysis tools. CONCLUSIONS We anticipate that SeqAn will continue to be a valuable resource, especially since it started to actively support various hardware acceleration techniques in a systematic manner.
Collapse
Affiliation(s)
- Knut Reinert
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany.
| | - Temesgen Hailemariam Dadi
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - Marcel Ehrhardt
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - Hannes Hauswedell
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - Svenja Mehringer
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - René Rahn
- Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - Jongkyu Kim
- Efficient Algorithms for -Omics Data, Max Planck Institute for Molecular Genetics, Ihnestrasse 62-73, 14195 Berlin, Germany
| | - Christopher Pockrandt
- Efficient Algorithms for -Omics Data, Max Planck Institute for Molecular Genetics, Ihnestrasse 62-73, 14195 Berlin, Germany
| | - Jörg Winkler
- Efficient Algorithms for -Omics Data, Max Planck Institute for Molecular Genetics, Ihnestrasse 62-73, 14195 Berlin, Germany
| | | | - Gianvito Urgese
- Department of Control and Computer Engineering, Politecnico di Torino, Italy
| | | |
Collapse
|
7
|
Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanicolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu NY, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang HJ, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol 2017; 15:63. [PMID: 28756777 PMCID: PMC5535293 DOI: 10.1186/s12915-017-0402-6] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/04/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.
Collapse
Affiliation(s)
- S L Pearce
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - D F Clarke
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - P D East
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - S Elfekih
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - K H J Gordon
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia.
| | - L S Jermiin
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - A McGaughran
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - J G Oakeshott
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia.
| | - A Papanicolaou
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Hawksbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - O P Perera
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS, USA
| | - R V Rane
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - S Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - W T Tay
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - T K Walsh
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - A Anderson
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - C J Anderson
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - S Asgari
- School of Biological Sciences, University of Queensland, Brisbane St Lucia, QLD, Australia
| | - P G Board
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | | | - P M Campbell
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - T Chertemps
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | | | - C W Coppin
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | | | - G Duan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - C A Farnsworth
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - R T Good
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - L B Han
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Y C Han
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - K Hatje
- Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - I Horne
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - Y P Huang
- Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - D S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - E Jacquin-Joly
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - W James
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - S Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - M Kollmar
- Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - S S Kuwar
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - S Li
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - N-Y Liu
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - M T Maibeche
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - J R Miller
- J. Craig Venter Institute, Rockville, MD, USA
| | - N Montagne
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
| | - T Perry
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - J Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - S V Song
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - G G Sutton
- J. Craig Venter Institute, Rockville, MD, USA
| | - H Vogel
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - B P Walenz
- J. Craig Venter Institute, Rockville, MD, USA
| | - W Xu
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - H-J Zhang
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Z Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - P Batterham
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | | | - R Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej, Denmark
| | - R A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - D G Heckel
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - A McGrath
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - C Robin
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - S E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - K C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Y D Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| |
Collapse
|