101
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Schmeitzl C, Varga E, Warth B, Kugler KG, Malachová A, Michlmayr H, Wiesenberger G, Mayer KFX, Mewes HW, Krska R, Schuhmacher R, Berthiller F, Adam G. Identification and Characterization of Carboxylesterases from Brachypodium distachyon Deacetylating Trichothecene Mycotoxins. Toxins (Basel) 2015; 8:E6. [PMID: 26712789 PMCID: PMC4728528 DOI: 10.3390/toxins8010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/03/2022] Open
Abstract
Increasing frequencies of 3-acetyl-deoxynivalenol (3-ADON)-producing strains of Fusarium graminearum (3-ADON chemotype) have been reported in North America and Asia. 3-ADON is nearly nontoxic at the level of the ribosomal target and has to be deacetylated to cause inhibition of protein biosynthesis. Plant cells can efficiently remove the acetyl groups of 3-ADON, but the underlying genes are yet unknown. We therefore performed a study of the family of candidate carboxylesterases (CXE) genes of the monocot model plant Brachypodium distachyon. We report the identification and characterization of the first plant enzymes responsible for deacetylation of trichothecene toxins. The product of the BdCXE29 gene efficiently deacetylates T-2 toxin to HT-2 toxin, NX-2 to NX-3, both 3-ADON and 15-acetyl-deoxynivalenol (15-ADON) into deoxynivalenol and, to a lesser degree, also fusarenon X into nivalenol. The BdCXE52 esterase showed lower activity than BdCXE29 when expressed in yeast and accepts 3-ADON, NX-2, 15-ADON and, to a limited extent, fusarenon X as substrates. Expression of these Brachypodium genes in yeast increases the toxicity of 3-ADON, suggesting that highly similar genes existing in crop plants may act as susceptibility factors in Fusarium head blight disease.
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Affiliation(s)
- Clemens Schmeitzl
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria.
| | - Elisabeth Varga
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Christian Doppler Laboratory for Mycotoxin Metabolism, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Benedikt Warth
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Karl G Kugler
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Alexandra Malachová
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Christian Doppler Laboratory for Mycotoxin Metabolism, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Herbert Michlmayr
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria.
| | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria.
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Hans-Werner Mewes
- Genome oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Germany.
| | - Rudolf Krska
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Franz Berthiller
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Christian Doppler Laboratory for Mycotoxin Metabolism, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria.
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102
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Sakai H, Naito K, Ogiso-Tanaka E, Takahashi Y, Iseki K, Muto C, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Itoh T, Kaga A, Tomooka N. The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome. Sci Rep 2015; 5:16780. [PMID: 26616024 PMCID: PMC4663752 DOI: 10.1038/srep16780] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 10/19/2015] [Indexed: 12/30/2022] Open
Abstract
Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.
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Affiliation(s)
- Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Ken Naito
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Eri Ogiso-Tanaka
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yu Takahashi
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kohtaro Iseki
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Chiaki Muto
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Akito Kaga
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
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103
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Spannagl M, Nussbaumer T, Bader KC, Martis MM, Seidel M, Kugler KG, Gundlach H, Mayer KFX. PGSB PlantsDB: updates to the database framework for comparative plant genome research. Nucleic Acids Res 2015; 44:D1141-7. [PMID: 26527721 PMCID: PMC4702821 DOI: 10.1093/nar/gkv1130] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/15/2015] [Indexed: 01/29/2023] Open
Abstract
PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).
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Affiliation(s)
- Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thomas Nussbaumer
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Kai C Bader
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Mihaela M Martis
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany BILS (Bioinformatics Infrastructure for Life Sciences), Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, SE-558185 Linköping, Sweden
| | - Michael Seidel
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Karl G Kugler
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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104
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Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KFX, Messing J. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 2015; 5:3311. [PMID: 24548928 PMCID: PMC3948053 DOI: 10.1038/ncomms4311] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/24/2014] [Indexed: 11/30/2022] Open
Abstract
The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications. Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.
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Affiliation(s)
- W Wang
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - G Haberer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - H Gundlach
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - C Gläßer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - T Nussbaumer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - M C Luo
- Department of Plant Sciences, University of California, 265 Hunt Hall, One Shields Avenue, Davis, California 95616, USA
| | - A Lomsadze
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - M Borodovsky
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - R A Kerstetter
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - J Shanklin
- Brookhaven National Laboratory, 50 Bell Ave, Upton, New York 11973, USA
| | - D W Byrant
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - T C Mockler
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - K J Appenroth
- Department of Plant Physiology, University of Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - J Grimwood
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Chow
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Choi
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Adam
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - X-H Cao
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - J Fuchs
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - I Schubert
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - D Rokhsar
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - J Schmutz
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - T P Michael
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - K F X Mayer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - J Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
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105
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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106
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How to Isolate a Plant's Hypomethylome in One Shot. BIOMED RESEARCH INTERNATIONAL 2015; 2015:570568. [PMID: 26421293 PMCID: PMC4573423 DOI: 10.1155/2015/570568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 11/17/2022]
Abstract
Genome assembly remains a challenge for large and/or complex plant genomes due to their abundant repetitive regions resulting in studies focusing on gene space instead of the whole genome. Thus, DNA enrichment strategies facilitate the assembly by increasing the coverage and simultaneously reducing the complexity of the whole genome. In this paper we provide an easy, fast, and cost-effective variant of MRE-seq to obtain a plant's hypomethylome by an optimized methyl filtration protocol followed by next generation sequencing. The method is demonstrated on three plant species with knowingly large and/or complex (polyploid) genomes: Oryza sativa, Picea abies, and Crocus sativus. The identified hypomethylomes show clear enrichment for genes and their flanking regions and clear reduction of transposable elements. Additionally, genomic sequences around genes are captured including regulatory elements in introns and up- and downstream flanks. High similarity of the results obtained by a de novo assembly approach with a reference based mapping in rice supports the applicability for studying and understanding the genomes of nonmodel organisms. Hence we show the high potential of MRE-seq in a wide range of scenarios for the direct analysis of methylation differences, for example, between ecotypes, individuals, within or across species harbouring large, and complex genomes.
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107
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Akpinar BA, Lucas SJ, Vrána J, Doležel J, Budak H. Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). PLANT BIOTECHNOLOGY JOURNAL 2015; 13:740-52. [PMID: 25516153 DOI: 10.1111/pbi.12302] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/08/2014] [Accepted: 10/25/2014] [Indexed: 05/11/2023]
Abstract
Flow cytometric sorting of individual chromosomes and chromosome-based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow-sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNA(L) (ys) and tRNA(M) (et) species, while the nonrepetitive assembly reveals tRNA(A) (la) species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome-specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome-level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor.
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Affiliation(s)
- Bala A Akpinar
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Stuart J Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Tuzla, Istanbul, Turkey
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Tuzla, Istanbul, Turkey
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108
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El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA. A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Res 2015; 43:e84. [PMID: 25813049 PMCID: PMC4513842 DOI: 10.1093/nar/gkv257] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/10/2015] [Accepted: 03/15/2015] [Indexed: 12/31/2022] Open
Abstract
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.
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Affiliation(s)
- Moaine El Baidouri
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Siwaret Arikit
- Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Olivier Panaud
- Université de Perpignan Via Domitia. Laboratoire Génome et Développement des Plantes. UMR5096 CNRS/UPVD., 52, avenue Paul Alduy. 66860 Perpignan Cedex, France
| | - Blake C Meyers
- Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
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109
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Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 2015. [PMID: 26206304 DOI: 10.1093/bioinformatics/btv422] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses. RESULTS Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. AVAILABILITY AND IMPLEMENTATION The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. CONTACT mhammell@cshl.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ying Jin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Eric Paniagua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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110
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Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci Rep 2015; 5:10763. [PMID: 26084265 PMCID: PMC4471722 DOI: 10.1038/srep10763] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.
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111
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Alter S, Bader KC, Spannagl M, Wang Y, Bauer E, Schön CC, Mayer KFX. DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav046. [PMID: 25979979 PMCID: PMC4433318 DOI: 10.1093/database/bav046] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/21/2015] [Indexed: 02/01/2023]
Abstract
Plants are sessile and therefore exposed to a number of biotic and abiotic stresses. Drought is the major abiotic stress restricting plant growth worldwide. A number of genes involved in drought stress response have already been characterized, mainly in the model species Arabidopsis thaliana and Oryza sativa. However, with the aim to produce drought tolerant crop varieties, it is of importance to identify the respective orthologs for each species. We have developed DroughtDB, a manually curated compilation of molecularly characterized genes that are involved in drought stress response. DroughtDB includes information about the originally identified gene, its physiological and/or molecular function and mutant phenotypes and provides detailed information about computed orthologous genes in nine model and crop plant species including maize and barley. All identified orthologs are interlinked with the respective reference entry in MIPS/PGSB PlantsDB, which allows retrieval of additional information like genome context and sequence information. Thus, DroughtDB is a valuable resource and information tool for researchers working on drought stress and will facilitate the identification, analysis and characterization of genes involved in drought stress tolerance in agriculturally important crop plants. Database URL:http://pgsb.helmholtz-muenchen.de/droughtdb/
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Affiliation(s)
- Svenja Alter
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Kai C Bader
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Manuel Spannagl
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Yu Wang
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Eva Bauer
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Chris-Carolin Schön
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Klaus F X Mayer
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany, Department of Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany and College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
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112
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Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 2015; 33:531-7. [PMID: 25893781 DOI: 10.1038/nbt.3207] [Citation(s) in RCA: 1019] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/15/2015] [Indexed: 02/06/2023]
Abstract
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
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113
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Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KFX, Asp T. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation. BMC Genomics 2015; 16:249. [PMID: 25886302 PMCID: PMC4389671 DOI: 10.1186/s12864-015-1447-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/06/2015] [Indexed: 01/18/2023] Open
Abstract
Background The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity. Results We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species. Conclusions Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is likely that the knowledge of the genomes will be largely transferable between species within the complex. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrian Czaban
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
| | - Sapna Sharma
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Stephen L Byrne
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
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114
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Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement. GENETICS RESEARCH INTERNATIONAL 2015; 2015:684321. [PMID: 25874133 PMCID: PMC4383144 DOI: 10.1155/2015/684321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/14/2014] [Accepted: 11/03/2014] [Indexed: 11/18/2022]
Abstract
The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.
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115
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Mun JH, Chung H, Chung WH, Oh M, Jeong YM, Kim N, Ahn BO, Park BS, Park S, Lim KB, Hwang YJ, Yu HJ. Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:259-272. [PMID: 25403353 DOI: 10.1007/s00122-014-2426-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.
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Affiliation(s)
- Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea
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116
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Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M. LAILAPS: the plant science search engine. PLANT & CELL PHYSIOLOGY 2015; 56:e8. [PMID: 25480116 PMCID: PMC4301746 DOI: 10.1093/pcp/pcu185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley.
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Affiliation(s)
- Maria Esch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Jinbo Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Matthias Klapperstück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Eva Grafahrend-Belau
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
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Nussbaumer T, Kugler KG, Schweiger W, Bader KC, Gundlach H, Spannagl M, Poursarebani N, Pfeifer M, Mayer KFX. chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. BMC PLANT BIOLOGY 2014; 14:348. [PMID: 25491094 PMCID: PMC4266971 DOI: 10.1186/s12870-014-0348-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner. DESCRIPTION We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering. CONCLUSIONS This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.
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Affiliation(s)
- Thomas Nussbaumer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Karl G Kugler
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Wolfgang Schweiger
- />Institute for Biotechnology in Plant Production, IFA-Tulln, University of
Natural Resources and Life Sciences, A-3430 Tulln, Austria
| | - Kai C Bader
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Heidrun Gundlach
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Manuel Spannagl
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Naser Poursarebani
- />Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Matthias Pfeifer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Klaus FX Mayer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
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118
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Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics 2014; 41:627-47. [DOI: 10.1016/j.jgg.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/16/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023]
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119
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014; 15:R78. [PMID: 24917130 PMCID: PMC4073093 DOI: 10.1186/gb-2014-15-6-r78] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/10/2014] [Indexed: 01/02/2023] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014. [PMID: 24917130 DOI: 10.1186/gb‐2014‐15‐6‐r78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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121
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Numa H, Itoh T. MEGANTE: a web-based system for integrated plant genome annotation. PLANT & CELL PHYSIOLOGY 2014; 55:e2. [PMID: 24253915 PMCID: PMC3894707 DOI: 10.1093/pcp/pct157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/.
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Affiliation(s)
| | - Takeshi Itoh
- *Corresponding author: E-mail, ; Fax, +81-29-838-7065
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122
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Tanaka T, Sakai H, Fujii N, Kobayashi F, Nakamura S, Itoh T, Matsumoto T, Wu J. bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes. BREEDING SCIENCE 2013; 63:430-434. [PMID: 24399916 PMCID: PMC3859355 DOI: 10.1270/jsbbs.63.430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/14/2013] [Indexed: 06/03/2023]
Abstract
Barley (Hordeum vulgare) is one of the world's most important cereal crops. Although its large and complex genome has held back barley genomics for quite a while, the whole genome sequence was released in 2012 by the International Barley Genome Sequencing Consortium (IBSC). Moreover, more than 30,000 barley full-length cDNAs (FLcDNAs) are now available in the public domain. Here we present the Barley Gene Expression Database (bex-db: http://barleyflc.dna.affrc.go.jp/bexdb/index.html) as a repository of transcriptome data including the sequences and the expression profiles of barley genes resulting from microarray analysis. In addition to FLcDNA sequences, bex-db also contains partial sequences of more than 309,000 novel expressed sequence tags (ESTs). Users can browse the data via keyword, sequence homology and expression profile search options. A genome browser was also developed to display the chromosomal locations of barley FLcDNAs and wheat (Triticum aestivum) transcripts as well as Aegilops tauschii gene models on the IBSC genome sequence for future comparative analysis of orthologs among Triticeae species. The bex-db should provide a useful resource for further genomics studies and development of genome-based tools to enhance the progress of the genetic improvement of cereal crops.
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Affiliation(s)
- Tsuyoshi Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Nobuyuki Fujii
- Bioinformatics Solution Group, Hitachi Government & Public Corporation System Engineering, Ltd.,
2-4-18 Toyo, Koto, Tokyo 135-8633,
Japan
| | - Fuminori Kobayashi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shingo Nakamura
- Wheat and Barley Research Division, National Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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123
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Narsai R, Devenish J, Castleden I, Narsai K, Xu L, Shou H, Whelan J. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:1057-73. [PMID: 24147765 PMCID: PMC4253041 DOI: 10.1111/tpj.12357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 05/04/2023]
Abstract
Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - James Devenish
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Ian Castleden
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Kabir Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Lin Xu
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang UniversityHangzhou, 310058, China
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
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124
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Tanaka T, Kobayashi F, Joshi GP, Onuki R, Sakai H, Kanamori H, Wu J, Simkova H, Nasuda S, Endo TR, Hayakawa K, Doležel J, Ogihara Y, Itoh T, Matsumoto T, Handa H. Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res 2013; 21:103-14. [PMID: 24086083 PMCID: PMC3989483 DOI: 10.1093/dnares/dst041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Common wheat (Triticum aestivum L.) is one of the most important cereals in the world. To improve wheat quality and productivity, the genomic sequence of wheat must be determined. The large genome size (∼17 Gb/1 C) and the hexaploid status of wheat have hampered the genome sequencing of wheat. However, flow sorting of individual chromosomes has allowed us to purify and separately shotgun-sequence a pair of telocentric chromosomes. Here, we describe a result from the survey sequencing of wheat chromosome 6B (914 Mb/1 C) using massively parallel 454 pyrosequencing. From the 4.94 and 5.51 Gb shotgun sequence data from the two chromosome arms of 6BS and 6BL, 235 and 273 Mb sequences were assembled to cover ∼55.6 and 54.9% of the total genomic regions, respectively. Repetitive sequences composed 77 and 86% of the assembled sequences on 6BS and 6BL, respectively. Within the assembled sequences, we predicted a total of 4798 non-repetitive gene loci with the evidence of expression from the wheat transcriptome data. The numbers and chromosomal distribution patterns of the genes for tRNAs and microRNAs in wheat 6B were investigated, and the results suggested a significant involvement of DNA transposon diffusion in the evolution of these non-protein-coding RNA genes. A comparative analysis of the genomic sequences of wheat 6B and monocot plants clearly indicated the evolutionary conservation of gene contents.
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Affiliation(s)
- Tsuyoshi Tanaka
- 1Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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Martis MM, Zhou R, Haseneyer G, Schmutzer T, Vrána J, Kubaláková M, König S, Kugler KG, Scholz U, Hackauf B, Korzun V, Schön CC, Doležel J, Bauer E, Mayer KF, Stein N. Reticulate evolution of the rye genome. THE PLANT CELL 2013; 25:3685-98. [PMID: 24104565 PMCID: PMC3877785 DOI: 10.1105/tpc.113.114553] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/23/2013] [Accepted: 09/20/2013] [Indexed: 05/18/2023]
Abstract
Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.
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Affiliation(s)
- Mihaela M. Martis
- Helmholtz Center Munich, German Research Centre for Environmental Health, Munich Information Center for Protein Sequences/IBIS, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany
| | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland (OT) Gatersleben, Germany
| | - Grit Haseneyer
- Technische Universität München, Centre of Life and Food Sciences Weihenstephan, Plant Breeding, 85354 Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland (OT) Gatersleben, Germany
| | - Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-783 71 Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-783 71 Olomouc, Czech Republic
| | - Susanne König
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland (OT) Gatersleben, Germany
| | - Karl G. Kugler
- Helmholtz Center Munich, German Research Centre for Environmental Health, Munich Information Center for Protein Sequences/IBIS, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland (OT) Gatersleben, Germany
| | - Bernd Hackauf
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, 18190 Sanitz, Germany
| | | | - Chris-Carolin Schön
- Technische Universität München, Centre of Life and Food Sciences Weihenstephan, Plant Breeding, 85354 Freising, Germany
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-783 71 Olomouc, Czech Republic
| | - Eva Bauer
- Technische Universität München, Centre of Life and Food Sciences Weihenstephan, Plant Breeding, 85354 Freising, Germany
| | - Klaus F.X. Mayer
- Helmholtz Center Munich, German Research Centre for Environmental Health, Munich Information Center for Protein Sequences/IBIS, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland (OT) Gatersleben, Germany
- Address correspondence to
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126
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Martinez M. From plant genomes to protein families: computational tools. Comput Struct Biotechnol J 2013; 8:e201307001. [PMID: 24688740 PMCID: PMC3962197 DOI: 10.5936/csbj.201307001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 01/28/2023] Open
Abstract
The development of new high-throughput sequencing technologies has increased dramatically the number of successful genomic projects. Thus, draft genomic sequences of more than 60 plant species are currently available. Suitable bioinformatics tools are being developed to assemble, annotate and analyze the enormous number of sequences produced. In this context, specific plant comparative genomic databases are become powerful tools for gene family annotation in plant clades. In this mini-review, the current state-of-art of genomic projects is glossed. Besides, the computational tools developed to compare genomic data are compiled.
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Affiliation(s)
- Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus Montegancedo, Universidad Politécnica de Madrid, Autovía M40 (Km 38), 28223-Pozuelo de Alarcón, Madrid, Spain
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