1
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Zhu C, Lv M, Huang J, Zhang C, Xie L, Gao T, Han B, Wang W, Feng G. Bloodstream infection and pneumonia caused by Chlamydia abortus infection in China: a case report. BMC Infect Dis 2022; 22:181. [PMID: 35197012 PMCID: PMC8867867 DOI: 10.1186/s12879-022-07158-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/15/2022] [Indexed: 11/29/2022] Open
Abstract
Background Chlamydia abortus is generally considered to cause abortion, stillbirth, and gestational sepsis in pregnant women, but it’s rare in bloodstream infection and pneumonia. Case presentation We present details of a patient with bloodstream infection and pneumonia caused by Chlamydia abortus. Both blood next-generation sequencing (NGS) and sputum NGS indicate Chlamydia abortus infection. The patient received intravenous infusion of piperacillin sodium and tazobactam sodium (4.5 g/8 h) and moxifloxacin (0.4 g/d) and oral oseltamivir (75 mg/day). Within one month of follow-up, the patient's clinical symptoms were significantly improved, and all laboratory parameters showed no marked abnormality. However, chest computer tomography (CT) showed the inflammation wasn’t completely absorbed. And we are still following up. Conclusions Chlamydia abortus can cause pneumonia in humans. NGS has the particular advantage of quickly and accurately identifying the infection of such rare pathogens. Pneumonia is generally not life-threatening, and has a good prognosis with appropriate treatment. However, Chlamydia infection can lead to serious visceral complications which clinicians should pay attention to.
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Affiliation(s)
- Changjun Zhu
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Minjie Lv
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Jianling Huang
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Changwen Zhang
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Lixu Xie
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Tianming Gao
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Bo Han
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Wenjing Wang
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China.
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2
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Li Y, Zang Y, Wang Y, Jin F, Liu W. Peripheral pulmonary nodule diagnosed as mycobacterium chelonae using electromagnetic navigation bronchoscopy combined with next generation sequencing: a case report. Am J Transl Res 2020; 12:4066-4073. [PMID: 32774760 PMCID: PMC7407723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
We report the case of a 29-year-old female with a 1.1 cm × 1.1 cm solitary nodule adjacent to the pleura in the upper lobe of the right lung that was diagnosed as Mycobacterium chelonae using electromagnetic navigation bronchoscopy combined with next generation sequencing. This diagnostics technology shows great promise in identifying peripheral pulmonary nodules, especially infectious lesions.
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Affiliation(s)
- Yanyan Li
- Department of Respiratory, The Second Affiliated Hospital, The Air Force Military Medical University Xi'an, Shaan Xi, China
| | - Yu Zang
- Department of Respiratory, The Second Affiliated Hospital, The Air Force Military Medical University Xi'an, Shaan Xi, China
| | - Yan Wang
- Department of Respiratory, The Second Affiliated Hospital, The Air Force Military Medical University Xi'an, Shaan Xi, China
| | - Faguang Jin
- Department of Respiratory, The Second Affiliated Hospital, The Air Force Military Medical University Xi'an, Shaan Xi, China
| | - Wei Liu
- Department of Respiratory, The Second Affiliated Hospital, The Air Force Military Medical University Xi'an, Shaan Xi, China
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3
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Second-Generation Sequencing with Deep Reinforcement Learning for Lung Infection Detection. JOURNAL OF HEALTHCARE ENGINEERING 2020; 2020:3264801. [PMID: 32184978 PMCID: PMC7060411 DOI: 10.1155/2020/3264801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
Recently, deep reinforcement learning, associated with medical big data generated and collected from medical Internet of Things, is prospective for computer-aided diagnosis and therapy. In this paper, we focus on the application value of the second-generation sequencing technology in the diagnosis and treatment of pulmonary infectious diseases with the aid of the deep reinforcement learning. Specifically, the rapid, comprehensive, and accurate identification of pathogens is a prerequisite for clinicians to choose timely and targeted treatment. Thus, in this work, we present representative deep reinforcement learning methods that are potential to identify pathogens for lung infection treatment. After that, current status of pathogenic diagnosis of pulmonary infectious diseases and their main characteristics are summarized. Furthermore, we analyze the common types of second-generation sequencing technology, which can be used to diagnose lung infection as well. Finally, we point out the challenges and possible future research directions in integrating deep reinforcement learning with second-generation sequencing technology to diagnose and treat lung infection, which is prospective to accelerate the evolution of smart healthcare with medical Internet of Things and big data.
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4
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Barley Genome Sequencing and Assembly—A First Version Reference Sequence. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-92528-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Thirugnanasambandam PP, Hoang NV, Henry RJ. The Challenge of Analyzing the Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:616. [PMID: 29868072 PMCID: PMC5961476 DOI: 10.3389/fpls.2018.00616] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 05/04/2023]
Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
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Affiliation(s)
- Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Prathima P. Thirugnanasambandam,
| | - Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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6
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Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 2017; 4:170044. [PMID: 28448065 PMCID: PMC5407242 DOI: 10.1038/sdata.2017.44] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022] Open
Abstract
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xiao-Qi Zhang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, South Perth, Western Australia 6151, Australia
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Micha Bayer
- The James Hutton Institute, Dundee DD2 5DA, UK
| | - Daniel Bolser
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alex Hastie
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Saki Chan
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - María Muñoz-Amatriaín
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Steve Wanamaker
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Stefano Grasso
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Jaakko Tanskanen
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Sujie Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Brett Chapman
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yong Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xuan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - John K McCooke
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Cong Tan
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Shuya Yin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gaofeng Zhou
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Jesse A Poland
- Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, Kansas 66506, USA
| | - Matthew I Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | | | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Peter Langridge
- School of Agriculture, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.,Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Paul Kersey
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Matthew D Clark
- Earlham Institute, Norwich NR4 7UH, UK.,School of Environmental Sciences, University of East Anglia, Norwich NR4 7UH, UK
| | - Mario Caccamo
- Earlham Institute, Norwich NR4 7UH, UK.,National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Timothy J Close
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Mats Hansson
- Department of Biology, Lund University, 22362 Lund, Sweden
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ilka Braumann
- Carlsberg Research Laboratory, 1799 Copenhagen, Denmark
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Agriculture and Food, Government of Western Australia, South Perth, Western Australia 6150, Australia.,Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei 434025, China
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK.,School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,School of Plant Biology, University of Western Australia, Crawley 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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7
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Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome. Nature 2017; 544:427-433. [DOI: 10.1038/nature22043] [Citation(s) in RCA: 966] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023]
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8
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Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
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9
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Pulido-Tamayo S, Duitama J, Marchal K. EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. Nucleic Acids Res 2016; 44:W142-6. [PMID: 27105844 PMCID: PMC4987886 DOI: 10.1093/nar/gkw298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/.
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Affiliation(s)
- Sergio Pulido-Tamayo
- Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jorge Duitama
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), 763537 Cali, Colombia
| | - Kathleen Marchal
- Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
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10
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Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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11
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Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:385-394. [PMID: 26332657 DOI: 10.1111/tpj.13006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
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Affiliation(s)
- Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Miroslava Karafiátová
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
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12
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Tavakol E, Okagaki R, Verderio G, Shariati J V, Hussien A, Bilgic H, Scanlon MJ, Todt NR, Close TJ, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer GJ, Rossini L. The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. PLANT PHYSIOLOGY 2015; 168:164-74. [PMID: 25818702 PMCID: PMC4424007 DOI: 10.1104/pp.114.252882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Tillers are vegetative branches that develop from axillary buds located in the leaf axils at the base of many grasses. Genetic manipulation of tillering is a major objective in breeding for improved cereal yields and competition with weeds. Despite this, very little is known about the molecular genetic bases of tiller development in important Triticeae crops such as barley (Hordeum vulgare) and wheat (Triticum aestivum). Recessive mutations at the barley Uniculme4 (Cul4) locus cause reduced tillering, deregulation of the number of axillary buds in an axil, and alterations in leaf proximal-distal patterning. We isolated the Cul4 gene by positional cloning and showed that it encodes a BROAD-COMPLEX, TRAMTRACK, BRIC-À-BRAC-ankyrin protein closely related to Arabidopsis (Arabidopsis thaliana) BLADE-ON-PETIOLE1 (BOP1) and BOP2. Morphological, histological, and in situ RNA expression analyses indicate that Cul4 acts at axil and leaf boundary regions to control axillary bud differentiation as well as the development of the ligule, which separates the distal blade and proximal sheath of the leaf. As, to our knowledge, the first functionally characterized BOP gene in monocots, Cul4 suggests the partial conservation of BOP gene function between dicots and monocots, while phylogenetic analyses highlight distinct evolutionary patterns in the two lineages.
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Affiliation(s)
- Elahe Tavakol
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ron Okagaki
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gabriele Verderio
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Vahid Shariati J
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ahmed Hussien
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Hatice Bilgic
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Mike J Scanlon
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Natalie R Todt
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Timothy J Close
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Arnis Druka
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Robbie Waugh
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Burkhard Steuernagel
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ruvini Ariyadasa
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Axel Himmelbach
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Nils Stein
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gary J Muehlbauer
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Laura Rossini
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
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Abstract
Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.
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Huang X, Peng X, Zhang L, Chen S, Cheng L, Liu G. Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing. BMC Genomics 2014; 15:1126. [PMID: 25516098 PMCID: PMC4320431 DOI: 10.1186/1471-2164-15-1126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 12/03/2014] [Indexed: 12/02/2022] Open
Abstract
Background Sheepgrass (Leymus chinensis) is an important perennial forage grass across the Eurasian Steppe and is adaptable to various environmental conditions, but little is known about its molecular mechanism responding to grazing and BSA deposition. Because it has a large genome, RNA sequencing is expensive and impractical except for the next-generation sequencing (NGS) technology. Results In this study, NGS technology was employed to characterize de novo the transcriptome of sheepgrass after defoliation and grazing treatments and to identify differentially expressed genes (DEGs) responding to grazing and BSA deposition. We assembled more than 47 M high-quality reads into 120,426 contigs from seven sequenced libraries. Based on the assembled transcriptome, we detected 2,002 DEGs responding to BSA deposition during grazing. Enrichment analysis of Gene ontology (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that the effects of grazing and BSA deposition involved more apoptosis and cell oxidative changes compared to defoliation. Analysis of DNA fragments, cell oxidative factors and the lengths of leaf scars after grazing provided physiological and morphological evidence that BSA deposition during grazing alters the oxidative and apoptotic status of cells. Conclusions This research greatly enriches sheepgrass transcriptome resources and grazing-stress-related genes, helping us to better understand the molecular mechanism of grazing in sheepgrass. The grazing-stress-related genes and pathways will be a valuable resource for further gene-phenotype studies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1126) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Shuangyan Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, People's Republic of China.
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Shang A, Liu Y, Wang J, Mo Z, Li G, Mou H. Complete nucleotide sequence of Klebsiella phage P13 and prediction of an EPS depolymerase gene. Virus Genes 2014; 50:118-28. [PMID: 25392088 DOI: 10.1007/s11262-014-1138-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/25/2014] [Indexed: 10/24/2022]
Abstract
The complete genome of Klebsiella phage P13 was sequenced and analyzed. Bacteriophage P13 has a double-stranded linear DNA with a length of 45,976 bp and a G+C content of 51.7 %, which is slightly lower than that of Klebsiella pneumoniae KCTC 2242. The codon biases of phage P13 are very similar to those of SP6-like phages and K. pneumoniae KCTC 2242. Bioinformatics analysis shows that the phage P13 genome has 282 open reading frames (ORFs) that are greater than 100 bp in length, and 50 of these ORFs were identified as predicted genes with an average length of 833 bp. Among these genes, 41 show homology to known proteins in the GenBank database. The functions of the 24 putative proteins were investigated, and 13 of these were found to be highly conserved. According to the homology analysis of the 50 predicted genes and the whole genome, phage P13 is homologous to SP6-like phages. Furthermore, the morphological characteristics of phage P13 suggest that it belongs to the SP6-like viral genus of the Podoviridae subfamily Autographivirinae. Two hypothetical genes encoding an extracellular polysaccharide depolymerase were predicted using PSI-BLAST. This analysis serves as groundwork for further research and application of the enzyme.
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Affiliation(s)
- Anqi Shang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003, Shandong, China
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16
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Kuczyńska A, Mikołajczak K, Ćwiek H. Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E. The barley Frost resistance-H2 locus. Funct Integr Genomics 2014; 14:85-100. [PMID: 24442711 DOI: 10.1007/s10142-014-0360-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Frost resistance-H2 (Fr-H2) is a major QTL affecting freezing tolerance in barley, yet its molecular basis is still not clearly understood. To gain a better insight into the structural characterization of the locus, a high-resolution linkage map developed from the Nure × Tremois cross was initially implemented to map 13 loci which divided the 0.602 cM total genetic distance into ten recombination segments. A PCR-based screening was then applied to identify positive bacterial artificial chromosome (BAC) clones from two genomic libraries of the reference genotype Morex. Twenty-six overlapping BACs from the integrated physical-genetic map were 454 sequenced. Reads assembled in contigs were subsequently ordered, aligned and manually curated in 42 scaffolds. In a total of 1.47 Mbp, 58 protein-coding sequences were identified, 33 of which classified according to similarity with sequences in public databases. As three complete barley C-repeat Binding Factors (HvCBF) genes were newly identified, the locus contained13 full-length HvCBFs, four Related to AP2 Triticeae (RAPT) genes, and at least five CBF pseudogenes. The final overall assembly of Fr-H2 includes more than 90 % of target region: all genes were identified along the locus, and a general survey of Repetitive Elements obtained. We believe that this gold-standard sequence for the Morex Fr-H2 will be a useful genomic tool for structural and evolutionary comparisons with Fr-H2 in winter-hardy cultivars along with Fr-2 of other Triticeae crops.
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Affiliation(s)
- Marianna Pasquariello
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy,
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Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. PLANT PHYSIOLOGY 2014; 164:412-23. [PMID: 24243933 PMCID: PMC3875818 DOI: 10.1104/pp.113.228213] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U. Kmasker--a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet Genome Res 2013; 142:66-78. [PMID: 24335088 DOI: 10.1159/000356460] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Specific localization of large genomic fragments by fluorescence in situ hybridization (FISH) is challenging in large- genome plant species due to the high content of repetitive sequences. We report the automated work flow (Kmasker) for in silico extraction of unique genomic sequences of large genomic fragments suitable for FISH in barley. This method can be widely used for the integration of genetic and cytogenetic maps in plants and other species with large and complex genomes if the probe sequence (e.g. BACs, sequence contigs) and a low coverage (8-fold) of unassembled sequences of the species of interest are available. Kmasker has been made publicly available as a web tool at http://webblast.ipk-gatersleben.de/kmasker.
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Affiliation(s)
- T Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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21
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Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön CC, Bauer E. BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genomics 2013; 14:628. [PMID: 24330545 PMCID: PMC3848877 DOI: 10.1186/1471-2164-14-628] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/31/2023] Open
Abstract
Background Sunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii (Farlow) Berlese & de Toni is one of the major diseases of cultivated sunflower (Helianthus annuus L.). In the search for new sources of downy mildew resistance, the locus PlARG on linkage group 1 (LG1) originating from H. argophyllus is promising since it confers resistance against all known races of the pathogen. However, the mapping resolution in the PlARG region is hampered by significantly suppressed recombination and by limited availability of polymorphic markers. Here we examined a strategy developed for the enrichment of molecular markers linked to this specific genomic region. We combined bulked segregant analysis (BSA) with next-generation sequencing (NGS) and de novo assembly of the sunflower transcriptome for single nucleotide polymorphism (SNP) discovery in a sequence resource combining reads originating from two sunflower species, H. annuus and H. argophyllus. Results A computational pipeline developed for SNP calling and pattern detection identified 219 candidate genes. For a proof of concept, 42 resistance gene-like sequences were subjected to experimental SNP validation. Using a high-resolution mapping population, 12 SNP markers were mapped to LG1. We successfully verified candidate sequences either co-segregating with or closely flanking PlARG. Conclusions This study is the first successful example to improve bulked segregant analysis with de novo transcriptome assembly using next generation sequencing. The BSTA pipeline we developed provides a useful guide for similar studies in other non-model organisms. Our results demonstrate this method is an efficient way to enrich molecular markers and to identify candidate genes in a specific mapping interval.
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Sangwan RS, Tripathi S, Singh J, Narnoliya LK, Sangwan NS. De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene 2013; 525:58-76. [DOI: 10.1016/j.gene.2013.04.057] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/15/2022]
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Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci U S A 2013; 110:13198-203. [PMID: 23878219 DOI: 10.1073/pnas.1221950110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inflorescence architecture of barley (Hordeum vulgare L.) is common among the Triticeae species, which bear one to three single-flowered spikelets at each rachis internode. Triple spikelet meristem is one of the unique features of barley spikes, in which three spikelets (one central and two lateral spikelets) are produced at each rachis internode. Fertility of the lateral spikelets at triple spikelet meristem gives row-type identity to barley spikes. Six-rowed spikes show fertile lateral spikelets and produce increased grain yield per spike, compared with two-rowed spikes with sterile lateral spikelets. Thus, far, two loci governing the row-type phenotype were isolated in barley that include Six-rowed spike1 (Vrs1) and Intermedium-C. In the present study, we isolated Six-rowed spike4 (Vrs4), a barley ortholog of the maize (Zea mays L.) inflorescence architecture gene RAMOSA2 (RA2). Eighteen coding mutations in barley RA2 (HvRA2) were specifically associated with lateral spikelet fertility and loss of spikelet determinacy. Expression analyses through mRNA in situ hybridization and microarray showed that Vrs4 (HvRA2) controls the row-type pathway through Vrs1 (HvHox1), a negative regulator of lateral spikelet fertility in barley. Moreover, Vrs4 may also regulate transcripts of barley SISTER OF RAMOSA3 (HvSRA), a putative trehalose-6-phosphate phosphatase involved in trehalose-6-phosphate homeostasis implicated to control spikelet determinacy. Our expression data illustrated that, although RA2 is conserved among different grass species, its down-stream target genes appear to be modified in barley and possibly other species of tribe Triticeae.
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Chen S, Huang X, Yan X, Liang Y, Wang Y, Li X, Peng X, Ma X, Zhang L, Cai Y, Ma T, Cheng L, Qi D, Zheng H, Yang X, Li X, Liu G. Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe. PLoS One 2013; 8:e67974. [PMID: 23861841 PMCID: PMC3701641 DOI: 10.1371/journal.pone.0067974] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. RESULTS The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. CONCLUSIONS This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.
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Affiliation(s)
- Shuangyan Chen
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- * E-mail: (SC); (XL); (GL)
| | - Xin Huang
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Xueqing Yan
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Ye Liang
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Xiaofeng Li
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
| | - Xingyong Ma
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Lexin Zhang
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Yueyue Cai
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Tian Ma
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
| | - Liqin Cheng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
| | - Dongmei Qi
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaoxia Li
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- Graduate Schoo1 of the Chinese Academy of Sciences, Beijing, P. R. China
- * E-mail: (SC); (XL); (GL)
| | - Gongshe Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, P. R. China
- * E-mail: (SC); (XL); (GL)
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Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G. Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1575-1586. [PMID: 23494394 DOI: 10.1007/s00122-013-2075-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/23/2013] [Indexed: 06/01/2023]
Abstract
The barley Rdg2a locus confers resistance to the leaf stripe pathogen Pyrenophora graminea and, in the barley genotype Thibaut, it is composed of a gene family with three highly similar paralogs. Only one member of the gene family (called as Rdg2a) encoding for a CC-NB-LRR protein is able to confer resistance to the leaf stripe isolate Dg2. To study the genome evolution and diversity at the Rdg2a locus, sequences spanning the Rdg2a gene were compared in two barley cultivars, Thibaut and Morex, respectively, resistant and susceptible to leaf stripe. An overall high level of sequence conservation interrupted by several rearrangements that included three main deletions was observed in the Morex contig. The main deletion of 13,692 bp was most likely derived from unequal crossing over between Rdg2a paralogs leading to the generation of a chimeric Morex rdg2a gene which was not associated to detectable level of resistance toward leaf stripe. PCR-based analyses of genic and intergenic regions at the Rdg2a locus in 29 H. vulgare lines and one H. vulgare ssp. spontaneum accession indicated large haplotype variability in the cultivated barley gene pool suggesting rapid and recent divergence at this locus. Barley genotypes showing the same haplotype as Thibaut at the Rdg2a locus were selected for a Rdg2a allele mining through allele re-sequencing and two lines with polymorphic nucleotides leading to amino acid changes in the CC-NB and LRR encoding domains, respectively, were identified. Analysis of nucleotide diversity of the Rdg2a alleles revealed that the polymorphic sites were subjected to positive selection. Moreover, strong positively selected sites were located in the LRR encoding domain suggesting that both positive selection and divergence at homologous loci are possibly representing the molecular mechanism for the generation of high diversity at the Rdg2a locus in the barley gene pool.
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Affiliation(s)
- Chiara Biselli
- Genomics Research Centre, CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Via S Protaso 302, 29017 Fiorenzuola d'Arda, Piacenza, Italy
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Lee MK, Zhang Y, Zhang M, Goebel M, Kim HJ, Triplett BA, Stelly DM, Zhang HB. Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). BMC Genomics 2013; 14:208. [PMID: 23537070 PMCID: PMC3623804 DOI: 10.1186/1471-2164-14-208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 02/11/2013] [Indexed: 11/25/2022] Open
Abstract
Background Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr. Results We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5). Conclusions The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii.
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Affiliation(s)
- Mi-Kyung Lee
- Department of Soil and Crop Sciences, 2474 TAMU, Texas A&M University, College Station, TX 77843-2474, USA
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Feltus FA, Vandenbrink JP. Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:80. [PMID: 23122416 PMCID: PMC3502489 DOI: 10.1186/1754-6834-5-80] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 10/05/2012] [Indexed: 05/19/2023]
Abstract
For lignocellulosic bioenergy to become a viable alternative to traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity in bioenergy production can be achieved through concomitant gains in processing efficiency as well as genetic improvement of feedstock that have the potential for bioenergy production at an industrial scale. The purpose of this review is to explore the genetic and genomic resource landscape for the improvement of a specific bioenergy feedstock group, the C4 bioenergy grasses. First, bioenergy grass feedstock traits relevant to biochemical conversion are examined. Then we outline genetic resources available bioenergy grasses for mapping bioenergy traits to DNA markers and genes. This is followed by a discussion of genomic tools and how they can be applied to understanding bioenergy grass feedstock trait genetic mechanisms leading to further improvement opportunities.
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Affiliation(s)
- Frank Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, 105 Collings Street. BRC #302C, Clemson, SC, 29634, USA
| | - Joshua P Vandenbrink
- Department of Genetics & Biochemistry, Clemson University, 105 Collings Street. BRC #302C, Clemson, SC, 29634, USA
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28
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A physical, genetic and functional sequence assembly of the barley genome. Nature 2012; 491:711-6. [PMID: 23075845 DOI: 10.1038/nature11543] [Citation(s) in RCA: 934] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/30/2012] [Indexed: 12/13/2022]
Abstract
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
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Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Nat Protoc 2012; 7:479-99. [PMID: 22343430 DOI: 10.1038/nprot.2011.456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine animals, insects, algae and microbes. These libraries have been used globally for different aspects of genomics research. Here we describe the procedure with the latest improvements that we have made and used for construction of BIBAC libraries. The procedure includes the preparation of BIBAC vectors, the preparation of clonable fragments of the desired size from the source DNA, the construction and transformation of BIBACs and, finally, the characterization and assembly of BIBAC libraries. We also specify the modifications necessary for construction of BAC libraries using the protocol. The entire protocol takes ∼7 d.
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Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, Zhang HB. Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nat Protoc 2012; 7:467-78. [PMID: 22343429 DOI: 10.1038/nprot.2011.455] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Megabase-sized DNA is crucial to modern genomics research of all organisms. Among the preparation methods developed, the nuclei method is the simplest and most widely used for preparing high-quality megabase-sized DNA from divergent organisms. In this method, nuclei are first isolated by physically grinding the source tissues. The nontarget cytoplast organellar genomes and metabolites are removed by centrifugation and washing, thus maximizing the utility of the method and substantially improving the digestibility and clonability of the resultant DNA. The nuclei are then embedded in an agarose matrix containing numerous pores, allowing the access of restriction enzymes while preventing the DNA from physical shearing. DNA is extracted from the nuclei, purified and subsequently manipulated in the agarose matrix. Here we describe the nuclei method that we have successfully used to prepare high-quality megabase-sized DNA from hundreds of plant, animal, fish, insect, algal and microbial species. The entire protocol takes ∼3 d.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA
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DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants. Methods Mol Biol 2012; 862:13-22. [PMID: 22419485 DOI: 10.1007/978-1-61779-609-8_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.
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Colmsee C, Flemming S, Klapperstück M, Lange M, Scholz U. A case study for efficient management of high throughput primary lab data. BMC Res Notes 2011; 4:413. [PMID: 22005096 PMCID: PMC3217054 DOI: 10.1186/1756-0500-4-413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In modern life science research it is very important to have an efficient management of high throughput primary lab data. To realise such an efficient management, four main aspects have to be handled: (I) long term storage, (II) security, (III) upload and (IV) retrieval. FINDINGS In this paper we define central requirements for a primary lab data management and discuss aspects of best practices to realise these requirements. As a proof of concept, we introduce a pipeline that has been implemented in order to manage primary lab data at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). It comprises: (I) a data storage implementation including a Hierarchical Storage Management system, a relational Oracle Database Management System and a BFiler package to store primary lab data and their meta information, (II) the Virtual Private Database (VPD) implementation for the realisation of data security and the LIMS Light application to (III) upload and (IV) retrieve stored primary lab data. CONCLUSIONS With the LIMS Light system we have developed a primary data management system which provides an efficient storage system with a Hierarchical Storage Management System and an Oracle relational database. With our VPD Access Control Method we can guarantee the security of the stored primary data. Furthermore the system provides high performance upload and download and efficient retrieval of data.
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Affiliation(s)
- Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr, 3, 06466 Gatersleben, Germany.
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Taudien S, Steuernagel B, Ariyadasa R, Schulte D, Schmutzer T, Groth M, Felder M, Petzold A, Scholz U, Mayer KF, Stein N, Platzer M. Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes 2011; 4:411. [PMID: 21999860 PMCID: PMC3213688 DOI: 10.1186/1756-0500-4-411] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 10/14/2011] [Indexed: 11/18/2022] Open
Abstract
Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.
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Affiliation(s)
- Stefan Taudien
- Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Beutenbergstr, 11, D-07745 Jena, Germany.
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Rapid flow-sorting to simultaneously resolve multiplex massively parallel sequencing products. Sci Rep 2011; 1:108. [PMID: 22355625 PMCID: PMC3216591 DOI: 10.1038/srep00108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/22/2011] [Indexed: 11/21/2022] Open
Abstract
Sample preparation for Roche/454, ABI/SOLiD and Life Technologies/Ion Torrent sequencing are based on amplification of library fragments on the surface of beads prior to sequencing. Commonly, libraries are barcoded and pooled, to maximise the sequence output of each sequence run. Here, we describe a novel approach for normalization of multiplex next generation sequencing libraries after emulsion PCR. Briefly, amplified libraries carrying unique barcodes are prepared by fluorescent tagging of complementary sequences and then resolved by high-speed flow cytometric sorting of labeled emulsion PCR beads. The protocol is simple and provides an even sequence distribution of multiplex libraries when sequencing the flow-sorted beads. Moreover, since many empty and mixed emulsion PCR beads are removed, the approach gives rise to a substantial increase in sequence quality and mean read length, as compared to that obtained by standard enrichment protocols.
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Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, BhanuPrakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, KaviKishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:922-31. [PMID: 21615673 PMCID: PMC3437486 DOI: 10.1111/j.1467-7652.2011.00625.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103,215 tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20,634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42,141 aligned TUSs with putative gene structures (including 39,281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44,639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.
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Affiliation(s)
- Pavana J Hiremath
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- Osmania University (OU)Hyderabad, India
| | - Andrew Farmer
- National Centre for Genome Resources (NCGR)Santa Fe, NM, USA
| | - Steven B Cannon
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit (USDA-ARS-CICGRU)Ames, IA, USA
- Department of Agronomy, Iowa State UniversityAmes, IA, USA
| | - Jimmy Woodward
- National Centre for Genome Resources (NCGR)Santa Fe, NM, USA
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Reetu Tuteja
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Ashish Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Amindala BhanuPrakash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | - Neha Gujaria
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Laxmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | | | - Trushar Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Ramamurthy Srinivasan
- National Research Centre on Plant Biotechnology (NRCPB), IARI CampusNew Delhi, India
| | - Marc Lohse
- Max Planck Institute for Molecular Plant Physiology (MPIMPP)Am Muehlenberg, Potsdam-Golm, Germany
| | - Yongli Xiao
- J. Craig Venter Institute (JCVI)Rockville, MD, USA
| | | | | | - Gregory D May
- National Centre for Genome Resources (NCGR)Santa Fe, NM, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- Generation Challenge Program (GCP)c/o CIMMYT, Mexico DF, Mexico
- *Correspondence (Tel +91 40 30713305; fax +91 40 30713074/3075; email )
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Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KFX, Bauer E. From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC PLANT BIOLOGY 2011; 11:131. [PMID: 21951788 PMCID: PMC3191334 DOI: 10.1186/1471-2229-11-131] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 09/28/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. RESULTS More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. CONCLUSIONS The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
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Affiliation(s)
- Grit Haseneyer
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
| | - Thomas Schmutzer
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Michael Seidel
- MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Ruonan Zhou
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Martin Mascher
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Chris-Carolin Schön
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
| | - Stefan Taudien
- Genome Analysis, Leibniz Institute for Age Research, Fritz-Lipmann-Institute (FLI), 07745 Jena, Germany
| | - Uwe Scholz
- Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
| | - Nils Stein
- Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Klaus FX Mayer
- MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Eva Bauer
- Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354 Freising, Germany
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Feltus FA, Saski CA, Mockaitis K, Haiminen N, Parida L, Smith Z, Ford J, Staton ME, Ficklin SP, Blackmon BP, Cheng CH, Schnell RJ, Kuhn DN, Motamayor JC. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. BMC Genomics 2011; 12:379. [PMID: 21794110 PMCID: PMC3154204 DOI: 10.1186/1471-2164-12-379] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/27/2011] [Indexed: 11/25/2022] Open
Abstract
Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.
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Affiliation(s)
- Frank A Feltus
- Clemson University Genomics Institute, Clemson University, 51 New Cherry Street, Clemson, SC 29634, USA.
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Kuhl H, Tine M, Beck A, Timmermann B, Kodira C, Reinhardt R. Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones. Genomics 2011; 98:202-12. [PMID: 21693181 DOI: 10.1016/j.ygeno.2011.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/31/2011] [Accepted: 06/03/2011] [Indexed: 02/02/2023]
Abstract
Dicentrarchus labrax is one of the major marine aquaculture species in the European Union. In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts. Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17-39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2 Mb, 17.5 Mb and 13.7 Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage. Combination of second generation sequencing technologies, Sanger sequencing and genome partitioning strategies allows "high-quality draft assemblies" of chromosome-sized superscaffolds, which are crucial for the prediction and annotation of complete genes.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
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Sato K, Motoi Y, Yamaji N, Yoshida H. 454 sequencing of pooled BAC clones on chromosome 3H of barley. BMC Genomics 2011. [PMID: 21592415 DOI: 10.1186/1471‐2164‐12‐246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000 Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. RESULTS We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. CONCLUSIONS We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Sato K, Motoi Y, Yamaji N, Yoshida H. 454 sequencing of pooled BAC clones on chromosome 3H of barley. BMC Genomics 2011; 12:246. [PMID: 21592415 PMCID: PMC3224129 DOI: 10.1186/1471-2164-12-246] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 05/19/2011] [Indexed: 12/02/2022] Open
Abstract
Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Haiminen N, Feltus FA, Parida L. Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes. BMC Genomics 2011; 12:194. [PMID: 21496274 PMCID: PMC3224119 DOI: 10.1186/1471-2164-12-194] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 04/15/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. RESULTS The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. CONCLUSIONS BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.
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Affiliation(s)
- Niina Haiminen
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA.
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Mayer KF, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N. Unlocking the barley genome by chromosomal and comparative genomics. THE PLANT CELL 2011; 23:1249-63. [PMID: 21467582 PMCID: PMC3101540 DOI: 10.1105/tpc.110.082537] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/10/2011] [Accepted: 03/18/2011] [Indexed: 05/18/2023]
Abstract
We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
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Affiliation(s)
- Klaus F.X. Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Mihaela Martis
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Pete E. Hedley
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Hui Liu
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Jenny A. Morris
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Stefan Taudien
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Stephan Roessner
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Pavla Suchánková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Florent Murat
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Marius Felder
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Thomas Nussbaumer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jerome Salse
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Takashi Endo
- Kyoto University, Laboratory of Plant Genetics, Kyoto 606-8502, Japan
| | - Hiroaki Sakai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Tsuyoshi Tanaka
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazuhiro Sato
- Okayama University, Institute of Plant Science and Resources, Kurashiki 710-0046, Japan
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Robbie Waugh
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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Abstract
SUMMARYSingle-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.
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JEUKENS J, BOYLE B, KUKAVICA‐IBRULJ I, ST‐CYR J, LÉVESQUE RC, BERNATCHEZ L. BAC library construction, screening and clone sequencing of lake whitefish (
Coregonus clupeaformis
, Salmonidae) towards the elucidation of adaptive species divergence. Mol Ecol Resour 2011; 11:541-9. [DOI: 10.1111/j.1755-0998.2011.02982.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. JEUKENS
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Quebec‐Ocean, Department of biology, Université Laval, Québec City, Québec, Canada
| | - B. BOYLE
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Arborea, Center for Forest Research, Université Laval, Québec City, Québec, Canada
| | - I. KUKAVICA‐IBRULJ
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Department of microbiology‐infectiology and immunology, Université Laval, Québec City, Québec, Canada
| | - J. ST‐CYR
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
| | - R. C. LÉVESQUE
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Department of microbiology‐infectiology and immunology, Université Laval, Québec City, Québec, Canada
| | - L. BERNATCHEZ
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Quebec‐Ocean, Department of biology, Université Laval, Québec City, Québec, Canada
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Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One 2011; 6:e16214. [PMID: 21283709 PMCID: PMC3025025 DOI: 10.1371/journal.pone.0016214] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/10/2010] [Indexed: 11/19/2022] Open
Abstract
Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb LP genome. To demonstrate the efficacy of the library in gene isolation, we screened macroarrays with overgos designed from a pine EST anchored on LP chromosome 10. A positive BAC was sequenced and found to contain the expected full-length target gene, several gene-like regions, and both known and novel repeats. Macroarray analysis using the retrotransposon IFG-7 (the most abundant repeat in the sequenced BAC) as a probe indicates that IFG-7 is found in roughly 210,557 copies and constitutes about 5.8% or 1.26 Gb of LP nuclear DNA; this DNA quantity is eight times the Arabidopsis genome. In addition to its use in genome characterization and gene isolation as demonstrated herein, the BAC library should hasten whole genome sequencing of LP via next-generation sequencing strategies/technologies and facilitate improvement of trees through molecular breeding and genetic engineering. The library and associated products are distributed by the Clemson University Genomics Institute (www.genome.clemson.edu).
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Bischof M, Eichmann R, Hückelhoven R. Pathogenesis-associated transcriptional patterns in Triticeae. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:9-19. [PMID: 20674077 DOI: 10.1016/j.jplph.2010.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 05/08/2023]
Abstract
The Triticeae tribe of the plant Poaceae family contains some of the most important cereal crop plants for nutrition of humans and livestock such as wheat and barley. Despite the agronomical relevance of plant immunity, knowledge on mechanisms of disease or resistance in Triticeae is limited. It is hardly understood what actually stops a microbial invader when restricted by the plant and in how far a susceptible host plant contributes to pathogenesis. Transcriptional reprogramming of the host plant may be involved in both immunity and disease. This paper gives an overview about recent analyses of global pathogenesis-related transcriptional patterns in response of Triticeae to biotrophic or non-biotrophic fungal pathogens and their toxins. It highlights enriched biological functions in association with successful plant defence or disease as well as experiments that successfully translated gene expression data into analysis of gene functions.
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Affiliation(s)
- Melanie Bischof
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, Freising-Weihenstephan, Germany
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González VM, Benjak A, Hénaff EM, Mir G, Casacuberta JM, Garcia-Mas J, Puigdomènech P. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC PLANT BIOLOGY 2010; 10:246. [PMID: 21073723 PMCID: PMC3095328 DOI: 10.1186/1471-2229-10-246] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 11/12/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb), which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods. RESULTS In order to gain insight into the structure of a significant portion of the melon genome we set out to perform massive sequencing of pools of BAC clones. For this, a set of 57 BAC clones from a double haploid line was sequenced in two pools with the 454 system using both shotgun and paired-end approaches. The final assembly consists of an estimated 95% of the actual size of the melon BAC clones, with most likely complete sequences for 50 of the BACs, and a total sequence coverage of 39x. The accuracy of the assembly was assessed by comparing the previously available Sanger sequence of one of the BACs against its 454 sequence, and the polymorphisms found involved only 1.7 differences every 10,000 bp that were localized in 15 homopolymeric regions and two dinucleotide tandem repeats. Overall, the study provides approximately 6.7 Mb or 1.5% of the melon genome. The analysis of this new data has allowed us to gain further insight into characteristics of the melon genome such as gene density, average protein length, or microsatellite and transposon content. The annotation of the BAC sequences revealed a high degree of collinearity and protein sequence identity between melon and its close relative Cucumis sativus (cucumber). Transposon content analysis of the syntenic regions suggests that transposition activity after the split of both cucurbit species has been low in cucumber but very high in melon. CONCLUSIONS The results presented here show that the strategy followed, which combines shotgun and BAC-end sequencing together with anchored marker information, is an excellent method for sequencing specific genomic regions, especially from relatively compact genomes such as that of melon. However, in agreement with other results, this map-based, BAC approach is confirmed to be an expensive way of sequencing a whole plant genome. Our results also provide a partial description of the melon genome's structure. Namely, our analysis shows that the melon genome is highly collinear with the smaller one of cucumber, the size difference being mainly due to the expansion of intergenic regions and proliferation of transposable elements.
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Affiliation(s)
- Víctor M González
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Andrej Benjak
- IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain
| | - Elizabeth Marie Hénaff
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Gisela Mir
- IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain
| | - Josep M Casacuberta
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain
| | - Pere Puigdomènech
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
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48
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Abstract
Next generation sequencing has already been used for genomic analysis of microorganis, human being, animals, and plants. Sample preparation is prerequisite and most important for large-scale sequencing. There are two major interferences for large-scale sequencing, polyA and abundant genes' concealment for rare genes. In order to solve these problems, we used total RNA extracted from violaceae leaves to produce double stranded cDNA. DSN nuclease was used to treat the ds cDNA prior to removing the polyA. Randomly sequencing 100 clones of the treated cDNA showed that there were 94 independent clones in the treated sample, and the sequences did not contained polyA. However, only 62 independent clones were found in the untreated sample, and 15 of the sequencing files were affected by polyA. By randomly sequencing of the treated cDNA, we also found two clones encoded two interested genes. We failed to isolate these genes although the protein mass peaks of them had been found in the MALDI-TOF trace. Furthermore, we designed primers from two known genes with different expression abundances. The PCR yields were approaching similar using the treated cDNAs as templates. These results showed that, removal of the polyA and enrichment of rare genes with DSN can meet the requirements of large-scale sequencing and discovery of new genes.
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49
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Knudsen B, Forsberg R, Miyamoto MM. A computer simulator for assessing different challenges and strategies of de novo sequence assembly. Genes (Basel) 2010; 1:263-82. [PMID: 24710045 PMCID: PMC3954094 DOI: 10.3390/genes1020263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/18/2010] [Accepted: 08/31/2010] [Indexed: 11/16/2022] Open
Abstract
This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly. The program uses reads from actual sequencing studies or from simulations with a reference genome that may also be real or simulated. The simulated reads can be created with our read simulator. They can be of differing length and coverage, consist of paired reads with varying distance, and include sequencing errors such as color space miscalls to imitate SOLiD data. The simulated or real reads are mapped to their reference genome and our assembly simulator is then used to obtain optimal assemblies that are limited only by the distribution of repeats. By way of this mapping, the assembly simulator determines which contigs are theoretically possible, or conversely (and perhaps more importantly), which are not. We illustrate the application and utility of our new simulation tools with several experiments that test the effects of genome complexity (repeats), read length and coverage, word size in De Bruijn graph assembly, and alternative sequencing strategies (e.g., BAC pooling) on sequence assemblies. These experiments highlight just some of the uses of our simulators in the experimental design of sequencing projects and in the further development of assembly algorithms.
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Affiliation(s)
| | | | - Michael M Miyamoto
- Department of Biology, Box 118525, University of Florida, Gainesville, Florida, 32611-8525, USA.
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50
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Taudien S, Groth M, Huse K, Petzold A, Szafranski K, Hampe J, Rosenstiel P, Schreiber S, Platzer M. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing. BMC Genomics 2010; 11:252. [PMID: 20403190 PMCID: PMC2873476 DOI: 10.1186/1471-2164-11-252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 04/19/2010] [Indexed: 01/10/2023] Open
Abstract
Background The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence variations (MSV) is less well understood and to date has only been reported for prostate cancer. Simultaneous assessment of MSVs and CNs can be achieved by PCR, cloning and Sanger sequencing, however, these methods are labour and cost intensive as well as prone to methodological bias introduced by bacterial cloning. Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel. Results Six PCR products spread over ~87 kb of DEFB and harbouring 24 known MSVs were amplified from 11 DNA samples, pooled and sequenced on a Roche 454 GS FLX sequencer. From ~142,000 reads, ~120,000 haplotype calls (HC) were inferred that identified 22 haplotypes ranging from 2 to 7 per amplicon. In addition to the 24 known MSVs, two additional sequence variations were detected. Minimal CNs were estimated from the ratio of HCs and compared to absolute CNs determined by alternative methods. Concordance in CNs was found for 7 samples, the CNs differed by one in 2 samples and the estimated minimal CN was half of the absolute in one sample. For 7 samples and 2 amplicons, the 454 haplotyping results were compared to those by cloning/Sanger sequencing. Intrinsic problems related to chimera formation during PCR and differences between haplotyping by 454 and cloning/Sanger sequencing are discussed. Conclusion Deep amplicon sequencing using the 454 technology yield thousands of HCs per amplicon for an affordable price and may represent an effective method for parallel haplotyping and CN estimation in small to medium-sized cohorts. The obtained haplotypes represent a valuable resource to facilitate further studies of the biomedical impact of highly CN variable loci such as the beta-defensin locus.
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Affiliation(s)
- Stefan Taudien
- Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany.
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