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Herbert DB, Gross T, Rupp O, Becker A. Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). BMC PLANT BIOLOGY 2021; 21:95. [PMID: 33588756 PMCID: PMC7885512 DOI: 10.1186/s12870-021-02867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense) is globally used as a fodder plant due its high nutritional value and soil improving qualities. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but the underlying molecular mechanisms and its role for plants grown in the field are unclear. RESULTS Here, we characterize the global transcriptional response to mowing of red clover by comparing plants grown under greenhouse conditions with plants growing on agriculturally used fields. Unexpectedly, we found that biotic and abiotic stress related changes of plants grown in the field overlay their regrowth related transcriptional changes and characterized transcription related protein families involved in these processes. Further, we can show that gibberellins, among other phytohormones, also contribute to the developmental processes related to regrowth after biomass-loss. CONCLUSIONS Our findings show that massive biomass loss triggers less transcriptional changes in field grown plants than their struggle with biotic and abiotic stresses and that gibberellins also play a role in the developmental program related to regrowth after mowing in red clover. Our results provide first insights into the physiological and developmental processes of mowing on red clover and may serve as a base for red clover yield improvement.
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Affiliation(s)
- Denise Brigitte Herbert
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Thomas Gross
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Oliver Rupp
- Department of Bioinformatics and Systems Biology, Justus Liebig University, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Annette Becker
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
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Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J. Bioinformatics for NGS-based metagenomics and the application to biogas research. J Biotechnol 2017; 261:10-23. [PMID: 28823476 DOI: 10.1016/j.jbiotec.2017.08.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.
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Affiliation(s)
- Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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Kracht ON, Ammann AC, Stockmann J, Wibberg D, Kalinowski J, Piotrowski M, Kerr R, Brück T, Kourist R. Transcriptome profiling of the Australian arid-land plant Eremophila serrulata (A.DC.) Druce (Scrophulariaceae) for the identification of monoterpene synthases. PHYTOCHEMISTRY 2017; 136:15-22. [PMID: 28162767 DOI: 10.1016/j.phytochem.2017.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 05/22/2023]
Abstract
Plant terpenoids are a large and highly diverse class of metabolites with an important role in the immune defense. They find wide industrial application as active pharmaceutical ingredients, aroma and fragrance compounds. Several Eremophila sp. derived terpenoids have been documented. To elucidate the terpenoid metabolism, the transcriptome of juvenile and mature Eremophila serrulata (A.DC.) Druce (Scrophulariaceae) leaves was sequenced and a transcript library was generated. We report on the first transcriptomic dataset of an Eremophila plant. IlluminaMiSeq sequencing (2 × 300 bp) revealed 7,093,266 paired reads, which could be assembled to 34,505 isogroups. To enable detection of terpene biosynthetic genes, leaves were separately treated with methyl jasmonate, a well-documented inducer of plant secondary metabolites. In total, 21 putative terpene synthase genes were detected in the transcriptome data. Two terpene synthase isoenzymatic genes, termed ES01 and ES02, were successfully expressed in E. coli. The resulting proteins catalyzed the conversion of geranyl pyrophosphate, the universal substrate of monoterpene synthases to myrcene and Z-(b)-ocimene, respectively. The transcriptomic data and the discovery of the first terpene synthases from Eremophila serrulata are the initial step for the understanding of the terpene metabolism in this medicinally important plant genus.
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Affiliation(s)
- Octavia Natascha Kracht
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Ann-Christin Ammann
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Julia Stockmann
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Daniel Wibberg
- Centre for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany
| | - Markus Piotrowski
- Chair of Plant Physiology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Russell Kerr
- Marine Natural Products Lab, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI, Canada
| | - Thomas Brück
- Chair of Industrial Biocatalysis, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany.
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Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, Dixelius C. Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC Genomics 2016; 17:245. [PMID: 26988094 PMCID: PMC4794925 DOI: 10.1186/s12864-016-2561-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. One of them is the basidiomycete Rhizoctonia solani. This fungal species has a compatibility system regulating hyphal fusions (anastomosis). Consequently, R. solani species are categorized in anastomosis groups (AGs). AG2-2IIIB isolates are most aggressive on sugar beet. In the present study, we report on the draft genome of R. solani AG2-2IIIB using the Illumina technology. Genome analysis, interpretation and comparative genomics of five sequenced R. solani isolates were carried out. Results The draft genome of R. solani AG2-2IIIB has an estimated size of 56.02 Mb. In addition, two normalized EST libraries were sequenced. In total 20,790 of 21,980 AG2-2IIIB isotigs (transcript isoforms) were mapped on the genome with more than 95 % sequence identity. The genome of R. solani AG2-2IIIB was predicted to harbor 11,897 genes and 4908 were found to be isolate-specific. R. solani AG2-2IIIB was predicted to contain 1142 putatively secreted proteins and 473 of them were found to be unique for this isolate. The R. solani AG2-2IIIB genome encodes a high number of carbohydrate active enzymes. The highest numbers were observed for the polysaccharide lyases family 1 (PL-1), glycoside hydrolase family 43 (GH-43) and carbohydrate estarase family 12 (CE-12). Transcription analysis of selected genes representing different enzyme clades revealed a mixed pattern of up- and down-regulation six days after infection on sugar beets featuring variable levels of resistance compared to mycelia of the fungus grown in vitro. Conclusions The established R. solani AG2-2IIIB genome and EST sequences provide important information on the gene content, gene structure and transcriptional activity for this sugar beet pathogen. The enriched genomic platform provides an important platform to enhance our understanding of R. solani biology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2561-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Louise Andersson
- Syngenta Seeds AB, Säbyholmsvägen 24, 26191, Landskrona, Sweden.,Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Georgios Tzelepis
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | | | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany.
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden.
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Wibberg D, Rupp O, Blom J, Jelonek L, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, Schlüter A. Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates. PLoS One 2015; 10:e0144769. [PMID: 26690577 PMCID: PMC4686921 DOI: 10.1371/journal.pone.0144769] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/23/2015] [Indexed: 12/22/2022] Open
Abstract
Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags—ESTs) were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI) and Average Amino-acid Identity (AAI) analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, Gießen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Gießen University, Gießen, Germany
| | - Lukas Jelonek
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
- Bioinformatics and Systems Biology, Gießen University, Gießen, Germany
| | - Magdalena Kröber
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Bart Verwaaijen
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Stefan Albaum
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetables and Ornamental Crops, Großbeeren, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
- * E-mail:
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Pauli M, Chakarov N, Rupp O, Kalinowski J, Goesmann A, Sorenson MD, Krüger O, Hoffman JI. De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC Genomics 2015; 16:1038. [PMID: 26645667 PMCID: PMC4673757 DOI: 10.1186/s12864-015-2254-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/27/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) is a widespread and common Eurasian raptor with three distinct plumage morphs that differ in several fitness-related traits, including parasite infestation. To provide a genomic resource for plumage polymorphic birds in general and to search for candidate genes relating to fitness, we generated a transcriptome from a single dead buzzard specimen plus easily accessible, minimally invasive samples from live chicks. RESULTS We not only de novo assembled a near-complete buzzard transcriptome, but also obtained a significant fraction of the transcriptome of its malaria-like parasite, Leucocytozoon buteonis. By identifying melanogenesis-related transcripts that are differentially expressed in light ventral and dark dorsal feathers, but which are also expressed in other regions of the body, we also identified a suite of candidate genes that could be associated with fitness differences among the morphs. These include several immune-related genes, providing a plausible link between melanisation and parasite load. qPCR analysis of a subset of these genes revealed significant differences between ventral and dorsal feathers and an additional effect of morph. CONCLUSION This new resource provides preliminary insights into genes that could be involved in fitness differences between the buzzard colour morphs, and should facilitate future studies of raptors and their malaria-like parasites.
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Affiliation(s)
- Martina Pauli
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
- Present address: Molecular Ecology and Evolution Lab, Lund University, 223 62, Lund, Sweden.
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University, 35390, Giessen, Germany
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University, 35390, Giessen, Germany
- Center for Biotechnology, Bielefeld University, 33501, Bielefeld, Germany
| | | | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - Joseph Ivan Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
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Hohnjec N, Czaja-Hasse LF, Hogekamp C, Küster H. Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1. BMC Genomics 2015; 16:994. [PMID: 26597293 PMCID: PMC4657205 DOI: 10.1186/s12864-015-2224-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/16/2015] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports nitrogen, mineral, and water aquisition. During the pre-contact stage, the AM symbiosis is controled by an exchange of diffusible factors from either partner. Amongst others, fungal signals were identified as a mix of sulfated and non-sulfated lipochitooligosaccharides (LCOs), being structurally related to rhizobial nodulation (Nod)-factor LCOs that in legumes induce the formation of nitrogen-fixing root nodules. LCO signals are transduced via a common symbiotic signaling pathway (CSSP) that activates a group of GRAS transcription factors (TFs). Using complex gene expression fingerprints as molecular phenotypes, this study primarily intended to shed light on the importance of the GRAS TFs NSP1 and RAM1 for LCO-activated gene expression during pre-symbiotic signaling. RESULTS We investigated the genome-wide transcriptional responses in 5 days old primary roots of the Medicago truncatula wild type and four symbiotic mutants to a 6 h challenge with LCO signals supplied at 10(-7/-8) M. We were able to show that during the pre-symbiotic stage, sulfated Myc-, non-sulfated Myc-, and Nod-LCO-activated gene expression almost exclusively depends on the LysM receptor kinase NFP and is largely controled by the CSSP, although responses independent of this pathway exist. Our results show that downstream of the CSSP, gene expression activation by Myc-LCOs supplied at 10(-7/-8) M strictly required both the GRAS transcription factors RAM1 and NSP1, whereas those genes either co- or specifically activated by Nod-LCOs displayed a preferential NSP1-dependency. RAM1, a central regulator of root colonization by AM fungi, controled genes activated by non-sulfated Myc-LCOs during the pre-symbiotic stage that are also up-regulated in areas with early physical contact, e.g. hyphopodia and infecting hyphae; linking responses to externally applied LCOs with early root colonization. CONCLUSIONS Since both RAM1 and NSP1 were essential for the pre-symbiotic transcriptional reprogramming by Myc-LCOs, we propose that downstream of the CSSP, these GRAS transcription factors act synergistically in the transduction of those diffusible signals that pre-announce the presence of symbiotic fungi.
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Affiliation(s)
- Natalija Hohnjec
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
| | - Lisa F Czaja-Hasse
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
- Present address: Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany.
| | - Claudia Hogekamp
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
| | - Helge Küster
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
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Wibberg D, Jelonek L, Rupp O, Kröber M, Goesmann A, Grosch R, Pühler A, Schlüter A. Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal Biol 2014; 118:800-13. [PMID: 25209639 DOI: 10.1016/j.funbio.2014.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/27/2014] [Accepted: 06/27/2014] [Indexed: 10/25/2022]
Abstract
Rhizoctonia solani is a soil-borne plant pathogenic fungus of the phylum Basidiomycota. It affects a wide range of agriculturally important crops and hence is responsible for economically relevant crop losses. Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14) by applying high-throughput sequencing and bioinformatics methods addressing Expressed Sequence Tag (EST) data interpretation provided new insights in expressed genes of this fungus. Two normalized cDNA libraries representing different cultivation conditions of the fungus were sequenced on the 454 FLX (Roche) system. Subsequent to cDNA sequence assembly and quality control, ESTs were analysed applying advanced bioinformatics methods. More than 14 000 transcript isoforms originating from approximately 10 000 predictable R. solani AG1-IB 7/3/14 genes are represented in each dataset. Comparative analyses revealed several differentially expressed genes depending on the growth conditions applied. Determinants with predicted functions in recognition processes between the fungus and the host plant were identified. Moreover, many R. solani AG1-IB ESTs were predicted to encode putative cellulose, pectin, and lignin degrading enzymes. Furthermore, genes playing a possible role in mitogen-activated protein (MAP) kinase cascades, 4-aminobutyric acid (GABA) metabolism, melanin synthesis, plant defence antagonism, phytotoxin, and mycotoxin synthesis were detected.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Magdalena Kröber
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetables and Ornamental Crops (IGZ), D-14979 Großbeeren, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
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10
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Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS One 2014; 9:e85568. [PMID: 24427317 PMCID: PMC3888431 DOI: 10.1371/journal.pone.0085568] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/03/2013] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters.
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Affiliation(s)
- Oliver Rupp
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
- * E-mail:
| | - Jennifer Becker
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Karina Brinkrolf
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Nicole Borth
- Department for Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
- ACIB, Austrian Center of Industrial Biotechnology, Graz and Vienna, Austria
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
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11
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Hogekamp C, Küster H. A roadmap of cell-type specific gene expression during sequential stages of the arbuscular mycorrhiza symbiosis. BMC Genomics 2013; 14:306. [PMID: 23647797 PMCID: PMC3667144 DOI: 10.1186/1471-2164-14-306] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/26/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND About 80% of today's land plants are able to establish an arbuscular mycorrhizal (AM) symbiosis with Glomeromycota fungi to improve their access to nutrients and water in the soil. On the molecular level, the development of AM symbioses is only partly understood, due to the asynchronous development of the microsymbionts in the host roots. Although many genes specifically activated during fungal colonization have been identified, genome-wide information on the exact place and time point of their activation remains limited. RESULTS In this study, we relied on a combination of laser-microdissection and the use of Medicago GeneChips to perform a genome-wide analysis of transcription patterns in defined cell-types of Medicago truncatula roots mycorrhized with Glomus intraradices. To cover major stages of AM development, we harvested cells at 5-6 and at 21 days post inoculation (dpi). Early developmental stages of the AM symbiosis were analysed by monitoring gene expression in appressorial and non-appressorial areas from roots harbouring infection units at 5-6 dpi. Here, the use of laser-microdissection for the first time enabled the targeted harvest of those sites, where fungal hyphae first penetrate the root. Circumventing contamination with developing arbuscules, we were able to specifically detect gene expression related to early infection events. To cover the late stages of AM formation, we studied arbusculated cells, cortical cells colonized by intraradical hyphae, and epidermal cells from mature mycorrhizal roots at 21 dpi. Taken together, the cell-specific expression patterns of 18014 genes were revealed, including 1392 genes whose transcription was influenced by mycorrhizal colonization at different stages, namely the pre-contact phase, the infection of roots via fungal appressoria, the subsequent colonization of the cortex by fungal hyphae, and finally the formation of arbuscules. Our cellular expression patterns identified distinct groups of AM-activated genes governing the sequential reprogramming of host roots towards an accommodation of microsymbionts, including 42 AM-activated transcription factor genes. CONCLUSIONS Our genome-wide analysis provides novel information on the cell-specific activity of AM-activated genes during both early and late stages of AM development, together revealing the road map of fine-tuned adjustments of transcript accumulation within root tissues during AM fungal colonization.
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Affiliation(s)
- Claudia Hogekamp
- Institut für Pflanzengenetik, Abteilung IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Helge Küster
- Institut für Pflanzengenetik, Abteilung IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
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12
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Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A. MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. J Biotechnol 2012; 167:156-65. [PMID: 23026555 DOI: 10.1016/j.jbiotec.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/21/2012] [Accepted: 09/21/2012] [Indexed: 12/01/2022]
Abstract
Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.
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Affiliation(s)
- Martha Zakrzewski
- Institute for Bioinformatics-IfB, Center for Biotechnology-CeBiTec, Bielefeld University, Bielefeld, Germany
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13
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Bassaglia Y, Bekel T, Da Silva C, Poulain J, Andouche A, Navet S, Bonnaud L. ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda). Gene 2012; 498:203-11. [PMID: 22548232 DOI: 10.1016/j.gene.2012.01.100] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
New molecular resources regarding the so-called “non-standard models” in biology extend the present knowledge and are essential for molecular evolution and diversity studies (especially during the development) and evolutionary inferences about these zoological groups, or more practically for their fruitful management. Sepia officinalis, an economically important cephalopod species, is emerging as a new lophotrochozoan developmental model. We developed a large set of expressed sequence tags (ESTs) from embryonic stages of S. officinalis, yielding 19,780 non-redundant sequences (NRS). Around 75% of these sequences have no homologs in existing available databases. This set is the first developmental ESTs library in cephalopods. By exploring these NRS for tubulin, a generic protein family, and reflectin, a cephalopod specific protein family,we point out for both families a striking molecular diversity in S. officinalis.
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Affiliation(s)
- Yann Bassaglia
- Muséum National d'Histoire Naturelle (MNHN), Département Milieux et Peuplements Aquatiques (DMPA), UMR Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), MNHN, CNRS 7208, IRD 207, UPMC. Paris, France.
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14
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Ellis JT, Sims RC, Miller CD. Monitoring microbial diversity of bioreactors using metagenomic approaches. Subcell Biochem 2012; 64:73-94. [PMID: 23080246 DOI: 10.1007/978-94-007-5055-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
With the rapid development of molecular techniques, particularly 'omics' technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.
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Affiliation(s)
- Joshua T Ellis
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
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15
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Rademacher A, Zakrzewski M, Schlüter A, Schönberg M, Szczepanowski R, Goesmann A, Pühler A, Klocke M. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol Ecol 2011; 79:785-99. [PMID: 22126587 DOI: 10.1111/j.1574-6941.2011.01265.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 11/28/2022] Open
Abstract
DNAs of two biofilms of a thermophilic two-phase leach-bed biogas reactor fed with rye silage and winter barley straw were sequenced by 454-pyrosequencing technology to assess the biofilm-based microbial community and their genetic potential for anaerobic digestion. The studied biofilms matured on the surface of the substrates in the hydrolysis reactor (HR) and on the packing in the anaerobic filter reactor (AF). The classification of metagenome reads showed Clostridium as most prevalent bacteria in the HR, indicating a predominant role for plant material digestion. Notably, insights into the genetic potential of plant-degrading bacteria were determined as well as further bacterial groups, which may assist Clostridium in carbohydrate degradation. Methanosarcina and Methanothermobacter were determined as most prevalent methanogenic archaea. In consequence, the biofilm-based methanogenesis in this system might be driven by the hydrogenotrophic pathway but also by the aceticlastic methanogenesis depending on metabolite concentrations such as the acetic acid concentration. Moreover, bacteria, which are capable of acetate oxidation in syntrophic interaction with methanogens, were also predicted. Finally, the metagenome analysis unveiled a large number of reads with unidentified microbial origin, indicating that the anaerobic degradation process may also be conducted by up to now unknown species.
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Affiliation(s)
- Antje Rademacher
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Potsdam, Germany
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16
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Kocabaş F, Can T, Baykal N. Metadata management and semantics in microarray repositories. Balkan J Med Genet 2011; 14:49-64. [PMID: 24052712 PMCID: PMC3776701 DOI: 10.2478/v10034-011-0047-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The number of microarray and other high-throughput experiments on primary repositories keeps increasing as do the size and complexity of the results in response to biomedical investigations. Initiatives have been started on standardization of content, object model, exchange format and ontology. However, there are backlogs and inability to exchange data between microarray repositories, which indicate that there is a great need for a standard format and data management. We have introduced a metadata framework that includes a metadata card and semantic nets that make experimental results visible, understandable and usable. These are encoded in syntax encoding schemes and represented in RDF (Resource Description Frame-word), can be integrated with other metadata cards and semantic nets, and can be exchanged, shared and queried. We demonstrated the performance and potential benefits through a case study on a selected microarray repository. We concluded that the backlogs can be reduced and that exchange of information and asking of knowledge discovery questions can become possible with the use of this metadata framework.
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Affiliation(s)
- F Kocabaş
- Middle East Technical University, Informatics Institute, Department of Health Informatics, 06531 Ankara, Turkey ; NATO HQ C3S, Information Services Branch, Blvd Leopold III B1110, Brussels, Belgium
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17
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Hogekamp C, Arndt D, Pereira PA, Becker JD, Hohnjec N, Küster H. Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. PLANT PHYSIOLOGY 2011; 157:2023-43. [PMID: 22034628 PMCID: PMC3327204 DOI: 10.1104/pp.111.186635] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 10/26/2011] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizae (AM) are the most widespread symbioses on Earth, promoting nutrient supply of most terrestrial plant species. To unravel gene expression in defined stages of Medicago truncatula root colonization by AM fungi, we here combined genome-wide transcriptome profiling based on whole mycorrhizal roots with real-time reverse transcription-PCR experiments that relied on characteristic cell types obtained via laser microdissection. Our genome-wide approach delivered a core set of 512 genes significantly activated by the two mycorrhizal fungi Glomus intraradices and Glomus mossae. Focusing on 62 of these genes being related to membrane transport, signaling, and transcriptional regulation, we distinguished whether they are activated in arbuscule-containing or the neighboring cortical cells harboring fungal hyphae. In addition, cortical cells from nonmycorrhizal roots served as a reference for gene expression under noncolonized conditions. Our analysis identified 25 novel arbuscule-specific genes and 37 genes expressed both in the arbuscule-containing and the adjacent cortical cells colonized by fungal hyphae. Among the AM-induced genes specifying transcriptional regulators were two members encoding CAAT-box binding transcription factors (CBFs), designated MtCbf1 and MtCbf2. Promoter analyses demonstrated that both genes were already activated by the first physical contact between the symbionts. Subsequently, and corresponding to our cell-type expression patterns, they were progressively up-regulated in those cortical areas colonized by fungal hyphae, including the arbuscule-containing cells. The encoded CBFs thus represent excellent candidates for regulators that mediate a sequential reprogramming of root tissues during the establishment of an AM symbiosis.
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Affiliation(s)
| | | | | | | | | | - Helge Küster
- Institut für Pflanzengenetik, Leibniz Universität Hannover, D–30419 Hannover, Germany (C.H., D.A., N.H., H.K.); Instituto Gulbenkian de Ciência, 2780–156 Oeiras, Portugal (P.A.P., J.D.B.)
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18
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Becker J, Hackl M, Rupp O, Jakobi T, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Pühler A, Tauch A, Brinkrolf K. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. J Biotechnol 2011; 156:227-35. [PMID: 21945585 DOI: 10.1016/j.jbiotec.2011.09.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 11/17/2022]
Abstract
The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were used to achieve a major step forward to unravel the transcriptome of Chinese hamster ovary (CHO) cells. Normalized cDNA libraries originating from several cell lines and diverse culture conditions were sequenced and the resulting 1.84 million reads were assembled into 32,801 contiguous sequences, 29,184 isotigs, and 24,576 isogroups. A taxonomic classification of the isotigs showed that more than 70% of the assembled data is most similar to the transcriptome of Mus musculus, with most of the remaining isotigs being homologous to DNA sequences from Rattus norvegicus. Mapping of the CHO cell line contigs to the mouse transcriptome demonstrated that 9124 mouse transcripts, representing 6701 genes, are covered by more than 95% of their sequence length. Metabolic pathways of the central carbohydrate metabolism and biosynthesis routes of sugars used for protein N-glycosylation were reconstructed from the transcriptome data. All relevant genes representing major steps in the N-glycosylation pathway of CHO cells were detected. The present manuscript represents a data set of assembled and annotated genes for CHO cells that can now be used for a detailed analysis of the molecular functioning of CHO cell lines.
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Affiliation(s)
- Jennifer Becker
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
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19
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De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS. Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite. BIOFOULING 2011; 27:367-374. [PMID: 21526438 DOI: 10.1080/08927014.2011.577211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In order to improve the genetic characterisation of the barnacle Balanus amphitrite, normalised EST libraries for the developmental stages, viz. nauplius (a mix of instars I and II), cyprid and adult, were generated. The libraries were sequenced independently using 454 technologies and 575,666 reads were generated. For adults, 4843 unique isotigs were estimated and 6754 and 7506 in the cyprid and naupliar stage, respectively. It was found that some of the previously proposed cyprid-specific bcs genes were also expressed during the naupliar and adult stage. Furthermore, as lectins have been hypothesised to influence settlement cue recognition in barnacles, the database was searched for lectin-like isotigs. Two proteins, uniquely expressed in either the cyprid or the adult stage, matched a mannose receptor, and their nucleotide sequences were 33% and 31% identical to a lectin (BRA-3) isolated from Megabalanus rosa. Further characterisation of these genes may suggest their involvement in settlement.
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20
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Henckel K, Küster H, Stutz LJ, Goesmann A. MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. BMC Res Notes 2010; 3:262. [PMID: 20958970 PMCID: PMC2972298 DOI: 10.1186/1756-0500-3-262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 10/19/2010] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Expressed Sequence Tags (ESTs) are in general used to gain a first insight into gene activities from a species of interest. Subsequently, and typically based on a combination of EST and genome sequences, microarray-based expression analyses are performed for a variety of conditions. In some cases, a multitude of EST and microarray experiments are conducted for one species, covering different tissues, cell states, and cell types. Under these circumstances, the challenge arises to combine results derived from the different expression profiling strategies, with the goal to uncover novel information on the basis of the integrated datasets. FINDINGS Using our new analysis tool, MediPlEx (MEDIcago truncatula multiPLe EXpression analysis), expression data from EST experiments, oligonucleotide microarrays and Affymetrix GeneChips® can be combined and analyzed, leading to a novel approach to integrated transcriptome analysis. We have validated our tool via the identification of a set of well-characterized AM-specific and AM-induced marker genes, identified by MediPlEx on the basis of in silico and experimental gene expression profiles from roots colonized with AM fungi. CONCLUSIONS MediPlEx offers an integrated analysis pipeline for different sets of expression data generated for the model legume Medicago truncatula. As expected, in silico and experimental gene expression data that cover the same biological condition correlate well. The collection of differentially expressed genes identified via MediPlEx provides a starting point for functional studies in plant mutants. MediPlEx can freely be used at http://www.cebitec.uni-bielefeld.de/mediplex.
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Affiliation(s)
- Kolja Henckel
- Bioinformatics of Signaling Networks, Center for Biotechnology, Bielefeld University, Germany
| | - Helge Küster
- Unit IV - Plant Genomics, Institute for Plant Genetics, Leibniz Universität Hannover, Germany
| | - Leonhard J Stutz
- Computational Genomics, Center for Biotechnology, Bielefeld University, Germany
- Technical Faculty, Bielefeld University, Germany
| | - Alexander Goesmann
- Computational Genomics, Center for Biotechnology, Bielefeld University, Germany
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Schmid J, Müller-Hagen D, Bekel T, Funk L, Stahl U, Sieber V, Meyer V. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics 2010; 11:329. [PMID: 20504312 PMCID: PMC2887420 DOI: 10.1186/1471-2164-11-329] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 --> 3)-beta-linked glucose with a (1 --> 6)-beta-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches. RESULTS Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding approximately 350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified approximately 800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields. CONCLUSIONS The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and oxalate synthesis and to identify important genes putatively involved in determining scleroglucan yields. Moreover, our data establish the first sequence database for S. rolfsii, which allows research into other biological processes of S. rolfsii, such as host-pathogen interaction.
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Affiliation(s)
- Jochen Schmid
- Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technische Universität München, Schulgasse 16, 94315 Straubing, Germany.
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Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010; 10:564-7. [PMID: 21565059 DOI: 10.1111/j.1755-0998.2010.02847.x] [Citation(s) in RCA: 9085] [Impact Index Per Article: 648.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.
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Affiliation(s)
- Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Krawczyk J, Goesmann A, Nolte R, Werber M, Weisshaar B. Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. SOURCE CODE FOR BIOLOGY AND MEDICINE 2009; 4:4. [PMID: 19622158 PMCID: PMC2722627 DOI: 10.1186/1751-0473-4-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 07/21/2009] [Indexed: 11/10/2022]
Abstract
Background Due to the advanced techniques in sequencing and fragment analysis, DNA sequencers and analyzers produce vast amounts of data within short time. To administrate the large data volume conveniently, efficient data management systems are used in order to process and to store sequencers' or analyzers' data outcome. The inclusion of graphical reports in such systems is necessary to achieve a comprehensive view of the integrated data. However, the resulting data of sequencing and fragment analysis runs are stored in a proprietary format, the so-called trace or fsa format, which is only readable by programs provided by the instrument's vendor operating on the machine itself or by commercial tools designed for editing the respective data. To allow for a quick conversion of the proprietary data format into a commonly used one, toolkits are required that reach this aim and can be easily integrated into workflow systems. Results We have developed the software toolkits Trace2PS and Fsa2PS which allow to convert sequence and fragment analysis raw data files to PostScript images, respectively. The toolkits are implemented as Perl modules that can be used as standalone command line applications in conjunction with a script-based analysis pipeline, or integrated in software applications for displaying the data content of trace and fsa files. The converter modules support the commonly used file formats for storage of sequencing (ABI and SCF) and fragment analysis data (FSA). Conclusion The software toolkits provide useful applications to convert sequencing and fragment analysis files from a proprietary into a more common, human-readable format. Trace2PS and FSA2PS are useful and capable in data management workflow systems like SAMS, or laboratory information systems that are used for displaying trace and fragment analysis results via web-based tools over an intranet or internet connection to users that can view their results directly on the screen.
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Affiliation(s)
- Justina Krawczyk
- Computational Genomics, Center for Biotechnology (CeBiTec), 33594 Bielefeld, Germany.
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Bacchetti De Gregoris T, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Mol Biol 2009; 10:62. [PMID: 19552808 PMCID: PMC2713238 DOI: 10.1186/1471-2199-10-62] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 06/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background Balanus amphitrite is a barnacle commonly used in biofouling research. Although many aspects of its biology have been elucidated, the lack of genetic information is impeding a molecular understanding of its life cycle. As part of a wider multidisciplinary approach to reveal the biogenic cues influencing barnacle settlement and metamorphosis, we have sequenced and annotated the first cDNA library for B. amphitrite. We also present a systematic validation of potential reference genes for normalization of quantitative real-time PCR (qRT-PCR) data obtained from different developmental stages of this animal. Results We generated a cDNA library containing expressed sequence tags (ESTs) from adult B. amphitrite. A total of 609 unique sequences (comprising 79 assembled clusters and 530 singlets) were derived from 905 reliable unidirectionally sequenced ESTs. Bioinformatics tools such as BLAST, HMMer and InterPro were employed to allow functional annotation of the ESTs. Based on these analyses, we selected 11 genes to study their ability to normalize qRT-PCR data. Total RNA extracted from 7 developmental stages was reverse transcribed and the expression stability of the selected genes was compared using geNorm, BestKeeper and NormFinder. These software programs produced highly comparable results, with the most stable gene being mt-cyb, while tuba, tubb and cp1 were clearly unsuitable for data normalization. Conclusion The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies.
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Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A. EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 2009; 10:50. [PMID: 19200358 PMCID: PMC2645365 DOI: 10.1186/1471-2105-10-50] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 02/06/2009] [Indexed: 11/10/2022] Open
Abstract
Background Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.
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Affiliation(s)
- Michael Dondrup
- Computational Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany.
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