1
|
Nguyen-Hoang A, Sandell FL, Himmelbauer H, Dohm JC. Spinach genomes reveal migration history and candidate genes for important crop traits. NAR Genom Bioinform 2024; 6:lqae034. [PMID: 38633427 PMCID: PMC11023180 DOI: 10.1093/nargab/lqae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.
Collapse
Affiliation(s)
- An Nguyen-Hoang
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Felix L Sandell
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| |
Collapse
|
2
|
Sandell FL, Holzweber T, Street NR, Dohm JC, Himmelbauer H. Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting. Plant Biotechnol J 2024; 22:1312-1324. [PMID: 38213076 PMCID: PMC11022794 DOI: 10.1111/pbi.14267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.
Collapse
Affiliation(s)
- Felix L. Sandell
- Department of Biotechnology, Institute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Thomas Holzweber
- Department of Biotechnology, Institute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversityUmeåSweden
- SciLifeLabUmeå UniversityUmeåSweden
| | - Juliane C. Dohm
- Department of Biotechnology, Institute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| |
Collapse
|
3
|
Sandell FL, Stralis-Pavese N, McGrath JM, Schulz B, Himmelbauer H, Dohm JC. Author Correction: Genomic distances reveal relationships of wild and cultivated beets. Nat Commun 2024; 15:1078. [PMID: 38316841 PMCID: PMC10844223 DOI: 10.1038/s41467-024-45401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Affiliation(s)
- Felix L Sandell
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | - Nancy Stralis-Pavese
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | | | | | - Heinz Himmelbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
| | - Juliane C Dohm
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
| |
Collapse
|
4
|
Yosief RHS, Lone IM, Nachshon A, Himmelbauer H, Gat‐Viks I, Iraqi FA. Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach. Animal Model Exp Med 2024; 7:36-47. [PMID: 38356021 PMCID: PMC10961901 DOI: 10.1002/ame2.12386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus (Af) using an RNAseq approach in CC lines and hepatic gene expression. METHODS We studied 31 male mice from 25 CC lines at 8 weeks old; the mice were infected with Af. Liver tissues were extracted from these mice 5 days post-infection, and next-generation RNA-sequencing (RNAseq) was performed. The GENE-E analysis platform was used to generate a clustered heat map matrix. RESULTS Significant variation in body weight changes between CC lines was observed. Hepatic gene expression revealed 12 top prioritized candidate genes differentially expressed in resistant versus susceptible mice based on body weight changes. Interestingly, three candidate genes are located within genomic intervals of the previously mapped quantitative trait loci (QTL), including Gm16270 and Stox1 on chromosome 10 and Gm11033 on chromosome 8. CONCLUSIONS Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af. As a next step, eQTL analysis will be performed for our RNA-Seq data. Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.
Collapse
Affiliation(s)
- Roa'a H. S. Yosief
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Iqbal M. Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 181190 ViennaAustria
| | - Irit Gat‐Viks
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| |
Collapse
|
5
|
Taylor BA, Taylor D, Bodrug‐Schepers A, Câmara Ferreira F, Stralis‐Pavese N, Himmelbauer H, Guigó R, Reuter M, Sumner S. Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp. Mol Ecol 2024; 33:e17217. [PMID: 38014715 PMCID: PMC10953455 DOI: 10.1111/mec.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Social insect reproductives and non-reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes in obligately social taxa such as honey bees, while relatively few studies have addressed the molecular correlates of reproductive differentiation in species in which the division of reproductive labour is established only in plastic dominance hierarchies. To address this knowledge gap, we generate the first genome for any stenogastrine wasp and analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social species Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive 'queues' exhibited by social colonies of this species, we show that reproductive division of labour in this species is associated with transcriptomic signatures that are more subtle and variable than those observed in social taxa in which colony living has become obligate; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that genes associated with reproductive division of labour overlap to some extent with those underlying division of labour in the separate polistine origin of wasp sociality but only explain a small portion of overall variation in this trait. These results indicate that broad patterns of within-colony transcriptomic differentiation in this species are similar to those in Polistinae but offer little support for the existence of a strongly conserved 'toolkit' for sociality.
Collapse
Affiliation(s)
- Benjamin A. Taylor
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Daisy Taylor
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Nancy Stralis‐Pavese
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Roderic Guigó
- Centre for Genomic RegulationBarcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
| | - Max Reuter
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
- Centre for Life's Origins and EvolutionUniversity College LondonLondonUK
| | - Seirian Sumner
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| |
Collapse
|
6
|
Felkel S, Dohm JC, Himmelbauer H. Genomic variation in the genus Beta based on 656 sequenced beet genomes. Sci Rep 2023; 13:8654. [PMID: 37244945 DOI: 10.1038/s41598-023-35691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, Macaronesia, and throughout the Mediterranean area exist. Thorough characterization of beet genomes is required for straightforward access to genes promoting genetic resistance against biotic and abiotic stress. Analysing short-read data of 656 sequenced beet genomes, we identified 10 million variant positions in comparison to the sugar beet reference genome RefBeet-1.2. The main groups of species and subspecies were distinguishable based on shared variation, and the separation of sea beets (Beta vulgaris ssp. maritima) into a Mediterranean and an Atlantic subgroup as suggested by previous studies could be confirmed. Complementary approaches of variant-based clustering were employed based on PCA, genotype likelihoods, tree calculations, and admixture analysis. Outliers suggested the occurrence of inter(sub)specific hybridisation, independently confirmed by different analyses. Screens for regions under artificial selection in the sugar beet genome identified 15 Mbp of the genome as variation-poor, enriched for genes involved in shoot system development, stress response, and carbohydrate metabolism. The resources presented herein will be valuable for crop improvement and wild species monitoring and conservation efforts, and for studies on beet genealogy, population structure and population dynamics. Our study provides a wealth of data for in-depth analyses of further aspects of the beet genome towards a thorough understanding of the biology of this important complex of a crop species and its wild relatives.
Collapse
Affiliation(s)
- Sabine Felkel
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| |
Collapse
|
7
|
Favreau E, Cini A, Taylor D, Câmara Ferreira F, Bentley MA, Cappa F, Cervo R, Privman E, Schneider J, Thiéry D, Mashoodh R, Wyatt CDR, Brown RL, Bodrug-Schepers A, Stralis-Pavese N, Dohm JC, Mead D, Himmelbauer H, Guigo R, Sumner S. Putting hornets on the genomic map. Sci Rep 2023; 13:6232. [PMID: 37085574 PMCID: PMC10121689 DOI: 10.1038/s41598-023-31932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/20/2023] [Indexed: 04/23/2023] Open
Abstract
Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.
Collapse
Affiliation(s)
- Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Alessandro Cini
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, Università di Pisa, Via Volta 6, 56126, Pisa, Italy
| | - Daisy Taylor
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Michael A Bentley
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Federico Cappa
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Rita Cervo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Abba Hushi 199, 3498838, Haifa, Israel
| | - Jadesada Schneider
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Denis Thiéry
- INRAe, UMR 1065 Santé et Agroécologie du Vignoble, Bordeaux Sciences Agro, ISVV, Université de Bordeaux, 33883, Villenave d'Ornon, France
| | - Rahia Mashoodh
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher D R Wyatt
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Robert L Brown
- Manaaki Whenua - Landcare Research, 54 Gerald Street, Lincoln, 7608, New Zealand
| | - Alexandrina Bodrug-Schepers
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Nancy Stralis-Pavese
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Daniel Mead
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Roderic Guigo
- Centre for Genomic Regulation, Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
8
|
Felkel S, Tremetsberger K, Moser D, Dohm JC, Himmelbauer H, Winkler M. Genome-environment associations along elevation gradients in two snowbed species of the North-Eastern Calcareous Alps. BMC Plant Biol 2023; 23:203. [PMID: 37076814 PMCID: PMC10114330 DOI: 10.1186/s12870-023-04187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Anthropogenic climate change leads to increasing temperatures and altered precipitation and snowmelt patterns, especially in alpine ecosystems. To understand species' responses to climate change, assessment of genetic structure and diversity is crucial as the basis for the evaluation of migration patterns, genetic adaptation potential as well as the identification of adaptive alleles. RESULTS We studied genetic structure, diversity and genome-environment associations of two snowbed species endemic to the Eastern Alps with a large elevational range, Achillea clusiana Tausch and Campanula pulla L. Genotyping-by-sequencing was employed to assemble loci de novo, call variants and perform population genetic analyses. Populations of either species were distinguishable by mountain, and to some extent by elevation. We found evidence for gene flow between elevations. Results of genome-environment associations suggested similar selective pressures acting on both species, emanating mainly from precipitation and exposition rather than temperature. CONCLUSIONS Given their genetic structure and amount of gene flow among populations the two study species are suitable to serve as a model for genetic monitoring of climate change adaptation along an elevation gradient. Consequences of climate change will predominantly manifest via changes in precipitation and, thus, duration of snow cover in the snowbeds and indirectly via shrub encroachment accompanied by increasing shading of snowbeds at lower range margins. Assembling genomes of the study species and studying larger sample sizes and time series will be necessary to functionally characterize and validate the herein identified genomic loci putatively involved in adaptive processes.
Collapse
Affiliation(s)
- Sabine Felkel
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Karin Tremetsberger
- Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Vienna, 1180, Austria
| | - Dietmar Moser
- Biodiversity Dynamics and Conservation Group, Department of Botany and Biodiversity Research, University of Vienna, Vienna, 1030, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Manuela Winkler
- GLORIA Coordination, Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Vienna, 1190, Austria.
- GLORIA Coordination, Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria.
| |
Collapse
|
9
|
Andolfo G, Dohm JC, Himmelbauer H. Prediction of NB-LRR resistance genes based on full-length sequence homology. Plant J 2022; 110:1592-1602. [PMID: 35365907 PMCID: PMC9322396 DOI: 10.1111/tpj.15756] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 05/11/2023]
Abstract
The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB-LRR genes using a protein motif/domain-based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB-LRR gene detection. Furthermore, R-genes have diversified in a species-specific manner, so that NB-LRR gene identification cannot be universally standardized. Here, we present the full-length Homology-based R-gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R-gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB-LRR gene loci, proving to be more performant than the well-established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full-length NB-LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R-gene allele mining, testified by the identification of hitherto undiscovered Fom-2 homologs in five Cucurbita sp. genomes. In summary, our high-performance method for full-length NB-LRR gene discovery will propel the identification of novel R-genes towards development of improved cultivars.
Collapse
Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural SciencesUniversity of Naples ‘Federico II’Via Università 10080055Portici (Naples)Italy
| | - Juliane C. Dohm
- Institute of Computational Biology, Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaMuthgasse 181190ViennaAustria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaMuthgasse 181190ViennaAustria
| |
Collapse
|
10
|
Sandell FL, Stralis-Pavese N, McGrath JM, Schulz B, Himmelbauer H, Dohm JC. Genomic distances reveal relationships of wild and cultivated beets. Nat Commun 2022; 13:2021. [PMID: 35440134 PMCID: PMC9019029 DOI: 10.1038/s41467-022-29676-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/28/2022] [Indexed: 12/01/2022] Open
Abstract
Cultivated beets (Beta vulgaris ssp. vulgaris), including sugar beet, rank among the most important crops. The wild ancestor of beet crops is the sea beet Beta vulgaris ssp. maritima. Species and subspecies of wild beets are readily crossable with cultivated beets and are thus available for crop improvement. To study genomic relationships in the genus Beta, we sequence and analyse 606 beet genomes, encompassing sugar beet, sea beet, B. v. adanensis, B. macrocarpa, and B. patula. We observe two genetically distinct groups of sea beets, one from the Atlantic coast and the other from the Mediterranean area. Genomic comparisons based on k-mers identify sea beets from Greece as the closest wild relatives of sugar beet, suggesting that domestication of the ancestors of sugar beet may be traced to this area. Our work provides comprehensive insight into the phylogeny of wild and cultivated beets and establishes a framework for classification of further accessions of unknown (sub-)species assignment.
Collapse
Affiliation(s)
- Felix L Sandell
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | - Nancy Stralis-Pavese
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | | | | | - Heinz Himmelbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
| | - Juliane C Dohm
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
| |
Collapse
|
11
|
Bodrug-Schepers A, Stralis-Pavese N, Buerstmayr H, Dohm JC, Himmelbauer H. Quinoa genome assembly employing genomic variation for guided scaffolding. Theor Appl Genet 2021; 134:3577-3594. [PMID: 34365519 PMCID: PMC8519820 DOI: 10.1007/s00122-021-03915-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.
Collapse
Affiliation(s)
- Alexandrina Bodrug-Schepers
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria
| | - Nancy Stralis-Pavese
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria
| | - Hermann Buerstmayr
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology and Department of Crop Sciences, Universität für Bodenkultur, Tulln, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria.
| |
Collapse
|
12
|
Schiavinato M, Bodrug‐Schepers A, Dohm JC, Himmelbauer H. Subgenome evolution in allotetraploid plants. Plant J 2021; 106:672-688. [PMID: 33547826 PMCID: PMC8251528 DOI: 10.1111/tpj.15190] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 05/02/2023]
Abstract
Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
Collapse
Affiliation(s)
- Matteo Schiavinato
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Alexandrina Bodrug‐Schepers
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Juliane C. Dohm
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| |
Collapse
|
13
|
Lehner R, Blazek L, Minoche AE, Dohm JC, Himmelbauer H. Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla). J Biotechnol 2021; 333:67-76. [PMID: 33932500 DOI: 10.1016/j.jbiotec.2021.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/09/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. While the genome of sugar beet, the most prominent beet crop, has been studied extensively, molecular data on other beet cultivars is scant. Here, we present a genome assembly of chard, a vegetable crop grown for its fleshy leaves. We report a de novo genome assembly of 604 Mbp, slightly larger than sugar beet assemblies presented so far. About 57 % of the assembly was annotated as repetitive sequence, of which LTR retrotransposons were the most abundant. Based on the presence of conserved genes, the chard assembly was estimated to be at least 96 % complete regarding its gene space. We predicted 34,521 genes of which 27,582 genes were supported by evidence from transcriptomic sequencing reads, and 5503 of the evidence-supported genes had multiple isoforms. We compared the chard gene set with gene sets from sugar beet and two wild beets (i.e. Beta vulgaris ssp. maritima and Beta patula) to find orthology relationships and identified genome-wide syntenic regions between chard and sugar beet. Lastly, we determined genomic variants that distinguish sugar beet and chard. Assessing the variation distribution along the chard chromosomes, we found extensive haplotype sharing between the two cultivars. In summary, our work provides a foundation for the molecular analysis of Beta vulgaris cultigroups as a basis for chard genomics and to unravel the domestication history of beet crops.
Collapse
Affiliation(s)
- Reinhard Lehner
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lisa Blazek
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
| |
Collapse
|
14
|
Schuller A, Cserjan-Puschmann M, Köppl C, Grabherr R, Wagenknecht M, Schiavinato M, Dohm JC, Himmelbauer H, Striedner G. Adaptive Evolution in Producing Microtiter Cultivations Generates Genetically Stable Escherichia coli Production Hosts for Continuous Bioprocessing. Biotechnol J 2020; 16:e2000376. [PMID: 33084246 DOI: 10.1002/biot.202000376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/06/2020] [Indexed: 01/01/2023]
Abstract
The production of recombinant proteins usually reduces cell fitness and the growth rate of producing cells. The growth disadvantage favors faster-growing non-producer mutants. Therefore, continuous bioprocessing is hardly feasible in Escherichia coli due to the high escape rate. The stability of E. coli expression systems under long-term production conditions and how metabolic load triggered by recombinant gene expression influences the characteristics of mutations are investigated. Iterated fed-batch-like microbioreactor cultivations are conducted under production conditions. The easy-to-produce green fluorescent protein (GFP) and a challenging antigen-binding fragment (Fab) are used as model proteins, and BL21(DE3) and BL21Q strains as expression hosts. In comparative whole-genome sequencing analyses, mutations that allowed cells to grow unhindered despite recombinant protein production are identified. A T7 RNA polymerase expression system is only conditionally suitable for long-term cultivation under production conditions. Mutations leading to non-producers occur in either the T7 RNA polymerase gene or the T7 promoter. The host RNA polymerase-based BL21Q expression system remains stable in the production of GFP in long-term cultivations. For the production of Fab, mutations in lacI of the BL21Q derivatives have positive effects on long-term stability. The results indicate that adaptive evolution carried out with genome-integrated E. coli expression systems in microtiter cultivations under industrial-relevant production conditions is an efficient strain development tool for production hosts.
Collapse
Affiliation(s)
- Artur Schuller
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Christoph Köppl
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna, A-1120, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| |
Collapse
|
15
|
Binenbaum I, Atamni HAT, Fotakis G, Kontogianni G, Koutsandreas T, Pilalis E, Mott R, Himmelbauer H, Iraqi FA, Chatziioannou AA. Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity. BMC Genomics 2020; 21:761. [PMID: 33143653 PMCID: PMC7640698 DOI: 10.1186/s12864-020-07173-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/21/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, underlying genetic mechanisms play a crucial role in the response to these factors. The interplay between the genetic background and the gene expression pattern can provide further insight into this response, but we lack robust and easily reproducible workflows to integrate genomic and transcriptomic information in the CC mouse population. RESULTS We established an automated and reproducible integrative workflow to analyse complex traits in the CC mouse genetic reference panel at the genomic and transcriptomic levels. We implemented the analytical workflow to assess the underlying genetic mechanisms of host susceptibility to diet induced obesity and integrated these results with diet induced changes in the hepatic gene expression of susceptible and resistant mice. Hepatic gene expression differs significantly between obese and non-obese mice, with a significant sex effect, where male and female mice exhibit different responses and coping mechanisms. CONCLUSION Integration of the data showed that different genes but similar pathways are involved in the genetic susceptibility and disturbed in diet induced obesity. Genetic mechanisms underlying susceptibility to high-fat diet induced obesity are different in female and male mice. The clear distinction we observed in the systemic response to the high-fat diet challenge and to obesity between male and female mice points to the need for further research into distinct sex-related mechanisms in metabolic disease.
Collapse
Affiliation(s)
- Ilona Binenbaum
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
- Department of Biology, University of Patras, Patras, Greece
| | - Hanifa Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Georgios Fotakis
- Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
- e-NIOS PC, Kallithea, Athens, Greece
| | - Georgia Kontogianni
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodoros Koutsandreas
- e-NIOS PC, Kallithea, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleftherios Pilalis
- e-NIOS PC, Kallithea, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Richard Mott
- Department of Genetics, University College of London, London, UK
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Vienna, Austria
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Aristotelis A Chatziioannou
- e-NIOS PC, Kallithea, Athens, Greece.
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| |
Collapse
|
16
|
Dittami SM, Corre E, Brillet-Guéguen L, Lipinska AP, Pontoizeau N, Aite M, Avia K, Caron C, Cho CH, Collén J, Cormier A, Delage L, Doubleau S, Frioux C, Gobet A, González-Navarrete I, Groisillier A, Hervé C, Jollivet D, KleinJan H, Leblanc C, Liu X, Marie D, Markov GV, Minoche AE, Monsoor M, Pericard P, Perrineau MM, Peters AF, Siegel A, Siméon A, Trottier C, Yoon HS, Himmelbauer H, Boyen C, Tonon T. The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga. Mar Genomics 2020; 52:100740. [PMID: 31937506 DOI: 10.1016/j.margen.2020.100740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/01/2020] [Indexed: 11/20/2022]
Abstract
Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
Collapse
Affiliation(s)
- Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France.
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Noé Pontoizeau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Meziane Aite
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Komlan Avia
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Université de Strasbourg, INRA, SVQV UMR-A 1131, F-68000 Colmar, France
| | - Christophe Caron
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Sylvie Doubleau
- IRD, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | | | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Irene González-Navarrete
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Agnès Groisillier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Cécile Hervé
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Hetty KleinJan
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Xi Liu
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - André E Minoche
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Misharl Monsoor
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Pierre Pericard
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Marie-Mathilde Perrineau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, United Kingdom
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Amandine Siméon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Camille Trottier
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France; Laboratory of Digital Sciences of Nantes (LS2N) - University of Nantes, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190 Vienna, Austria
| | - Catherine Boyen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Thierry Tonon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| |
Collapse
|
17
|
Dohm JC, Peters P, Stralis-Pavese N, Himmelbauer H. Benchmarking of long-read correction methods. NAR Genom Bioinform 2020; 2:lqaa037. [PMID: 33575591 PMCID: PMC7671305 DOI: 10.1093/nargab/lqaa037] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/02/2020] [Accepted: 05/15/2020] [Indexed: 01/25/2023] Open
Abstract
Third-generation sequencing technologies provided by Pacific Biosciences and Oxford Nanopore Technologies generate read lengths in the scale of kilobasepairs. However, these reads display high error rates, and correction steps are necessary to realize their great potential in genomics and transcriptomics. Here, we compare properties of PacBio and Nanopore data and assess correction methods by Canu, MARVEL and proovread in various combinations. We found total error rates of around 13% in the raw datasets. PacBio reads showed a high rate of insertions (around 8%) whereas Nanopore reads showed similar rates for substitutions, insertions and deletions of around 4% each. In data from both technologies the errors were uniformly distributed along reads apart from noisy 5' ends, and homopolymers appeared among the most over-represented kmers relative to a reference. Consensus correction using read overlaps reduced error rates to about 1% when using Canu or MARVEL after patching. The lowest error rate in Nanopore data (0.45%) was achieved by applying proovread on MARVEL-patched data including Illumina short-reads, and the lowest error rate in PacBio data (0.42%) was the result of Canu correction with minimap2 alignment after patching. Our study provides valuable insights and benchmarks regarding long-read data and correction methods.
Collapse
Affiliation(s)
- Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Philipp Peters
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Nancy Stralis-Pavese
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
18
|
Schiavinato M, Marcet‐Houben M, Dohm JC, Gabaldón T, Himmelbauer H. Parental origin of the allotetraploid tobacco Nicotiana benthamiana. Plant J 2020; 102:541-554. [PMID: 31833111 PMCID: PMC7317763 DOI: 10.1111/tpj.14648] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 05/12/2023]
Abstract
Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4-5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long-term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.
Collapse
Affiliation(s)
- Matteo Schiavinato
- Department of BiotechnologyInstitute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Marina Marcet‐Houben
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)The Barcelona Institute of Science and Technology08003BarcelonaSpain
- ICREABarcelonaSpain
| | - Juliane C. Dohm
- Department of BiotechnologyInstitute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Toni Gabaldón
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)The Barcelona Institute of Science and Technology08003BarcelonaSpain
- ICREABarcelonaSpain
- Present address:
Barcelona Supercomputing Centre (BSC‐CNS) and Institute for Research in Biomedicine (IRB)BarcelonaSpain
| | - Heinz Himmelbauer
- Department of BiotechnologyInstitute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| |
Collapse
|
19
|
Zwickl NF, Stralis-Pavese N, Schäffer C, Dohm JC, Himmelbauer H. Comparative genome characterization of the periodontal pathogen Tannerella forsythia. BMC Genomics 2020; 21:150. [PMID: 32046654 PMCID: PMC7014623 DOI: 10.1186/s12864-020-6535-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tannerella forsythia is a bacterial pathogen implicated in periodontal disease. Numerous virulence-associated T. forsythia genes have been described, however, it is necessary to expand the knowledge on T. forsythia's genome structure and genetic repertoire to further elucidate its role within pathogenesis. Tannerella sp. BU063, a putative periodontal health-associated sister taxon and closest known relative to T. forsythia is available for comparative analyses. In the past, strain confusion involving the T. forsythia reference type strain ATCC 43037 led to discrepancies between results obtained from in silico analyses and wet-lab experimentation. RESULTS We generated a substantially improved genome assembly of T. forsythia ATCC 43037 covering 99% of the genome in three sequences. Using annotated genomes of ten Tannerella strains we established a soft core genome encompassing 2108 genes, based on orthologs present in > = 80% of the strains analysed. We used a set of known and hypothetical virulence factors for comparisons in pathogenic strains and the putative periodontal health-associated isolate Tannerella sp. BU063 to identify candidate genes promoting T. forsythia's pathogenesis. Searching for pathogenicity islands we detected 38 candidate regions in the T. forsythia genome. Only four of these regions corresponded to previously described pathogenicity islands. While the general protein O-glycosylation gene cluster of T. forsythia ATCC 43037 has been described previously, genes required for the initiation of glycan synthesis are yet to be discovered. We found six putative glycosylation loci which were only partially conserved in other bacteria. Lastly, we performed a comparative analysis of translational bias in T. forsythia and Tannerella sp. BU063 and detected highly biased genes. CONCLUSIONS We provide resources and important information on the genomes of Tannerella strains. Comparative analyses enabled us to assess the suitability of T. forsythia virulence factors as therapeutic targets and to suggest novel putative virulence factors. Further, we report on gene loci that should be addressed in the context of elucidating T. forsythia's protein O-glycosylation pathway. In summary, our work paves the way for further molecular dissection of T. forsythia biology in general and virulence of this species in particular.
Collapse
Affiliation(s)
- Nikolaus F. Zwickl
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Nancy Stralis-Pavese
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology unit, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Juliane C. Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| |
Collapse
|
20
|
Abu-Toamih Atamni HJ, Kontogianni G, Binenbaum I, Mott R, Himmelbauer H, Lehrach H, Chatziioannou A, Iraqi FA. Hepatic gene expression variations in response to high-fat diet-induced impaired glucose tolerance using RNAseq analysis in collaborative cross mouse population. Mamm Genome 2019; 30:260-275. [PMID: 31650267 DOI: 10.1007/s00335-019-09816-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022]
Abstract
Hepatic gene expression is known to differ between healthy and type 2 diabetes conditions. Identifying these variations will provide better knowledge to the development of gene-targeted therapies. The aim of this study is to assess diet-induced hepatic gene expression of susceptible versus resistant CC lines to T2D development. Next-generation RNA-sequencing was performed for 84 livers of diabetic and non-diabetic mice of 41 different CC lines (both sexes) following 12 weeks on high-fat diet (42% fat). Data analysis revealed significant variations of hepatic gene expression in diabetic versus non-diabetic mice with significant sex effect, where 601 genes were differentially expressed (DE) in overall population (males and females), 718 genes in female mice, and 599 genes in male mice. Top prioritized DE candidate genes were Lepr, Ins2, Mb, Ckm, Mrap2, and Ckmt2 for the overall population; for females-only group were Hdc, Serpina12, Socs1, Socs2, and Mb, while for males-only group were Serpine1, Mb, Ren1, Slc4a1, and Atp2a1. Data analysis for sex differences revealed 193 DE genes in health (Top: Lepr, Cav1, Socs2, Abcg2, and Col5a3), and 389 genes DE between diabetic females versus males (Top: Lepr, Clps, Ins2, Cav1, and Mrap2). Furthermore, integrating gene expression results with previously published QTL, we identified significant variants mapped at chromosomes at positions 36-49 Mb, 62-71 Mb, and 79-99 Mb, on chromosomes 9, 11, and 12, respectively. Our findings emphasize the complexity of T2D development and that significantly controlled by host complex genetic factors. As well, we demonstrate the significant sex differences between males and females during health and increasing to extent levels during disease/diabetes. Altogether, opening the venue for further studies targets the discovery of effective sex-specific and personalized preventions and therapies.
Collapse
Affiliation(s)
- H J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel
| | - G Kontogianni
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - I Binenbaum
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, University of Patras, Patras, Greece
| | - R Mott
- Department of Genetics, University College of London, London, UK
| | - H Himmelbauer
- Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - H Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, 17671, Kallithea, Greece
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel.
| |
Collapse
|
21
|
Rodríguez del Río Á, Minoche AE, Zwickl NF, Friedrich A, Liedtke S, Schmidt T, Himmelbauer H, Dohm JC. Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima. Plant J 2019; 99:1242-1253. [PMID: 31104348 PMCID: PMC9546096 DOI: 10.1111/tpj.14413] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 05/04/2023]
Abstract
We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence-based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome-wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.
Collapse
Affiliation(s)
- Álvaro Rodríguez del Río
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
- Present address:
Centro de Biotecnología y Genómica de PlantasUPM – INIA28223MadridSpain
| | - André E. Minoche
- Garvan Institute of Medical ResearchDarlinghurst2010NSWAustralia
| | - Nikolaus F. Zwickl
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Anja Friedrich
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
- Present address:
FH Campus WienUniversity of Applied Sciences1030ViennaAustria
| | | | | | - Heinz Himmelbauer
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Juliane C. Dohm
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| |
Collapse
|
22
|
Schiavinato M, Strasser R, Mach L, Dohm JC, Himmelbauer H. Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT. BMC Genomics 2019; 20:594. [PMID: 31324144 PMCID: PMC6642603 DOI: 10.1186/s12864-019-5960-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/08/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant's genomic and transcriptomic features. Most N. benthamiana accessions currently used in research lack proper documentation of their breeding history and provenance. One of these, the glycoengineered N. benthamiana line ΔXT/FT is increasingly used for the production of biopharmaceutical proteins. RESULTS Based on an existing draft assembly of the N. benthamiana genome we predict 50,516 protein -encoding genes (62,216 transcripts) supported by expression data derived from 2.35 billion mRNA-seq reads. Using single-copy core genes we show high completeness of the predicted gene set. We functionally annotate more than two thirds of the gene set through sequence homology to genes from other Nicotiana species. We demonstrate that the expression profiles from leaf tissue of ΔXT/FT and its wild type progenitor only show minimal differences. We identify the transgene insertion sites in ΔXT/FT and show that one of the transgenes was inserted inside another predicted gene that most likely lost its function upon insertion. Based on publicly available mRNA-seq data, we confirm that the N. benthamiana accessions used by different research institutions most likely derive from a single source. CONCLUSIONS This work provides gene annotation of the N. benthamiana genome, a genomic and transcriptomic characterization of a transgenic N. benthamiana line in comparison to its wild-type progenitor, and sheds light onto the relatedness of N. benthamiana accessions that are used in laboratories around the world.
Collapse
Affiliation(s)
- Matteo Schiavinato
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Juliane C. Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
23
|
Dhiman H, Gerstl MP, Ruckerbauer D, Hanscho M, Himmelbauer H, Clarke C, Barron N, Zanghellini J, Borth N. Genetic and Epigenetic Variation across Genes Involved in Energy Metabolism and Mitochondria of Chinese Hamster Ovary Cell Lines. Biotechnol J 2019; 14:e1800681. [DOI: 10.1002/biot.201800681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/14/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Heena Dhiman
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Matthias P. Gerstl
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - David Ruckerbauer
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Michael Hanscho
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
| | - Colin Clarke
- National Institute for Bioprocessing Research and TrainingBlackrock, Co Dublin Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and TrainingBlackrock, Co Dublin Ireland
- School of Chemical and Bioprocess EngineeringUniversity College DublinGlasnevin Whitehall Dublin Ireland
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
- Austrian Biotech University of Applied SciencesKonrad Lorenz Strasse 10 3430 Tulln Austria
| | - Nicole Borth
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesVienna Austria
- Austrian Centre of Industrial BiotechnologyMuthgasse 11 1190 Vienna Austria
| |
Collapse
|
24
|
Tomek MB, Maresch D, Windwarder M, Friedrich V, Janesch B, Fuchs K, Neumann L, Nimeth I, Zwickl NF, Dohm JC, Everest-Dass A, Kolarich D, Himmelbauer H, Altmann F, Schäffer C. A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications. Front Microbiol 2018; 9:2008. [PMID: 30210478 PMCID: PMC6120980 DOI: 10.3389/fmicb.2018.02008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
The cell surface of the oral pathogen Tannerella forsythia is heavily glycosylated with a unique, complex decasaccharide that is O-glycosidically linked to the bacterium’s abundant surface (S-) layer, as well as other proteins. The S-layer glycoproteins are virulence factors of T. forsythia and there is evidence that protein O-glycosylation underpins the bacterium’s pathogenicity. To elucidate the protein O-glycosylation pathway, genes suspected of encoding pathway components were first identified in the genome sequence of the ATCC 43037 type strain, revealing a 27-kb gene cluster that was shown to be polycistronic. Using a gene deletion approach targeted at predicted glycosyltransferases (Gtfs) and methyltransferases encoded in this gene cluster, in combination with mass spectrometry of the protein-released O-glycans, we show that the gene cluster encodes the species-specific part of the T. forsythia ATCC 43037 decasaccharide and that this is assembled step-wise on a pentasaccharide core. The core was previously proposed to be conserved within the Bacteroidetes phylum, to which T. forsythia is affiliated, and its biosynthesis is encoded elsewhere on the bacterial genome. Next, to assess the prevalence of protein O-glycosylation among Tannerella sp., the publicly available genome sequences of six T. forsythia strains were compared, revealing gene clusters of similar size and organization as found in the ATCC 43037 type strain. The corresponding region in the genome of a periodontal health-associated Tannerella isolate showed a different gene composition lacking most of the genes commonly found in the pathogenic strains. Finally, we investigated whether differential cell surface glycosylation impacts T. forsythia’s overall immunogenicity. Release of proinflammatory cytokines by dendritic cells (DCs) upon stimulation with defined Gtf-deficient mutants of the type strain was measured and their T cell-priming potential post-stimulation was explored. This revealed that the O-glycan is pivotal to modulating DC effector functions, with the T. forsythia-specific glycan portion suppressing and the pentasaccharide core activating a Th17 response. We conclude that complex protein O-glycosylation is a hallmark of pathogenic T. forsythia strains and propose it as a valuable target for the design of novel antimicrobials against periodontitis.
Collapse
Affiliation(s)
- Markus B Tomek
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Markus Windwarder
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Valentin Friedrich
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Bettina Janesch
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Kristina Fuchs
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Laura Neumann
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Irene Nimeth
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Nikolaus F Zwickl
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Juliane C Dohm
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Arun Everest-Dass
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Heinz Himmelbauer
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Friedrich Altmann
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Christina Schäffer
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| |
Collapse
|
25
|
Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T. nextPARS: parallel probing of RNA structures in Illumina. RNA 2018; 24:609-619. [PMID: 29358234 PMCID: PMC5855959 DOI: 10.1261/rna.063073.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
Abstract
RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing.
Collapse
Affiliation(s)
- Ester Saus
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jesse R Willis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Ahmed Hafez
- Biotechvana, 46980 Paterna (Valencia), Spain
| | | | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
26
|
Koczka K, Peters P, Ernst W, Himmelbauer H, Nika L, Grabherr R. Comparative transcriptome analysis of a Trichoplusia ni cell line reveals distinct host responses to intracellular and secreted protein products expressed by recombinant baculoviruses. J Biotechnol 2018; 270:61-69. [PMID: 29432775 DOI: 10.1016/j.jbiotec.2018.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 01/12/2018] [Accepted: 02/02/2018] [Indexed: 12/17/2022]
Abstract
The baculovirus insect cell expression system has become a firmly established production platform in biotechnology. Various complex proteins, multi-subunit particles including veterinary and human vaccines are manufactured with this system on a commercial scale. Apart from baculovirus infected Spodoptera frugiperda (Sf9) cells, the Trichoplusia ni (HighFive) cell line is alternatively used as host organism. In this study, we explored the protein production capabilities of Tnms42 insect cells, a new derivative of HighFive, which is free of latent nodavirus infection. As a model system, a cytosolic (mCherry) and a secreted (hemagglutinin) protein were overexpressed in Tnms42 cells. The response of the host cells was followed in a time course experiment over the infection cycle by comparative transcriptome analysis (RNA-seq). As expected, the baculovirus infection per se had a massive impact on the host cell transcriptome, which was observed by the huge total number of differentially expressed transcripts (>14,000). Despite this severe overall cellular reaction, a specific response could be clearly attributed to the overexpression of secreted hemagglutinin, revealing limits in the secretory capacity of the host cell. About 400 significantly regulated transcripts were identified and assigned to biochemical pathways and gene ontology (GO) categories, all related to protein processing, folding and response to unfolded protein. The identification of relevant target genes will serve to design specific virus engineering concepts for improving the yield of proteins that are dependent on the secretory pathway.
Collapse
Affiliation(s)
- Krisztina Koczka
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Philipp Peters
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Wolfgang Ernst
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| | - Lisa Nika
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.
| |
Collapse
|
27
|
Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin JC, Notredame C, Späth GF. Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani. Nat Ecol Evol 2017; 1:1961-1969. [DOI: 10.1038/s41559-017-0361-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/26/2017] [Indexed: 11/09/2022]
|
28
|
Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Soerensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ. Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes. Nat Commun 2017; 8:15708. [PMID: 28585529 PMCID: PMC5467160 DOI: 10.1038/ncomms15708] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/21/2017] [Indexed: 01/13/2023] Open
Abstract
Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing. Variation among wild relatives of crop plants can be used to identify genes underlying traits of agronomic importance. Here, the authors show that a modified mapping-by-sequencing approach can rapidly identify the genetic basis for viral resistance in sugar beet using wild beet populations in their natural habitat.
Collapse
Affiliation(s)
| | - D Ries
- CeBiTec &Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - D Holtgräwe
- CeBiTec &Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - A Minoche
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, Berlin 14195, Germany.,Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney NSW 2010, Australia
| | - T Kraft
- Syngenta Seeds AB, Box 302, Landskrona 26123, Sweden
| | - S L M Frerichmann
- Plant Breeding Institute, Kiel University, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - T Rosleff Soerensen
- CeBiTec &Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - J C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - I González
- Centre for Genomic Regulation (CRG), Carrer del Dr. Aiguader 88, Barcelona 08003, Spain
| | - M Schilhabel
- Plant Breeding Institute, Kiel University, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - M Varrelmann
- Department of Phytopathology, Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, Göttingen 37079, Germany
| | - H Tschoep
- SESVanderHave N.V., Industriepark, Tienen 3300, Belgium
| | - H Uphoff
- Syngenta Seeds AB, Box 302, Landskrona 26123, Sweden
| | - K Schütze
- KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| | - D Borchardt
- KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| | - O Toerjek
- KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| | - W Mechelke
- KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| | - J C Lein
- KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| | - A W Schechert
- Strube Research GmbH &Co. KG, Hauptstraße 1, Söllingen 38387, Germany
| | - L Frese
- Federal Research Centre for Cultivated Plants (JKI), Erwin-Baur-Str. 27, Quedlinburg 06484, Germany
| | - H Himmelbauer
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, Berlin 14195, Germany.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Centre for Genomic Regulation (CRG), Carrer del Dr. Aiguader 88, Barcelona 08003, Spain
| | - B Weisshaar
- CeBiTec &Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - F J Kopisch-Obuch
- Plant Breeding Institute, Kiel University, Am Botanischen Garten 1-9, Kiel 24118, Germany.,KWS SAAT SE, Grimsehlstraße 31, Einbeck 37555, Germany
| |
Collapse
|
29
|
Nachshon A, Abu-Toamih Atamni HJ, Steuerman Y, Sheikh-Hamed R, Dorman A, Mott R, Dohm JC, Lehrach H, Sultan M, Shamir R, Sauer S, Himmelbauer H, Iraqi FA, Gat-Viks I. Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains. Front Genet 2016; 7:172. [PMID: 27761138 PMCID: PMC5050206 DOI: 10.3389/fgene.2016.00172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/09/2016] [Indexed: 12/26/2022] Open
Abstract
A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences.
Collapse
Affiliation(s)
- Aharon Nachshon
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| | - Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Yael Steuerman
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| | - Roa'a Sheikh-Hamed
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Alexandra Dorman
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Richard Mott
- Genetics Institute, University College of London London, UK
| | - Juliane C Dohm
- Genomics Unit, Center for Genomic RegulationBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU)Vienna, Austria
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
| | - Sascha Sauer
- Department of Vertebrate Genomics, Max Planck Institute for Molecular GeneticsBerlin, Germany; CU Systems Medicine, University of WürzburgWürzburg, Germany
| | - Heinz Himmelbauer
- Genomics Unit, Center for Genomic RegulationBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU)Vienna, Austria
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel- Aviv University Tel-Aviv, Israel
| | - Irit Gat-Viks
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel-Aviv University Tel-Aviv, Israel
| |
Collapse
|
30
|
Harnisch C, Cuzic-Feltens S, Dohm JC, Götze M, Himmelbauer H, Wahle E. Oligoadenylation of 3' decay intermediates promotes cytoplasmic mRNA degradation in Drosophila cells. RNA 2016; 22:428-42. [PMID: 26786835 PMCID: PMC4748820 DOI: 10.1261/rna.053942.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
Post-transcriptional 3' end addition of nucleotides is important in a variety of RNA decay pathways. We have examined the 3' end addition of nucleotides during the decay of the Hsp70 mRNA and a corresponding reporter RNA in Drosophila S2 cells by conventional sequencing of cDNAs obtained after mRNA circularization and by deep sequencing of dedicated libraries enriched for 3' decay intermediates along the length of the mRNA. Approximately 5%-10% of 3' decay intermediates carried nonencoded oligo(A) tails with a mean length of 2-3 nucleotides. RNAi experiments showed that the oligoadenylated RNA fragments were intermediates of exosomal decay and the noncanonical poly(A) polymerase Trf4-1 was mainly responsible for A addition. A hot spot of A addition corresponded to an intermediate of 3' decay that accumulated upon inhibition of decapping, and knockdown of Trf4-1 increased the abundance of this intermediate, suggesting that oligoadenylation facilitates 3' decay. Oligoadenylated 3' decay intermediates were found in the cytoplasmic fraction in association with ribosomes, and fluorescence microscopy revealed a cytoplasmic localization of Trf4-1. Thus, oligoadenylation enhances exosomal mRNA degradation in the cytoplasm.
Collapse
Affiliation(s)
- Christiane Harnisch
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Simona Cuzic-Feltens
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Juliane C Dohm
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Michael Götze
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| |
Collapse
|
31
|
Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
Collapse
Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
| |
Collapse
|
32
|
Schwichtenberg K, Wenke T, Zakrzewski F, Seibt KM, Minoche A, Dohm JC, Weisshaar B, Himmelbauer H, Schmidt T. Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species. Plant J 2016; 85:229-44. [PMID: 26676716 DOI: 10.1111/tpj.13103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
Short interspersed nuclear elements (SINEs) are non-autonomous non-long terminal repeat retrotransposons which are widely distributed in eukaryotic organisms. While SINEs have been intensively studied in animals, only limited information is available about plant SINEs. We analysed 22 SINE families from seven genomes of the Amaranthaceae family and identified 34 806 SINEs, including 19 549 full-length copies. With the focus on sugar beet (Beta vulgaris), we performed a comparative analysis of the diversity, genomic and chromosomal organization and the methylation of SINEs to provide a detailed insight into the evolution and age of Amaranthaceae SINEs. The lengths of consensus sequences of SINEs range from 113 nucleotides (nt) up to 224 nt. The SINEs show dispersed distribution on all chromosomes but were found with higher incidence in subterminal euchromatic chromosome regions. The methylation of SINEs is increased compared with their flanking regions, and the strongest effect is visible for cytosines in the CHH context, indicating an involvement of asymmetric methylation in the silencing of SINEs.
Collapse
Affiliation(s)
| | - Torsten Wenke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Falk Zakrzewski
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Kathrin M Seibt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - André Minoche
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia
| | - Juliane C Dohm
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Bernd Weisshaar
- CeBiTec & Department of Biology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Heinz Himmelbauer
- Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| |
Collapse
|
33
|
Minoche AE, Dohm JC, Schneider J, Holtgräwe D, Viehöver P, Montfort M, Sörensen TR, Weisshaar B, Himmelbauer H. Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. Genome Biol 2015; 16:184. [PMID: 26328666 PMCID: PMC4556409 DOI: 10.1186/s13059-015-0729-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 07/22/2015] [Indexed: 12/20/2022] Open
Abstract
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.
Collapse
Affiliation(s)
- André E Minoche
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Jessica Schneider
- Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Prisca Viehöver
- Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Magda Montfort
- Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Thomas Rosleff Sörensen
- Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
| | - Heinz Himmelbauer
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Centre for Genomic Regulation (CRG), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
| |
Collapse
|
34
|
Holtgräwe D, Sörensen TR, Viehöver P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B. Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris). PLoS One 2014; 9:e110113. [PMID: 25302600 PMCID: PMC4193868 DOI: 10.1371/journal.pone.0110113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/07/2014] [Indexed: 02/03/2023] Open
Abstract
Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers.
Collapse
Affiliation(s)
- Daniela Holtgräwe
- CeBiTec & Department of Biology, University of Bielefeld, Bielefeld, Germany
- * E-mail:
| | | | - Prisca Viehöver
- CeBiTec & Department of Biology, University of Bielefeld, Bielefeld, Germany
| | - Jessica Schneider
- CeBiTec & Department of Biology, University of Bielefeld, Bielefeld, Germany
| | - Britta Schulz
- Molecular Breeding Sugarbeet, KWS Saat AG, Einbeck, Germany
| | | | | | - Heinz Himmelbauer
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Centre for Genomic Regulation, Barcelona, Spain
| | - Bernd Weisshaar
- CeBiTec & Department of Biology, University of Bielefeld, Bielefeld, Germany
| |
Collapse
|
35
|
Bellmunt J, Selvarajah S, Rodig S, Salido M, de Muga S, Costa I, Bellosillo B, Werner L, Mullane S, Fay AP, O'Brien R, Barretina J, Minoche AE, Signoretti S, Montagut C, Himmelbauer H, Berman DM, Kantoff P, Choueiri TK, Rosenberg JE. Identification of ALK gene alterations in urothelial carcinoma. PLoS One 2014; 9:e103325. [PMID: 25083769 PMCID: PMC4118868 DOI: 10.1371/journal.pone.0103325] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022] Open
Abstract
Background Anaplastic lymphoma kinase (ALK) genomic alterations have emerged as a potent predictor of benefit from treatment with ALK inhibitors in several cancers. Currently, there is no information about ALK gene alterations in urothelial carcinoma (UC) and its correlation with clinical or pathologic features and outcome. Methods Samples from patients with advanced UC and correlative clinical data were collected. Genomic imbalances were investigated by array comparative genomic hybridization (aCGH). ALK gene status was evaluated by fluorescence in situ hybridization (FISH). ALK expression was assessed by immunohistochemistry (IHC) and high-throughput mutation analysis with Oncomap 3 platform. Next generation sequencing was performed using Illumina Genome Analyzer IIx, and Illumina HiSeq 2000 in the FISH positive case. Results 70 of 96 patients had tissue available for all the tests performed. Arm level copy number gains at chromosome 2 were identified in 17 (24%) patients. Minor copy number alterations (CNAs) in the proximity of ALK locus were found in 3 patients by aCGH. By FISH analysis, one of these samples had a deletion of the 5′ALK. Whole genome next generation sequencing was inconclusive to confirm the deletion at the level of the ALK gene at the coverage level used. We did not observe an association between ALK CNA and overall survival, ECOG PS, or development of visceral disease. Conclusions ALK genomic alterations are rare and probably without prognostic implications in UC. The potential for testing ALK inhibitors in UC merits further investigation but might be restricted to the identification of an enriched population.
Collapse
Affiliation(s)
- Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
- Hospital del Mar Research Institute-IMIM, Barcelona, Spain
- * E-mail:
| | - Shamini Selvarajah
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Scott Rodig
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marta Salido
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Silvia de Muga
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | | | - Beatriz Bellosillo
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Lillian Werner
- Biostatistics and Computational Biology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Stephanie Mullane
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - André P. Fay
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert O'Brien
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jordi Barretina
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - André E. Minoche
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Sabina Signoretti
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Clara Montagut
- Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - David M. Berman
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Philip Kantoff
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Toni K. Choueiri
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan E. Rosenberg
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| |
Collapse
|
36
|
Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B, Schmidt T. Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades. Plant J 2014; 79:385-97. [PMID: 24862340 DOI: 10.1111/tpj.12565] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 05/03/2023]
Abstract
A large fraction of eukaryotic genomes is made up of long interspersed nuclear elements (LINEs). Due to their capability to create novel copies via error-prone reverse transcription, they generate multiple families and reach high copy numbers. Although mammalian LINEs have been well described, plant LINEs have been only poorly investigated. Here, we present a systematic cross-species survey of LINEs in higher plant genomes shedding light on plant LINE evolution as well as diversity, and facilitating their annotation in genome projects. Applying a Hidden Markov Model (HMM)-based analysis, 59 390 intact LINE reverse transcriptases (RTs) were extracted from 23 plant genomes. These fall in only two out of 28 LINE clades (L1 and RTE) known in eukaryotes. While plant RTE LINEs are highly homogenous and mostly constitute only a single family per genome, plant L1 LINEs are extremely diverse and form numerous families. Despite their heterogeneity, all members across the 23 species fall into only seven L1 subclades, some of them defined here. Exemplarily focusing on the L1 LINEs of a basal reference plant genome (Beta vulgaris), we show that the subclade classification level does not only reflect RT sequence similarity, but also mirrors structural aspects of complete LINE retrotransposons, like element size, position and type of encoded enzymatic domains. Our comprehensive catalogue of plant LINE RTs serves the classification of highly diverse plant LINEs, while the provided subclade-specific HMMs facilitate their annotation.
Collapse
Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | | | | | | | | | | | | |
Collapse
|
37
|
Schmidt M, Hense S, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T, Zakrzewski F. Cytosine methylation of an ancient satellite family in the wild beet Beta procumbens. Cytogenet Genome Res 2014; 143:157-67. [PMID: 24994030 DOI: 10.1159/000363485] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.
Collapse
Affiliation(s)
- Martin Schmidt
- Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, Germany
| | | | | | | | | | | | | |
Collapse
|
38
|
Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T. The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation. Plant J 2014; 78:937-50. [PMID: 24661787 DOI: 10.1111/tpj.12519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 05/03/2023]
Abstract
Methylation of DNA is important for the epigenetic silencing of repetitive DNA in plant genomes. Knowledge about the cytosine methylation status of satellite DNAs, a major class of repetitive DNA, is scarce. One reason for this is that arrays of tandemly arranged sequences are usually collapsed in next-generation sequencing assemblies. We applied strategies to overcome this limitation and quantified the level of cytosine methylation and its pattern in three satellite families of sugar beet (Beta vulgaris) which differ in their abundance, chromosomal localization and monomer size. We visualized methylation levels along pachytene chromosomes with respect to small satellite loci at maximum resolution using chromosome-wide fluorescent in situ hybridization complemented with immunostaining and super-resolution microscopy. Only reduced methylation of many satellite arrays was obtained. To investigate methylation at the nucleotide level we performed bisulfite sequencing of 1569 satellite sequences. We found that the level of methylation of cytosine strongly depends on the sequence context: cytosines in the CHH motif show lower methylation (44-52%), while CG and CHG motifs are more strongly methylated. This affects the overall methylation of satellite sequences because CHH occurs frequently while CG and CHG are rare or even absent in the satellite arrays investigated. Evidently, CHH is the major target for modulation of the cytosine methylation level of adjacent monomers within individual arrays and contributes to their epigenetic function. This strongly indicates that asymmetric cytosine methylation plays a role in the epigenetic modification of satellite repeats in plant genomes.
Collapse
Affiliation(s)
- Falk Zakrzewski
- Department of Plant Cell and Molecular Biology, TU Dresden, D-01062, Dresden, Germany
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Bendadani C, Meinl W, Monien B, Dobbernack G, Florian S, Engst W, Nolden T, Himmelbauer H, Glatt H. Determination of Sulfotransferase Forms Involved in the Metabolic Activation of the Genotoxicant 1-Hydroxymethylpyrene Using Bacterially Expressed Enzymes and Genetically Modified Mouse Models. Chem Res Toxicol 2014; 27:1060-9. [DOI: 10.1021/tx500129g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carolin Bendadani
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Walter Meinl
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Bernhard Monien
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Gisela Dobbernack
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Simone Florian
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Wolfram Engst
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Tobias Nolden
- Department
of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Heinz Himmelbauer
- Department
of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Hansruedi Glatt
- Department
of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| |
Collapse
|
40
|
Aksoy I, Giudice V, Delahaye E, Wianny F, Aubry M, Mure M, Chen J, Jauch R, Bogu GK, Nolden T, Himmelbauer H, Xavier Doss M, Sachinidis A, Schulz H, Hummel O, Martinelli P, Hübner N, Stanton LW, Real FX, Bourillot PY, Savatier P. Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in embryonic stem cells. Nat Commun 2014; 5:3719. [PMID: 24770696 DOI: 10.1038/ncomms4719] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/24/2014] [Indexed: 01/04/2023] Open
Abstract
Krüppel-like factors (Klf) 4 and 5 are two closely related members of the Klf family, known to play key roles in cell cycle regulation, somatic cell reprogramming and pluripotency. Here we focus on the functional divergence between Klf4 and Klf5 in the inhibition of mouse embryonic stem (ES) cell differentiation. Using microarrays and chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing, we show that Klf4 negatively regulates the expression of endodermal markers in the undifferentiated ES cells, including transcription factors involved in the commitment of pluripotent stem cells to endoderm differentiation. Knockdown of Klf4 enhances differentiation towards visceral and definitive endoderm. In contrast, Klf5 negatively regulates the expression of mesodermal markers, some of which control commitment to the mesoderm lineage, and knockdown of Klf5 specifically enhances differentiation towards mesoderm. We conclude that Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in murine ES cells.
Collapse
Affiliation(s)
- Irène Aksoy
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France [4] Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore [5]
| | - Vincent Giudice
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France [4]
| | - Edwige Delahaye
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Florence Wianny
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Maxime Aubry
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Magali Mure
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Jiaxuan Chen
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Ralf Jauch
- 1] Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore [2] Genome Regulation Laboratory, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Gireesh K Bogu
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Tobias Nolden
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Heinz Himmelbauer
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany [2] Center for Genomic Regulation (CRG), C. Dr. Aiguader 88, Barcelona 08003, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, Barcelona 08003, Spain
| | - Michael Xavier Doss
- 1] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, Barcelona 08003, Spain [2]
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, Robert-Koch-Strasse. 39, Cologne 50931, Germany
| | - Herbert Schulz
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Oliver Hummel
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Paola Martinelli
- Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Lawrence W Stanton
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Francisco X Real
- 1] Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro 3, Madrid 28029, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Pierre-Yves Bourillot
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Pierre Savatier
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| |
Collapse
|
41
|
Leiva-Eriksson N, Pin PA, Kraft T, Dohm JC, Minoche AE, Himmelbauer H, Bülow L. Differential expression patterns of non-symbiotic hemoglobins in sugar beet (Beta vulgaris ssp. vulgaris). Plant Cell Physiol 2014; 55:834-44. [PMID: 24486763 DOI: 10.1093/pcp/pcu027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biennial sugar beet (Beta vulgaris spp. vulgaris) is a Caryophyllidae that has adapted its growth cycle to the seasonal temperature and daylength variation of temperate regions. This is the first time a holistic study of the expression pattern of non-symbiotic hemoglobins (nsHbs) is being carried out in a member of this group and under two essential environmental conditions for flowering, namely vernalization and length of photoperiod. BvHb genes were identified by sequence homology searches against the latest draft of the sugar beet genome. Three nsHb genes (BvHb1.1, BvHb1.2 and BvHb2) and one truncated Hb gene (BvHb3) were found in the genome of sugar beet. Gene expression profiling of the nsHb genes was carried out by quantitative PCR in different organs and developmental stages, as well as during vernalization and under different photoperiods. BvHb1.1 and BvHb2 showed differential expression during vernalization as well as during long and short days. The high expression of BvHb2 indicates that it has an active role in the cell, maybe even taking over some BvHb1.2 functions, except during germination where BvHb1.2 together with BvHb1.1-both Class 1 nsHbs-are highly expressed. The unprecedented finding of a leader peptide at the N-terminus of BvHb1.1, for the first time in an nsHb from higher plants, together with its observed expression indicate that it may have a very specific role due to its suggested location in chloroplasts. Our findings open up new possibilities for research, breeding and engineering since Hbs could be more involved in plant development than previously was anticipated.
Collapse
Affiliation(s)
- Nélida Leiva-Eriksson
- Department of Pure and Applied Biochemistry, Lund University, Box 124, 221.00 Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
42
|
Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 2013; 505:546-9. [PMID: 24352233 DOI: 10.1038/nature12817] [Citation(s) in RCA: 326] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 10/29/2013] [Indexed: 01/25/2023]
Abstract
Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
Collapse
Affiliation(s)
- Juliane C Dohm
- 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4]
| | - André E Minoche
- 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4]
| | - Daniela Holtgräwe
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Salvador Capella-Gutiérrez
- 1] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Falk Zakrzewski
- TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Hakim Tafer
- University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Oliver Rupp
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Thomas Rosleff Sörensen
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Ralf Stracke
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Alexander Goesmann
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Britta Schulz
- KWS SAAT AG, Grimsehlstraße 31, 37574 Einbeck, Germany
| | - Peter F Stadler
- University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Thomas Schmidt
- TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Toni Gabaldón
- 1] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Bernd Weisshaar
- Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Heinz Himmelbauer
- 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain
| |
Collapse
|
43
|
Herrmann K, Engst W, Meinl W, Florian S, Cartus AT, Schrenk D, Appel KE, Nolden T, Himmelbauer H, Glatt H. Formation of hepatic DNA adducts by methyleugenol in mouse models: drastic decrease by Sult1a1 knockout and strong increase by transgenic human SULT1A1/2. Carcinogenesis 2013; 35:935-41. [PMID: 24318996 DOI: 10.1093/carcin/bgt408] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Methyleugenol--a natural constituent of herbs and spices--is hepatocarcinogenic in rodent models. It can form DNA adducts after side-chain hydroxylation and sulfation. We previously demonstrated that human sulfotransferases (SULTs) 1A1 and 1A2 as well as mouse Sult1a1, expressed in Salmonella target strains, are able to activate 1'-hydroxymethyleugenol (1'-OH-ME) and 3'-hydroxymethylisoeugenol (3'-OH-MIE) to mutagens. Now we investigated the role of these enzymes in the formation of hepatic DNA adducts by methyleugenol in the mouse in vivo. We used FVB/N mice [wild-type (wt)] and genetically modified strains in this background: Sult1a1 knockout (ko), transgenic for human SULT1A1/2 (tg) and the combination of both modifications (ko-tg). Methyleugenol (50mg/kg body mass) formed 23, 735, 3770 and 4500 N (2)-(trans-methylisoeugenol-3'-yl)-2'-deoxyguanosine adducts per 10(8) 2'-deoxyribonucleosides (dN) in ko, wt, ko-tg and tg mice, respectively. The corresponding values for an equimolar dose of 1'-OH-ME were 12, 1490, 12 400 and 13 300 per 10(8) dN. Similar relative levels were observed for the minor adduct, N (6)-(trans-methylisoeugenol-3'-yl)-2'-deoxyadenosine. Thus, the adduct formation by both compounds was nearly completely dependent on the presence of SULT1A enzymes, with human SULT1A1/2 producing stronger effects than mouse Sult1a1. Moreover, a dose of 0.05 mg/kg methyleugenol (one-fourth of the estimated average daily exposure of humans) was sufficient to form detectable adducts in humanized (ko-tg) mice. Although 3'-OH-MIE was equally mutagenic to 1'-OH-ME in Salmonella strains expressing human SULT1A1 or 1A2, it only formed 0.14% of hepatic adducts in ko-tg mice compared with an equimolar dose of 1'-OH-ME, suggesting an important role of detoxifying pathways for this isomer in vivo.
Collapse
Affiliation(s)
- Kristin Herrmann
- Department of Nutritional Toxicology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Dokas J, Chadt A, Nolden T, Himmelbauer H, Zierath JR, Joost HG, Al-Hasani H. Conventional knockout of Tbc1d1 in mice impairs insulin- and AICAR-stimulated glucose uptake in skeletal muscle. Endocrinology 2013; 154:3502-14. [PMID: 23892475 DOI: 10.1210/en.2012-2147] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the obesity-resistant SJL mouse strain, we previously identified a naturally occurring loss-of-function mutation in the gene for Tbc1d1. Characterization of recombinant inbred mice that carried the Tbc1d1(SJL) allele on a C57BL/6J background indicated that loss of TBC1D1 protects from obesity, presumably by increasing the use of fat as energy source. To provide direct functional evidence for an involvement of TBC1D1 in energy substrate metabolism, we generated and characterized conventional Tbc1d1 knockout mice. TBC1D1-deficient mice showed moderately reduced body weight, decreased respiratory quotient, and an elevated resting metabolic rate. Ex vivo analysis of intact isolated skeletal muscle revealed a severe impairment in insulin- and AICAR-stimulated glucose uptake in glycolytic extensor digitorum longus muscle and a substantially increased rate of fatty acid oxidation in oxidative soleus muscle. Our results provide direct evidence that TBC1D1 plays a major role in glucose and lipid utilization, and energy substrate preference in skeletal muscle.
Collapse
Affiliation(s)
- Janine Dokas
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at the Heinrich-Heine-University Düsseldorf, Auf'm Hennekamp 65, 40225 Düsseldorf, Germany.
| | | | | | | | | | | | | |
Collapse
|
45
|
Llorens F, Hummel M, Pantano L, Pastor X, Vivancos A, Castillo E, Mattlin H, Ferrer A, Ingham M, Noguera M, Kofler R, Dohm JC, Pluvinet R, Bayés M, Himmelbauer H, del Rio JA, Martí E, Sumoy L. Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor. BMC Genomics 2013; 14:371. [PMID: 23724959 PMCID: PMC3680220 DOI: 10.1186/1471-2164-14-371] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 05/20/2013] [Indexed: 01/04/2023] Open
Abstract
Background Epidermal Growth Factor (EGF) plays an important function in the regulation of cell growth, proliferation, and differentiation by binding to its receptor (EGFR) and providing cancer cells with increased survival responsiveness. Signal transduction carried out by EGF has been extensively studied at both transcriptional and post-transcriptional levels. Little is known about the involvement of microRNAs (miRNAs) in the EGF signaling pathway. miRNAs have emerged as major players in the complex networks of gene regulation, and cancer miRNA expression studies have evidenced a direct involvement of miRNAs in cancer progression. Results In this study, we have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by reverse transcription quantitative PCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomiRs) among regulated miRNAs. Conclusions We propose that the use of global genomic miRNA cross-validation derived from high throughput technologies can be used to generate more reliable datasets inferring more robust networks of co-regulated predicted miRNA target genes.
Collapse
Affiliation(s)
- Franc Llorens
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Weber B, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T. Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration. Mob DNA 2013; 4:8. [PMID: 23448600 PMCID: PMC3605345 DOI: 10.1186/1759-8753-4-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 01/22/2013] [Indexed: 12/25/2022] Open
Abstract
Background Chromoviruses are one of the three genera of Ty3-gypsy long terminal repeat (LTR) retrotransposons, and are present in high copy numbers in plant genomes. They are widely distributed within the plant kingdom, with representatives even in lower plants such as green and red algae. Their hallmark is the presence of a chromodomain at the C-terminus of the integrase. The chromodomain exhibits structural characteristics similar to proteins of the heterochromatin protein 1 (HP1) family, which mediate the binding of each chromovirus type to specific histone variants. A specific integration via the chromodomain has been shown for only a few chromoviruses. However, a detailed study of different chromoviral clades populating a single plant genome has not yet been carried out. Results We conducted a comprehensive survey of chromoviruses within the Beta vulgaris (sugar beet) genome, and found a highly diverse chromovirus population, with significant differences in element size, primarily caused by their flanking LTRs. In total, we identified and annotated full-length members of 16 families belonging to the four plant chromoviral clades: CRM, Tekay, Reina, and Galadriel. The families within each clade are structurally highly conserved; in particular, the position of the chromodomain coding region relative to the polypurine tract is clade-specific. Two distinct groups of chromodomains were identified. The group II chromodomain was present in three chromoviral clades, whereas families of the CRM clade contained a more divergent motif. Physical mapping using representatives of all four clades identified a clade-specific integration pattern. For some chromoviral families, we detected the presence of expressed sequence tags, indicating transcriptional activity. Conclusions We present a detailed study of chromoviruses, belonging to the four major clades, which populate a single plant genome. Our results illustrate the diversity and family structure of B. vulgaris chromoviruses, and emphasize the role of chromodomains in the targeted integration of these viruses. We suggest that the diverse sets of plant chromoviruses with their different localization patterns might help to facilitate plant-genome organization in a structural and functional manner.
Collapse
Affiliation(s)
- Beatrice Weber
- Institute of Botany, Dresden University of Technology, Dresden D-01062, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J. Comparative transcriptomics of early dipteran development. BMC Genomics 2013; 14:123. [PMID: 23432914 PMCID: PMC3616871 DOI: 10.1186/1471-2164-14-123] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/19/2013] [Indexed: 12/24/2022] Open
Abstract
Background Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). Results We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. Conclusions We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).
Collapse
Affiliation(s)
- Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Wollrab C, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T. Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. Plant J 2012; 72:636-51. [PMID: 22804913 DOI: 10.1111/j.1365-313x.2012.05107.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
LTR retrotransposons and retroviruses are closely related. Although a viral envelope gene is found in some LTR retrotransposons and all retroviruses, only the latter show infectivity. The identification of Ty3-gypsy-like retrotransposons possessing putative envelope-like open reading frames blurred the taxonomical borders and led to the establishment of the Errantivirus, Metavirus and Chromovirus genera within the Metaviridae. Only a few plant Errantiviruses have been described, and their evolutionary history is not well understood. In this study, we investigated 27 retroelements of four abundant Elbe retrotransposon families belonging to the Errantiviruses in Beta vulgaris (sugar beet). Retroelements of the Elbe lineage integrated between 0.02 and 5.59 million years ago, and show family-specific variations in autonomy and degree of rearrangements: while Elbe3 members are highly fragmented, often truncated and present in a high number of solo LTRs, Elbe2 members are mainly autonomous. We observed extensive reshuffling of structural motifs across families, leading to the formation of new retrotransposon families. Elbe retrotransposons harbor a typical envelope-like gene, often encoding transmembrane domains. During the course of Elbe evolution, the additional open reading frames have been strongly modified or independently acquired. Taken together, the Elbe lineage serves as retrotransposon model reflecting the various stages in Errantivirus evolution, and allows a detailed analysis of retrotransposon family formation.
Collapse
Affiliation(s)
- Cora Wollrab
- Department of Biology, Dresden University of Technology, D-01062, Dresden, Germany
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Dohm JC, Lange C, Holtgräwe D, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris). Plant J 2012; 70:528-540. [PMID: 22211633 DOI: 10.1111/j.1365-313x.2011.04898.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.
Collapse
Affiliation(s)
- Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Berndt H, Harnisch C, Rammelt C, Stöhr N, Zirkel A, Dohm JC, Himmelbauer H, Tavanez JP, Hüttelmaier S, Wahle E. Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming. RNA 2012; 18:958-72. [PMID: 22442037 PMCID: PMC3334704 DOI: 10.1261/rna.032292.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/14/2012] [Indexed: 05/17/2023]
Abstract
Small nucleolar and small Cajal body RNAs (snoRNAs and scaRNAs) of the H/ACA box and C/D box type are generated by exonucleolytic shortening of longer precursors. Removal of the last few nucleotides at the 3' end is known to be a distinct step. We report that, in human cells, knock-down of the poly(A) specific ribonuclease (PARN), previously implicated only in mRNA metabolism, causes the accumulation of oligoadenylated processing intermediates of H/ACA box but not C/D box RNAs. In agreement with a role of PARN in snoRNA and scaRNA processing, the enzyme is concentrated in nucleoli and Cajal bodies. Oligo(A) tails are attached to a short stub of intron sequence remaining beyond the mature 3' end of the snoRNAs. The noncanonical poly(A) polymerase PAPD5 is responsible for addition of the oligo(A) tails. We suggest that deadenylation is coupled to clean 3' end trimming, which might serve to enhance snoRNA stability.
Collapse
Affiliation(s)
- Heike Berndt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Harnisch
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Nadine Stöhr
- Section for Molecular Cell Biology, Department of Medicine, Martin Luther University Halle-Wittenberg, 06097 Halle, Germany
| | - Anne Zirkel
- Section for Molecular Cell Biology, Department of Medicine, Martin Luther University Halle-Wittenberg, 06097 Halle, Germany
| | - Juliane C. Dohm
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | | | - Joao-Paulo Tavanez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Stefan Hüttelmaier
- Section for Molecular Cell Biology, Department of Medicine, Martin Luther University Halle-Wittenberg, 06097 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
- Corresponding author.E-mail .
| |
Collapse
|