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Bleker C, Ramšak Ž, Bittner A, Podpečan V, Zagorščak M, Wurzinger B, Baebler Š, Petek M, Križnik M, van Dieren A, Gruber J, Afjehi-Sadat L, Weckwerth W, Županič A, Teige M, Vothknecht UC, Gruden K. Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. Plant Commun 2024:100920. [PMID: 38616489 DOI: 10.1016/j.xplc.2024.100920] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
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Affiliation(s)
- Carissa Bleker
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Andras Bittner
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Vid Podpečan
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Bernhard Wurzinger
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Annelotte van Dieren
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Juliane Gruber
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Leila Afjehi-Sadat
- Mass Spectrometry Unit, Core Facility Shared Services, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Anže Županič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Markus Teige
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ute C Vothknecht
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia.
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2
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Romero-Rodríguez B, Petek M, Jiao C, Križnik M, Zagorščak M, Fei Z, Bejarano ER, Gruden K, Castillo AG. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato. BMC Plant Biol 2023; 23:651. [PMID: 38110861 PMCID: PMC10726652 DOI: 10.1186/s12870-023-04534-y] [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] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/17/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). RESULTS We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. CONCLUSION We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
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Affiliation(s)
- Beatriz Romero-Rodríguez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- The Key Lab of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain.
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3
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Dermastia M, Tomaž Š, Strah R, Lukan T, Coll A, Dušak B, Anžič B, Čepin T, Wienkoop S, Kladnik A, Zagorščak M, Riedle-Bauer M, Schönhuber C, Weckwerth W, Gruden K, Roitsch T, Pompe Novak M, Brader G. Candidate pathogenicity factor/effector proteins of ' Candidatus Phytoplasma solani' modulate plant carbohydrate metabolism, accelerate the ascorbate-glutathione cycle, and induce autophagosomes. Front Plant Sci 2023; 14:1232367. [PMID: 37662165 PMCID: PMC10471893 DOI: 10.3389/fpls.2023.1232367] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including 'Candidiatus Phytoplasma solani' are unknown. Six putative pathogenicity factors/effectors from six different strains of 'Ca. P. solani' were selected by bioinformatic analysis. The way in which they manipulate the host cellular machinery was elucidated by analyzing Nicotiana benthamiana leaves after Agrobacterium-mediated transient transformation with the pathogenicity factor/effector constructs using confocal microscopy, pull-down, and co-immunoprecipitation, and enzyme assays. Candidate pathogenicity factors/effectors were shown to modulate plant carbohydrate metabolism and the ascorbate-glutathione cycle and to induce autophagosomes. PoStoSP06, PoStoSP13, and PoStoSP28 were localized in the nucleus and cytosol. The most active effector in the processes studied was PoStoSP06. PoStoSP18 was associated with an increase in phosphoglucomutase activity, whereas PoStoSP28, previously annotated as an antigenic membrane protein StAMP, specifically interacted with phosphoglucomutase. PoStoSP04 induced only the ascorbate-glutathione cycle along with other pathogenicity factors/effectors. Candidate pathogenicity factors/effectors were involved in reprogramming host carbohydrate metabolism in favor of phytoplasma own growth and infection. They were specifically associated with three distinct metabolic pathways leading to fructose-6-phosphate as an input substrate for glycolysis. The possible significance of autophagosome induction by PoStoSP28 is discussed.
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Affiliation(s)
- Marina Dermastia
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Tomaž
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Rebeka Strah
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Barbara Dušak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Barbara Anžič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Timotej Čepin
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Stefanie Wienkoop
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Aleš Kladnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Monika Riedle-Bauer
- Federal College and Research Institute for Viticulture and Pomology Klosterneuburg, Klosterneuburg, Austria
| | - Christina Schönhuber
- Bioresources Unit, Health & Environment Department, Austrian Institute of Technology, Tulln, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Maruša Pompe Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Faculty of Viticulture and Enology, University of Nova Gorica, Vipava, Slovenia
| | - Günter Brader
- Bioresources Unit, Health & Environment Department, Austrian Institute of Technology, Tulln, Austria
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4
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Ferrer L, Mindt M, Suarez-Diez M, Jilg T, Zagorščak M, Lee JH, Gruden K, Wendisch VF, Cankar K. Fermentative Indole Production via Bacterial Tryptophan Synthase Alpha Subunit and Plant Indole-3-Glycerol Phosphate Lyase Enzymes. J Agric Food Chem 2022; 70:5634-5645. [PMID: 35500281 PMCID: PMC9100643 DOI: 10.1021/acs.jafc.2c01042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 02/10/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L-1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat.
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Affiliation(s)
- Lenny Ferrer
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Melanie Mindt
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
- Axxence
Aromatic GmbH, 46446 Emmerich am Rhein, Germany
| | - Maria Suarez-Diez
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708WE Wageningen, The Netherlands
| | - Tatjana Jilg
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Maja Zagorščak
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Jin-Ho Lee
- Department
of Food Science & Biotechnology, Kyungsung
University, 608-736 Busan, Republic of Korea
| | - Kristina Gruden
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Volker F. Wendisch
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Katarina Cankar
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
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5
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Foix L, Nadal A, Zagorščak M, Ramšak Ž, Esteve-Codina A, Gruden K, Pla M. Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni. BMC Genomics 2021; 22:360. [PMID: 34006221 PMCID: PMC8132438 DOI: 10.1186/s12864-021-07571-9] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which are of them being plant elicitor peptides (Peps). Exogenous application of Peps activates defense mechanisms and reduces the symptoms of pathogen infection in various pathosystems. We have previously identified the Rosaceae Peps and showed, in an ex vivo system, that their topical application efficiently enhanced resistance to the bacterial pathogen Xanthomonas arboricola pv. pruni (Xap). RESULTS Here we demonstrate the effectiveness of Prunus persica peptides PpPep1 and PpPep2 in protecting peach plants in vivo at nanomolar doses, with 40% reduction of the symptoms following Xap massive infection. We used deep sequencing to characterize the transcriptomic response of peach plants to preventive treatment with PpPep1 and PpPep2. The two peptides induced highly similar massive transcriptomic reprogramming in the plant. One hour, 1 day and 2 days after peptide application there were changes in expression in up to 8% of peach genes. We visualized the transcriptomics dynamics in a background knowledge network and detected the minor variations between plant responses to PpPep1 and PpPep2, which might explain their slightly different protective effects. By designing a P. persica Pep background knowledge network, comparison of our data and previously published immune response datasets was possible. CONCLUSIONS Topical application of P. persica Peps mimics the PTI natural response and protects plants against massive Xap infection. This makes them good candidates for deployment of natural, targeted and environmental-friendly strategies to enhance resistance in Prunus species and prevent important biotic diseases.
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Affiliation(s)
- Laura Foix
- Institute for Agricultural and Food Technology, Universitat de Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Anna Nadal
- Institute for Agricultural and Food Technology, Universitat de Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maria Pla
- Institute for Agricultural and Food Technology, Universitat de Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain.
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6
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Lukan T, Pompe‐Novak M, Baebler Š, Tušek‐Žnidarič M, Kladnik A, Križnik M, Blejec A, Zagorščak M, Stare K, Dušak B, Coll A, Pollmann S, Morgiewicz K, Hennig J, Gruden K. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato. Plant J 2020; 104:645-661. [PMID: 32772469 PMCID: PMC7692943 DOI: 10.1111/tpj.14953] [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: 03/29/2020] [Accepted: 07/21/2020] [Indexed: 05/18/2023]
Abstract
Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA-seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.
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Affiliation(s)
- Tjaša Lukan
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | | | - Špela Baebler
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | | | - Aleš Kladnik
- Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Maja Križnik
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Andrej Blejec
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Maja Zagorščak
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Katja Stare
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Barbara Dušak
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Anna Coll
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Stephan Pollmann
- Centre for Plant Biotechnology and GenomicsCampus de Montegancedo Crta M‐40, Km 38Pozuelo de Alarcón, Madrid28223UPM–INIA Spain
| | - Karolina Morgiewicz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Kristina Gruden
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
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7
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Petek M, Zagorščak M, Ramšak Ž, Sanders S, Tomaž Š, Tseng E, Zouine M, Coll A, Gruden K. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato. Sci Data 2020; 7:249. [PMID: 32709858 PMCID: PMC7382494 DOI: 10.1038/s41597-020-00581-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 11/27/2019] [Accepted: 06/19/2020] [Indexed: 01/25/2023] Open
Abstract
Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes. Measurement(s) | genome • RNA • sequence_assembly • transcriptome | Technology Type(s) | digital curation • RNA sequencing • sequence assembly process | Factor Type(s) | cultivar | Sample Characteristic - Organism | Solanum tuberosum |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12562733
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Affiliation(s)
- Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Sheri Sanders
- National Center for Genome Analysis and Support (NCGAS), Indiana University, Bloomington, USA
| | - Špela Tomaž
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | | | - Mohamed Zouine
- Laboratoire Génomique et Biotechnologie des Fruits, INRA-INP/ENSAT, Castanet-Tolosan, France
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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8
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Rabar B, Zagorščak M, Ristov S, Rosenzweig M, Goldstein P. IGLOSS: iterative gapless local similarity search. Bioinformatics 2019; 35:3491-3492. [PMID: 30721953 DOI: 10.1093/bioinformatics/btz086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/07/2019] [Accepted: 02/04/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available sequences calls for novel methods to explore local sequence similarity. We have developed a new method for iterative motif scanning that will look for ungapped sequence patterns similar to a submitted query. Using careful parameter estimation and an adaptation of a fast string-matching algorithm, the method performs significantly better in this context than the existing software. AVAILABILITY AND IMPLEMENTATION The IGLOSS web server is available at http://compbioserv.math.hr/igloss/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Braslav Rabar
- Mathematics Department, Faculty of Natural Sciences and Mathematics, Zagreb, Croatia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Strahil Ristov
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Martin Rosenzweig
- Mathematics Department, Faculty of Natural Sciences and Mathematics, Zagreb, Croatia
| | - Pavle Goldstein
- Mathematics Department, Faculty of Natural Sciences and Mathematics, Zagreb, Croatia
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Zagorščak M, Blejec A, Ramšak Ž, Petek M, Stare T, Gruden K. DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R. Plant Methods 2018; 14:78. [PMID: 30186360 PMCID: PMC6117943 DOI: 10.1186/s13007-018-0345-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous. RESULTS We have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the Arabidopsis thaliana and Solanum tuberosum datasets, but it is set to handle any biological instances. CONCLUSIONS DiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo.
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Affiliation(s)
- Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Andrej Blejec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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Gonçalves J, Gutiérrez-Aguirre I, Balasubramanian MN, Zagorščak M, Ravnikar M, Turk V. Surveillance of human enteric viruses in coastal waters using concentration with methacrylate monolithic supports prior to detection by RT-qPCR. Mar Pollut Bull 2018; 128:307-317. [PMID: 29571377 PMCID: PMC5884306 DOI: 10.1016/j.marpolbul.2018.01.040] [Citation(s) in RCA: 8] [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: 10/17/2017] [Revised: 12/07/2017] [Accepted: 01/18/2018] [Indexed: 05/04/2023]
Abstract
This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel farm areas. RoV and NoV are released into the Bay of Koper, with higher rates close to the discharge of the wastewater treatment plant, however, they can be detected at recreational and mussel farming areas. Our results showed that water bodies considered safe based on FC concentrations, can still have low, yet potentially infective, concentrations of human viruses.
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Affiliation(s)
- José Gonçalves
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, SI-6330 Piran, Slovenia; Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia.
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | | | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, SI-6330 Piran, Slovenia; University of Nova Gorica, Vipavska 15, SI-5000 Nova Gorica, Slovenia
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Lukan T, Baebler Š, Pompe-Novak M, Guček K, Zagorščak M, Coll A, Gruden K. Cell Death Is Not Sufficient for the Restriction of Potato Virus Y Spread in Hypersensitive Response-Conferred Resistance in Potato. Front Plant Sci 2018; 9:168. [PMID: 29497431 PMCID: PMC5818463 DOI: 10.3389/fpls.2018.00168] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/30/2018] [Indexed: 05/25/2023]
Abstract
Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by the induction of cell death, manifested as the formation of necrotic lesions. While it is known that salicylic acid is the key component in the orchestration of the events restricting viral spread in HR, the exact function of the cell death in resistance is still unknown. We show that potato virus Y (PVY) can be detected outside the cell death zone in Ny-1-mediated HR in potato plants (cv. Rywal), observed as individual infected cells or small clusters of infected cells outside the cell death zone. By exploiting the features of temperature dependent Ny-1-mediated resistance, we confirmed that the cells at the border of the cell death zone are alive and harbor viable PVY that is able to reinitiate infection. To get additional insights into this phenomenon we further studied the dynamics of both cell death zone expansion and occurrence of viral infected cell islands outside it. We compared the response of Rywal plants to their transgenic counterparts, impaired in SA accumulation (NahG-Rywal), where the lesions occur but the spread of the virus is not restricted. We show that the virus is detected outside the cell death zone in all lesion developmental stages of HR lesions. We also measured the dynamics of lesions expansion in both genotypes. We show that while rapid lesion expansion is observed in SA-depleted plants, virus spread is even faster. On the other hand the majority of analyzed lesions slowly expand also in HR-conferred resistance opening the possibility that the infected cells are eventually engulfed by cell death zone. Taken altogether, we suggest that the HR cell death is separated from the resistance mechanisms which lead to PVY restriction in Ny-1 genetic background. We propose that HR should be regarded as a process where the dynamics of events is crucial for effectiveness of viral arrest albeit the exact mechanism conferring this resistance remains unknown.
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Affiliation(s)
- Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maruša Pompe-Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Katja Guček
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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