| 1. |
- Alexandersson, Erik, et al.
(author)
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Field-omics-understanding large-scale molecular data from field crops
- 2014
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 5
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Journal article (peer-reviewed)abstract
- The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: "Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with '-omics' data."
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| 2. |
- Alexandersson, Erik, et al.
(author)
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Plant secretome proteomics
- 2013
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 4
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Research review (peer-reviewed)abstract
- The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extracellular space commonly referred to as the apoplast. Secreted proteins maintain cell structure and acts in signaling and are crucial for stress responses where they can interact with pathogen effectors and control the extracellular environment. Typically, secreted proteins contain an N-terminal signal peptide and are directed through the endoplasmic reticulum/Golgi pathway. However, in plants many proteins found in the secretome lack such a signature and might follow alternative ways of secretion. This review covers techniques to isolate plant secretomes and how to identify and quantify their constituent proteins. Furthermore, bioinformatical tools to predict secretion signals and define the putative secretome are presented. Findings from proteomic studies and important protein families of plant secretomes, such as proteases and hydrolases, are highlighted.
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| 3. |
- Ali, Ashfaq, et al.
(author)
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Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Journal article (peer-reviewed)abstract
- Background: In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. Conclusions: In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.
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| 4. |
- Bengtsson, Therese, et al.
(author)
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Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Journal article (peer-reviewed)abstract
- Background: Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. beta-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. Results: Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. Conclusions: BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.
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| 5. |
- Burra, Dharani, et al.
(author)
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Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
- 2014
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14
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Journal article (peer-reviewed)abstract
- Background: Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling. Results: Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with beta-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid. Conclusions: Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.
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| 6. |
- Iciar, Frades, et al.
(author)
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Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case
- 2014
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14
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Journal article (peer-reviewed)abstract
- Background: For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available.Results: We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard.Conclusions: We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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| 7. |
- Lager, Ida, et al.
(author)
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Changes in external pH rapidly alter plant gene expression and modulate auxin and elicitor responses
- 2010
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In: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 33:9, s. 1513-1528
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Journal article (peer-reviewed)abstract
- pH is a highly variable environmental factor for the root, and plant cells can modify apoplastic pH for nutrient acquisition and in response to extracellular signals. Nevertheless, surprisingly few effects of external pH on plant gene expression have been reported. We have used microarrays to investigate whether external pH affects global gene expression. In Arabidopsis thaliana roots, 881 genes displayed at least twofold changes in transcript abundance 8 h after shifting medium pH from 6.0 to 4.5, identifying pH as a major affector of global gene expression. Several genes responded within 20 min, and gene responses were also observed in leaves of seedling cultures. The pH 4.5 treatment was not associated with abiotic stress, as evaluated from growth and transcriptional response. However, the observed patterns of global gene expression indicated redundancies and interactions between the responses to pH, auxin and pathogen elicitors. In addition, major shifts in gene expression were associated with cell wall modifications and Ca2+ signalling. Correspondingly, a marked overrepresentation of Ca2+/calmodulin-associated motifs was observed in the promoters of pH-responsive genes. This strongly suggests that plant pH recognition involves intracellular Ca2+. Overall, the results emphasize the previously underappreciated role of pH in plant responses to the environment.
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| 8. |
- Persson, Erik, et al.
(author)
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Cultural Relict Plants in the Nordic Region
- 2014
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In: Sources to the history of gardening : Four interdisciplinary seminars 2010-2013 arranged by the Nordic Network for the Archaeology and Archaeobotany of Gardening - Four interdisciplinary seminars 2010-2013 arranged by the Nordic Network for the Archaeology and Archaeobotany of Gardening. - 9789187117862 ; 2014:25, s. 299-312
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Book chapter (peer-reviewed)
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| 9. |
- Persson, Erik, et al.
(author)
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What’s in a name? : Exploring the definition of ‘Cultural Relict Plant’
- 2014
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In: Sources to the history of gardening : Four Interdisciplinary Seminars 2010–2013 Arranged By the Nordic Network for the Archaeology and Archaeobotany of Gardening (NTAA) - Four Interdisciplinary Seminars 2010–2013 Arranged By the Nordic Network for the Archaeology and Archaeobotany of Gardening (NTAA). - 9789187117862 ; 2014:25, s. 289-298
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Book chapter (peer-reviewed)
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| 10. |
- Walter, Abigail, et al.
(author)
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GENE TRANSCRIPTION CHANGES DURING COMPATIBLE AND INCOMPATIBLE INFECTIONS OF POTATO BY GLOBODERA ROSTOCHIENSIS
- 2014
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In: Journal of Nematology. - 0022-300X. ; 46, s. 253-253
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Conference paper (other academic/artistic)abstract
- The golden potato cyst nematode,Globodera rostochiensis, is one of the most important pests of potato in Sweden. Several pathotypes of the nematode exist, and they may be controlled by one of several sources of single-gene resistance in potato. Here we report that SW93-1015, a breeding line from the potato breeding program at SLU Alnarp, has phenotypic resistance to the Ro1/4 pathotype ofG. rostochiensis. Reproduction ofG. rostochiensispathotype Ro1/4 on SW93-1015 is approximately 5% of reproduction on the susceptible cultivar Desiree. To further investigate the interaction between potato cyst nematodes and susceptible and resistant host plants, changes in gene transcription were monitored just after root penetration and during syncytium formation in Desiree and SW93-1015 potato plants infected with Ro1/4G. rostochiensis.RNA expression in root tissue was analysed on a microarray at 0, 8, and 48 h post-infection, corresponding to pre-infection, root penetration, and early syncytium formation. Changes in gene transcription over the process of infection in susceptible and resistant genotypes are discussed. The resistance will be further investigated using a crossing population if Desiree and SW93-1015.
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