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Sjödin, A., Street, N. R., Sandberg, G., Gustafsson, P. & Jansson, S. (2009). The populus genome integrative explorer (PopGenIE): a new resource for exploring the populus genome. New Phytologist, 182(4), 1013-1025
Open this publication in new window or tab >>The populus genome integrative explorer (PopGenIE): a new resource for exploring the populus genome
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2009 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 182, no 4, p. 1013-1025Article in journal (Refereed) Published
Abstract [en]

* Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. * As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. * Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. * PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at http://www.popgenie.org or via http://www.populusgenome.info.

National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-25706 (URN)10.1111/j.1469-8137.2009.02807.x (DOI)19383103 (PubMedID)
Available from: 2009-08-31 Created: 2009-08-31 Last updated: 2018-06-08Bibliographically approved
Street, N. R., Sjödin, A., Bylesjö, M., Gustafsson, P., Trygg, J. & Jansson, S. (2008). A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics, 9(1), 539
Open this publication in new window or tab >>A cross-species transcriptomics approach to identify genes involved in leaf development
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2008 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 9, no 1, p. 539-Article in journal (Other (popular science, discussion, etc.)) Published
Abstract [en]

Background

We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.

Results

Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.

Conclusion

This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-2743 (URN)10.1186/1471-2164-9-589 (DOI)19061504 (PubMedID)
Available from: 2007-11-07 Created: 2007-11-07 Last updated: 2018-06-09
Bylesjö, M., Segura, V., Soolanayakanahally, R. Y., Rae, A. M., Trygg, J., Gustafsson, P., . . . Street, N. R. (2008). LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biology, 8(82), 1-9
Open this publication in new window or tab >>LAMINA: a tool for rapid quantification of leaf size and shape parameters
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2008 (English)In: BMC Plant Biology, ISSN 1471-2229, Vol. 8, no 82, p. 1-9Article in journal (Refereed) Published
Abstract [en]

Background

An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.

Results

We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.

Conclusion

We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.

Keywords
Image Processing; Computer-Assisted/*methods, Plant Leaves/*anatomy & histology, Populus/anatomy & histology, Principal Component Analysis, Software Validation
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-10579 (URN)doi:10.1186/1471-2229-8-82 (DOI)18647399 (PubMedID)
Available from: 2008-12-10 Created: 2008-12-10 Last updated: 2018-06-09
Svalastog, A. L., Gustafsson, P. & Jansson, S. (2006). Comparative analysis of the risk-handling procedures for gene technology applications in medical and plant science. Science and Engineering Ethics, 12(3), 465-479
Open this publication in new window or tab >>Comparative analysis of the risk-handling procedures for gene technology applications in medical and plant science
2006 (English)In: Science and Engineering Ethics, Vol. 12, no 3, p. 465-479Article in journal (Refereed) Published
Abstract [en]

In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk — focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.

Identifiers
urn:nbn:se:umu:diva-18092 (URN)doi:10.1007/s11948-006-0045-4 (DOI)
Available from: 2007-04-16 Created: 2007-04-16 Last updated: 2018-06-09Bibliographically approved
Mouillon, J.-M., Gustafsson, P. & Harryson, P. (2006). Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments.. Plant Physiology, 141(2), 638-50
Open this publication in new window or tab >>Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments.
2006 (English)In: Plant Physiology, ISSN 0032-0889, Vol. 141, no 2, p. 638-50Article in journal (Refereed) Published
Abstract [en]

Dehydrins constitute a class of intrinsically disordered proteins that are expressed under conditions of water-related stress. Characteristic of the dehydrins are some highly conserved stretches of seven to 17 residues that are repetitively scattered in their sequences, the K-, S-, Y-, and Lys-rich segments. In this study, we investigate the putative role of these segments in promoting structure. The analysis is based on comparative analysis of four full-length dehydrins from Arabidopsis (Arabidopsis thaliana; Cor47, Lti29, Lti30, and Rab18) and isolated peptide mimics of the K-, Y-, and Lys-rich segments. In physiological buffer, the circular dichroism spectra of the full-length dehydrins reveal overall disordered structures with a variable content of poly-Pro helices, a type of elongated secondary structure relying on bridging water molecules. Similar disordered structures are observed for the isolated peptides of the conserved segments. Interestingly, neither the full-length dehydrins nor their conserved segments are able to adopt specific structure in response to altered temperature, one of the factors that regulate their expression in vivo. There is also no structural response to the addition of metal ions, increased protein concentration, or the protein-stabilizing salt Na2SO4. Taken together, these observations indicate that the dehydrins are not in equilibrium with high-energy folded structures. The result suggests that the dehydrins are highly evolved proteins, selected to maintain high configurational flexibility and to resist unspecific collapse and aggregation. The role of the conserved segments is thus not to promote tertiary structure, but to exert their biological function more locally upon interaction with specific biological targets, for example, by acting as beads on a string for specific recognition, interaction with membranes, or intermolecular scaffolding. In this perspective, it is notable that the Lys-rich segment in Cor47 and Lti29 shows sequence similarity with the animal chaperone HSP90.

Keywords
Amino Acid Sequence, Circular Dichroism, Guanidine, Heat-Shock Proteins/*chemistry, Metals/chemistry, Molecular Sequence Data, Peptides/*chemistry, Plant Proteins/*chemistry, Protein Conformation, Protein Denaturation, Sequence Homology; Amino Acid, Sulfates/chemistry, Temperature
Identifiers
urn:nbn:se:umu:diva-15822 (URN)doi:10.1104/pp.106.079848 (DOI)16565295 (PubMedID)
Available from: 2007-08-02 Created: 2007-08-02 Last updated: 2018-06-09Bibliographically approved
Barker-Åström, K., Schelin, J., Gustafsson, P., Clarke, A. K. & Campbell, D. A. (2005). Chlorosis during nitrogen starvation is altered by carbon dioxide and temperature status and is mediated by the ClpP1 protease in Synechococcus elongatus.. Archives of Microbiology, 183(1), 66-9
Open this publication in new window or tab >>Chlorosis during nitrogen starvation is altered by carbon dioxide and temperature status and is mediated by the ClpP1 protease in Synechococcus elongatus.
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2005 (English)In: Archives of Microbiology, ISSN 0302-8933, Vol. 183, no 1, p. 66-9Article in journal (Refereed) Published
Abstract [en]

The interactive effects of inorganic carbon status, temperature and light on chlorosis induced by nitrogen deficiency, and the roles of Clp proteases in this process were investigated. In wild-type cultures grown in high or ambient CO2, following transfer to media lacking combined nitrogen, phycocyanin per cell dropped primarily through dilution of the pigment through cell division, and also suffered variable degrees of net degradation. When grown at high CO2 (5%), chlorophyll (Chl) suffered net degradation to a greater extent than phycocyanin. In marked contrast, growth at ambient CO2 resulted in Chl per cell dropping through dilution. Conditions that drove net Chl degradation in the wild-type resulted in little or no net Chl degradation in a clpPI inactivation mutant, with Chl content dropping largely through growth dilution in the mutant. The chlorotic response of a clpPII inactivation strain was nearly the same as that of wild-type, although phycocyanin degradation may have been slightly accelerated in the former.

Keywords
Bacterial Proteins/metabolism, Bacteriochlorophylls/*metabolism, Carbon Dioxide/*metabolism, Endopeptidase Clp/*metabolism, Nitrogen Compounds/*metabolism, Phycocyanin/analysis/*metabolism, Synechococcus/*enzymology
Identifiers
urn:nbn:se:umu:diva-15818 (URN)doi:10.1007/s00203-004-0741-x (DOI)15549267 (PubMedID)
Available from: 2007-08-09 Created: 2007-08-09 Last updated: 2018-06-09Bibliographically approved
Sterky, F., Bhalerao, R. R., Unneberg, P., Segerman, B., Nilsson, P., Brunner, A. M., . . . Jansson, S. (2004). A Populus EST resource for plant functional genomics.. Proceedings of the National Academy of Sciences of the United States of America, 101(38), 13951-6
Open this publication in new window or tab >>A Populus EST resource for plant functional genomics.
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2004 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, Vol. 101, no 38, p. 13951-6Article in journal (Refereed) Published
Abstract [en]

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

Keywords
Ecosystem, Expressed Sequence Tags, Genome; Plant, Genomics/*methods, Humans, Phylogeny, Plant Proteins/*genetics, Populus/*genetics, Species Specificity
Identifiers
urn:nbn:se:umu:diva-14231 (URN)doi:10.1073/pnas.0401641101 (DOI)15353603 (PubMedID)
Available from: 2007-08-10 Created: 2007-08-10 Last updated: 2018-06-09Bibliographically approved
Andersson, A., Keskitalo, J., Sjödin, A., Bhalerao, R., Sterky, F., Wissel, K., . . . Nilsson, P. (2004). A transcriptional timetable of autumn senescence. Genome Biology, 5(4), R24
Open this publication in new window or tab >>A transcriptional timetable of autumn senescence
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2004 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, no 4, p. R24-Article in journal (Refereed) Published
Abstract [en]

Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

Keywords
Aging/*genetics, Cell Death/genetics, Chronobiology/*genetics, DNA; Complementary/genetics, DNA; Plant/genetics, Expressed Sequence Tags, Gene Expression Profiling/methods, Gene Expression Regulation; Plant/genetics, Gene Library, Oligonucleotide Array Sequence Analysis/methods, Plant Leaves/genetics, Populus/cytology/genetics, RNA; Plant/genetics, Seasons, Sequence Analysis; DNA/methods, Transcription; Genetic/*genetics
Identifiers
urn:nbn:se:umu:diva-5065 (URN)15059257 (PubMedID)
Available from: 2006-04-12 Created: 2006-04-12 Last updated: 2018-06-09Bibliographically approved
Strand, Å., Foyer, C. H., Gustafsson, P., Gardeström, P. & Hurry, V. (2003). Altering flux through the sucrose biosynthesis pathway in transgenic Arabidopsis thaliana modifies photosynthetic acclimation at low temperatures and the development of freezing tolerance. Plant, Cell and Environment, 26(4), 523-535
Open this publication in new window or tab >>Altering flux through the sucrose biosynthesis pathway in transgenic Arabidopsis thaliana modifies photosynthetic acclimation at low temperatures and the development of freezing tolerance
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2003 (English)In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 26, no 4, p. 523-535Article in journal (Refereed) Published
Abstract [en]

To test the hypothesis that the up-regulation of sucrose biosynthesis during cold acclimation is essential for the development of freezing tolerance, the acclimation responses of wild-type (WT) Arabidopsis thaliana (Heynh.) were compared with transgenic plants over-expressing sucrose phosphate synthase (over-sps) or with antisense repression of either cytosolic fructose-1,6-bisphosphatase (antifbp) or sucrose phosphate synthase (antisps). Plants were grown at 23 degreesC and then shifted to 5 degreesC. The leaves shifted to 5 degreesC for 10 d and the new leaves that developed at 5 degreesC were compared with control leaves on plants at 23 degreesC. Plants over-expressing sucrose phosphate synthase showed improved photosynthesis and increased flux of fixed carbon into sucrose when shifted to 5 degreesC, whereas both antisense lines showed reduced flux into soluble sugars relative to WT. The improved photosynthetic performance by the over-sps plants shifted to 5 degreesC was associated with an increase in freezing tolerance relative to WT (-9.1 and -7.2 degreesC, respectively). In contrast, both antisense lines showed impaired development of freezing tolerance (- 5.2 and -5.8 degreesC for antifbp and antisps, respectively) when shifted to 5 degreesC. In the new leaves developed at 5 degreesC the recovery of photosynthesis as typically seen in WT was strongly inhibited in both antisense lines and this inhibition was associated with a further failure of both antisense lines to cold acclimate. Thus, functional sucrose biosynthesis at low temperature in the over-sps plants reduced the inhibition of photosynthesis, maintained the mobilization of carbohydrates from source leaves to sinks and increased the rate at which freezing tolerance developed. Modification of sucrose metabolism therefore represents an additional approach that will have benefits both for the development of freezing tolerance and over-wintering, and for the supply of exportable carbohydrate to support growth at low temperatures.

Keywords
Arabidopsis, carbon metabolism, cold acclimation, photosynthesis, sucrose phosphate synthase, sucrose
Identifiers
urn:nbn:se:umu:diva-44652 (URN)000182009600005 ()
Available from: 2011-08-12 Created: 2011-06-09 Last updated: 2018-06-08
Bhalerao, R., Keskitalo, J., Sterky, F., Erlandsson, R., Björkbacka, H., Birve, S. J., . . . Jansson, S. (2003). Gene expression in autumn leaves. Plant Physiology, 131(2), 430-442
Open this publication in new window or tab >>Gene expression in autumn leaves
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2003 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 131, no 2, p. 430-442Article in journal (Refereed) Published
Abstract [en]

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula x tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

Identifiers
urn:nbn:se:umu:diva-5064 (URN)10.1104/pp.012732 (DOI)12586868 (PubMedID)
Available from: 2006-04-12 Created: 2006-04-12 Last updated: 2018-06-09Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-2147-7428

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