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  1. Article ; Online: Solanaceae

    Usadel, Björn

    aBIOTECH

    2022  Volume 3, Issue 4, Page(s) 233–236

    Abstract: Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single ... ...

    Abstract Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.
    Language English
    Publishing date 2022-11-14
    Publishing country Singapore
    Document type Journal Article
    ISSN 2662-1738
    ISSN (online) 2662-1738
    DOI 10.1007/s42994-022-00087-0
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  2. Article: Understanding protein import in diverse non-green plastids.

    Christian, Ryan / Labbancz, June / Usadel, Bjorn / Dhingra, Amit

    Frontiers in genetics

    2023  Volume 14, Page(s) 969931

    Abstract: The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the ... ...

    Abstract The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
    Language English
    Publishing date 2023-03-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.969931
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  3. Article ; Online: Advances in fruit development and ripening.

    Osorio, Sonia / Costa, Fabrizio / Gibon, Yves / Usadel, Björn / Vicente, Ariel

    Journal of experimental botany

    2023  Volume 74, Issue 20, Page(s) 6205–6206

    MeSH term(s) Fruit/physiology
    Language English
    Publishing date 2023-11-06
    Publishing country England
    Document type Introductory Journal Article
    ZDB-ID 2976-2
    ISSN 1460-2431 ; 0022-0957
    ISSN (online) 1460-2431
    ISSN 0022-0957
    DOI 10.1093/jxb/erad379
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  4. Article ; Online: Characterization of Bioactive Phenolic Compounds in Seeds of Chilean Quinoa (Chenopodium quinoa Willd.) Germplasm

    Pandya, Archis / Thiele, Björn / Köppchen, Stephan / Zurita-Silva, Andres / Usadel, Björn / Fiorani, Fabio

    Agronomy. 2023 Aug. 18, v. 13, no. 8

    2023  

    Abstract: In recent years, quinoa (Chenopodium quinoa Willd.), an ancient Andean region crop, has received increased research attention because it is an excellent source of nutrients and also of bioactive phenolic compounds, which are potentially beneficial for ... ...

    Abstract In recent years, quinoa (Chenopodium quinoa Willd.), an ancient Andean region crop, has received increased research attention because it is an excellent source of nutrients and also of bioactive phenolic compounds, which are potentially beneficial for human health. However, variation in the content and type of these metabolites in quinoa genetic resources remains, to a large extent, unexplored. We evaluated the composition of free and bound phenolic forms in the seeds of 111 Chilean quinoa accessions by using LC-DAD-MS/MS. The relative phenolic content ranged from 35.51 mg/100 g to 93.23 mg/100 g of seed dry weight. The free phenolic fraction accounted for 72% of the total phenolic content, while the bound fraction represented the remaining 28% of the total phenolic content. Our study also revealed a significant degree of variation in terms of individual phenolic compounds such as rutin, vanillic acid, quercetin, and their derivatives, which can have important implications for quinoa’s nutritional and functional properties. We conclude that our data reveal a significant phenotypic variation of bioactive phenolic content in the examined germplasm, which could be exploited in current and future genetic improvement programs in quinoa.
    Keywords Chenopodium quinoa ; agronomy ; genetic improvement ; germplasm ; human health ; metabolites ; phenotypic variation ; quercetin ; rutin ; vanillic acid ; Andes region
    Language English
    Dates of publication 2023-0818
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2607043-1
    ISSN 2073-4395
    ISSN 2073-4395
    DOI 10.3390/agronomy13082170
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  5. Article: Seed hemicelluloses tailor mucilage properties and salt tolerance

    Yang, Bo / Hofmann, Florian / Usadel, Björn / Voiniciuc, Cătălin

    new phytologist. 2021 Feb., v. 229, no. 4

    2021  

    Abstract: While Arabidopsis seed coat epidermal cells have become an excellent genetic system to study the biosynthesis and structural roles of various cell wall polymers, the physiological function of the secreted mucilaginous polysaccharides remains ambiguous. ... ...

    Abstract While Arabidopsis seed coat epidermal cells have become an excellent genetic system to study the biosynthesis and structural roles of various cell wall polymers, the physiological function of the secreted mucilaginous polysaccharides remains ambiguous. Seed mucilage is shaped by two distinct classes of highly substituted hemicelluloses along with cellulose and structural proteins, but their interplay has not been explored. We deciphered the functions of four distinct classes of cell wall polymers by generating a series of double mutants with defects in heteromannan, xylan, cellulose, or the arabinogalactan protein SALT‐OVERLY SENSITIVE 5 (SOS5), and evaluating their impact on mucilage architecture and seed germination during salt stress. We discovered that muci10 seeds, lacking heteromannan branches, had elevated tolerance to salt stress, while heteromannan elongation mutants exhibited reduced germination in calcium chloride (CaCl₂). By contrast, xylan made by MUCILAGE‐RELATED21 (MUCI21) was found to be required for the adherence of mucilage pectin to microfibrils made by CELLULOSE SYNTHASE5 (CESA5) as well as to a SOS5‐mediated network. Our results indicate that the substitution of xylan and glucomannan in seeds can fine‐tune mucilage adherence and salt tolerance, respectively. The study of germinating seeds can thus provide insights into the synthesis, modification and function of complex glycans.
    Keywords Arabidopsis ; arabinogalactan proteins ; calcium chloride ; cell wall components ; cell walls ; cellulose ; cellulose synthase ; epidermis (plant) ; glucomannans ; mucilages ; mutants ; pectins ; salt stress ; salt tolerance ; seed coat ; seed germination ; structural proteins ; xylan
    Language English
    Dates of publication 2021-02
    Size p. 1946-1954.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note golden set ; JOURNAL ARTICLE
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.17056
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    In stock of ZB MED Bonn / Germany

    Z 868: Show issues

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  6. Article ; Online: Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites.

    Nemati, Zahra / Kazemi-Shahandashti, Seyyedeh-Sanam / Garibay-Hernández, Adriana / Mock, Hans-Peter / Schmidt, Maximilian H-W / Usadel, Björn / Blattner, Frank R

    BMC plant biology

    2024  Volume 24, Issue 1, Page(s) 369

    Abstract: Background: The increasing demand for saffron metabolites in various commercial industries, including medicine, food, cosmetics, and dyeing, is driven by the discovery of their diverse applications. Saffron, derived from Crocus sativus stigmas, is the ... ...

    Abstract Background: The increasing demand for saffron metabolites in various commercial industries, including medicine, food, cosmetics, and dyeing, is driven by the discovery of their diverse applications. Saffron, derived from Crocus sativus stigmas, is the most expensive spice, and there is a need to explore additional sources to meet global consumption demands. In this study, we focused on yellow-flowering crocuses and examined their tepals to identify saffron-like compounds.
    Results: Through metabolomic and transcriptomic approaches, our investigation provides valuable insights into the biosynthesis of compounds in yellow-tepal crocuses that are similar to those found in saffron. The results of our study support the potential use of yellow-tepal crocuses as a source of various crocins (crocetin glycosylated derivatives) and flavonoids.
    Conclusions: Our findings suggest that yellow-tepal crocuses have the potential to serve as a viable excessive source of some saffron metabolites. The identification of crocins and flavonoids in these crocuses highlights their suitability for meeting the demands of various industries that utilize saffron compounds. Further exploration and utilization of yellow-tepal crocuses could contribute to addressing the growing global demand for saffron-related products.
    MeSH term(s) Crocus/genetics ; Crocus/metabolism ; Carotenoids/metabolism ; Metabolomics ; Flowers/genetics ; Flowers/metabolism ; Flavonoids/metabolism ; Gene Expression Profiling ; Transcriptome ; Metabolome
    Chemical Substances Carotenoids (36-88-4) ; crocin (877GWI46C2) ; Flavonoids
    Language English
    Publishing date 2024-05-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2059868-3
    ISSN 1471-2229 ; 1471-2229
    ISSN (online) 1471-2229
    ISSN 1471-2229
    DOI 10.1186/s12870-024-05036-1
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  7. Article ; Online: MapMan Visualization of RNA-Seq Data Using Mercator4 Functional Annotations.

    Bolger, Marie / Schwacke, Rainer / Usadel, Björn

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2354, Page(s) 195–212

    Abstract: Plant omics research has advanced to the stage where it is feasible to generate data from multiple samples and multiple time points to gain insight into biological processes. This impressive array of data can prove challenging to interpret. In this ... ...

    Abstract Plant omics research has advanced to the stage where it is feasible to generate data from multiple samples and multiple time points to gain insight into biological processes. This impressive array of data can prove challenging to interpret. In this chapter, we describe a solution to this problem, consisting of the MapMan transcript visualization application and the associated MapMan4 ontology and Mercator4 online annotation process.
    MeSH term(s) Molecular Sequence Annotation ; RNA-Seq ; Whole Exome Sequencing
    Language English
    Publishing date 2021-08-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1609-3_9
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  8. Article ; Online: Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

    Gui, Songtao / Martinez‐Rivas, Felix Juan / Wen, Weiwei / Meng, Minghui / Yan, Jianbing / Usadel, Björn / Fernie, Alisdair R.

    The Plant Journal. 2023 Feb., v. 113, no. 3 p.446-459

    2023  

    Abstract: Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high‐quality genomic and transcriptomic data has been collected and most of this has been publicly released. ... ...

    Abstract Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high‐quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome‐wide association and transcriptome‐wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
    Keywords domestication ; evolution ; genome ; genomics ; plant physiology ; transcriptome ; transcriptomics
    Language English
    Dates of publication 2023-02
    Size p. 446-459.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note REVIEW
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.16070
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    In stock of ZB MED Bonn / Germany

    Z 6071: Show issues

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  9. Article: Interview: Professor Dr. Björn Usadel. Ein Computer hat keine Intuition

    Usadel, Björn

    Genomxpress scholae

    2015  Volume 4, Issue -, Page(s) 22

    Language German
    Document type Article
    ZDB-ID 2564735-0
    ISSN 2190-524X
    Database Current Contents Medicine

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6902 -Scholae-: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: The Multifaceted Role of Pectin Methylesterase Inhibitors (PMEIs).

    Wormit, Alexandra / Usadel, Björn

    International journal of molecular sciences

    2018  Volume 19, Issue 10

    Abstract: Plant cell walls are complex and dynamic structures that play important roles in growth and development, as well as in response to stresses. Pectin is a major polysaccharide of cell walls rich in galacturonic acid (GalA). Homogalacturonan (HG) is ... ...

    Abstract Plant cell walls are complex and dynamic structures that play important roles in growth and development, as well as in response to stresses. Pectin is a major polysaccharide of cell walls rich in galacturonic acid (GalA). Homogalacturonan (HG) is considered the most abundant pectic polymer in plant cell walls and is partially methylesterified at the C6 atom of galacturonic acid. Its degree (and pattern) of methylation (DM) has been shown to affect biomechanical properties of the cell wall by making pectin susceptible for enzymatic de-polymerization and enabling gel formation. Pectin methylesterases (PMEs) catalyze the removal of methyl-groups from the HG backbone and their activity is modulated by a family of proteinaceous inhibitors known as pectin methylesterase inhibitors (PMEIs). As such, the interplay between PME and PMEI can be considered as a determinant of cell adhesion, cell wall porosity and elasticity, as well as a source of signaling molecules released upon cell wall stress. This review aims to highlight recent updates in our understanding of the PMEI gene family, their regulation and structure, interaction with PMEs, as well as their function in response to stress and during development.
    MeSH term(s) Carboxylic Ester Hydrolases/metabolism ; Gene Expression Regulation, Plant ; Pectins/metabolism ; Plant Proteins/metabolism
    Chemical Substances Plant Proteins ; Pectins (89NA02M4RX) ; Carboxylic Ester Hydrolases (EC 3.1.1.-) ; pectinesterase (EC 3.1.1.11)
    Language English
    Publishing date 2018-09-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms19102878
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