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Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. We introduce a novel strategy for the assembly of polyploid genomes and present an assembly of the autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from an offspring population to achieve chromosomal clustering and haplotype phasing on the assembly graph. Our approach generates high-quality assemblies of individual chromosomes with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.

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.

The horticultural production of bell peppers generates large quantities of residual biomass. Abiotic stress stimulates the production of protective flavonoids, so the deliberate application of stress to the plants after fruit harvest could provide a strategy to valorize horticultural residuals by increasing flavonoid concentrations, facilitating their industrial extraction. Here we exposed two Capsicumcultivars, a chilli and a bell pepper, to cold and salt stress and combinations thereof to determine their valorization potential. Noninvasive image-based phenotyping and multiparametric fluorescence measurements indicated that all stress treatments inhibited plant growth and reduced the leaf chlorophyll fluorescence index, with the chilli cultivar showing greater sensitivity. The fluorescence-based FLAV index allowed the noninvasive assessment of foliar luteolin glycosides. High-performance liquid chromatography–mass spectrometry (HPLC-MS) analysis showed that moderate cold increased the levels of two foliar antioxidant luteolin glycosides in both cultivars, with bell pepper containing the highest amounts (induced to maximum 5.5 mg g–1DW cynaroside and 37.0 mg g–1DW graveobioside A) after combined stress treatment. These data confirm the potential of abiotic stress for the valorization of residual leaf biomass to enhance the industrial extraction of antioxidant and bioactive flavonoids.

As one of the most popular beverages globally, tea has enormous economic, cultural, and medicinal importance that necessitates a comprehensive metabolomics study of this species. In this study, a large-scale targeted metabolomics analysis on two types of leaf tissues of nine tea cultivars from five representative geographical origins within China was carried out using the liquid chromatography-mass spectrometry technique. RNA-seq-based transcriptomic analysis was in parallel conducted on the same samples, and gene expression and metabolic differentiation between tissues as well as between the multiple tea cultivars were investigated. The data obtained provide an accessible resource for further studies of naturally occurring metabolic variation of tea plants, which will aid in thoroughly interpreting the underlying genetic and molecular mechanisms of biosynthesis of specialized metabolites in this critical species. Candidate genes including a transcription factor (CsMYB5-like), which were highly correlated with both the content of flavonoids and the expression level of genes participating in the phenylpropanoid and flavonoid biosynthesis pathway, were identified as potential targets for quality improvement of tea.

Potato (Solanum tuberosum) is a major agricultural crop cultivated worldwide. To meet market demand, breeding programs focus on enhancing important agricultural traits such as disease resistance and improvement of tuber palatability. However, while potato tubers get a lot of attention from research, potato berries are mostly overlooked due to their level of toxicity and lack of usefulness for the food production sector. Generally, they remain unused in the production fields after harvesting the tuber. These berries are toxic due to high levels of glycoalkaloids, which might confer some interesting bioactivities. Berries of various solanaceous species contain bioactive secondary metabolites, suggesting that potato berries might contain similarly valuable metabolites. Therefore, possible applications of potato berries, e.g., in the protection of plants against pests and pathogens, as well as the medical exploitation of their anti-inflammatory, anticarcinogenic, and antifungal properties, are plausible. The presence of valuable compounds in potato berries could also contribute to the bioeconomy by providing a novel use for otherwise discarded agricultural side streams. Here we review the potential use of these berries for the extraction of compounds that can be exploited to produce pharmaceuticals and plant protection products.

Strawberry (Fragaria× ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F1population derived from parental lines ‘Candonga’ and ‘Senga Sengana’, adapted to distinct Southern and Northern European areas. To account for environmental effects, the F1and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A),and the chloroplast-located AsA transporter gene FaPHT4;4(7C)might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A)inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A)was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.

Pathogen components, such as lipopolysaccharides of Gram-negative bacteria that activate Toll-like receptor 4, induce mitogen activated protein kinases and NFκB through different downstream pathways to stimulate pro- and anti-inflammatory cytokine expression. Importantly, post-transcriptional control of the expression of Toll-like receptor 4 downstream signaling molecules contributes to the tight regulation of inflammatory cytokine synthesis in macrophages. Emerging evidence highlights the role of RNA-binding proteins (RBPs) in the post-transcriptional control of the innate immune response. To systematically identify macrophage RBPs and their response to LPS stimulation, we employed RNA interactome capture in LPS-induced and untreated murine RAW 264.7 macrophages. This combines RBP-crosslinking to RNA, cell lysis, oligo(dT) capture of polyadenylated RNAs and mass spectrometry analysis of associated proteins. Our data revealed 402 proteins of the macrophage RNA interactome including 91 previously not annotated as RBPs. A comparison with published RNA interactomes classified 32 RBPs uniquely identified in RAW 264.7 macrophages. Of these, 19 proteins are linked to biochemical activities not directly related to RNA. From this group, we validated the HSP90 cochaperone P23 that was demonstrated to exhibit cytosolic prostaglandin E2 synthase 3 (PTGES3) activity, and the hematopoietic cell-specific LYN substrate 1 (HCLS1 or HS1), a hematopoietic cell-specific adapter molecule, as novel macrophage RBPs. Our study expands the mammalian RBP repertoire, and identifies macrophage RBPs that respond to LPS. These RBPs are prime candidates for the post-transcriptional regulation and execution of LPS-induced signaling pathways and the innate immune response. Macrophage RBP data have been deposited to ProteomeXchange with identifier PXD002890.

The integration of natural materials in today's product development gains more and more importance. Society's demand for ecologically produced and sustainably operable goods is a key driver for material scientists and engineers to substitute conventional substances such as metals or plastics. In addition, the entire lifecycle sets multiple requirements for the product developers entailing strategies for reuse and recycling. Most of these eco-design approaches are limited to the selection of the right material and the industrial processing, to shape and manufacture to the desired design. The authors of this contribution are scientists from the areas of cell-biology, eco-toxicology, structural-, engineering- and industrial-design, and teamed up to use directed natural growth of bio-materials (e.g. plants). The aim is to minimize conventional production steps and decrease the amount of resources for manufacturing. In the first step the team categorizes and analyzes potential plants in general and on a structural cell level. In addition, requirements for different sorts of products are defined, and matching parts of both databases are identified. The full paper will show first results and research of the potential function-plant relation and will give an overview of characteristic parameters for the holistic evaluation of near net shape grown products. These include exemplarily the amount of fertilizer needed, ecotoxicological implications, plant area needed, growth time, mechanical properties, design restrictions and possible surface quality.

The data explosion in the biological sciences has led to many novel challenges for the individual researcher. One of these is to interpret the sheer mass of data at hand. Typical high-throughput data sets from transcriptomic data can easily comprise hundred thousand data points. It is thus necessary to provide tools to interactively visualize these data sets in a way that aids in their interpretation. Thus we have developed the MAPMAN application. This application renders individual data points from different domains as different glyphs that are color coded to reflect underlying changes in the magnitude/abundance of the underlying data. In order to augment the human comprehensibility of the biologist domain experts these data are organized on meaningful pathway diagrams that the biologist has encountered numerous times. Using these representations together with a high level organization thus helps to quickly realize the main outcome of such a high throughput study and to further decide on additional tasks that should be performed to explore the data.

The tomato microarray TOM1 offers the possibility to monitor the levels of several thousand transcripts in parallel. The microelements represented on this tomato microarray have been putatively assigned to unigenes, and organised in functional classes using the MapMan ontology (Thimm  et al., 2004. Plant J. 37: 914–939). This ontology was initially developed for use with the ArabidopsisATH1 array, has a low level of redundancy, and can be combined with the MapMan software to provide a biologically structured overview of changes of transcripts, metabolites and enzyme activities. Use of this application is illustrated using three case studies with published or novel TOM1 array data sets for Solanaceousspecies. Comparison of previously reported data on transcript levels in potato leaves in the middle of the day and the middle of the night identified coordinated changes in the levels of transcripts of genes involved in various metabolic pathways and cellular events. Comparison with diurnal changes of gene expression in Arabidopsisrevealed common features, illustrating how MapMan can be used to compare responses in different organisms. Comparison of transcript levels in new experiments performed on the leaves of the cultivated tomato S. lycopersicumand the wild relative S. pennelliirevealed a general decrease of levels of transcripts of genes involved in terpene and, phenylpropanoid metabolism as well as chorismate biosynthesis in the crop compared to the wild relative. This matches the recently reported decrease of the levels of secondary metabolites in the latter. In the third case study, new expression array data for two genotypes deficient in TCA cycle enzymes is analysed to show that these genotypes have elevated levels of transcripts associated with photosynthesis. This in part explains the previously documented enhanced rates of photosynthesis in these genotypes. Since the SolanaceousMapMan is intended to be a community resource it will be regularly updated on improvements in tomato gene annotation and transcript profiling resources.The tomato microarray TOM1 offers the possibility to monitor the levels of several thousand transcripts in parallel. The microelements represented on this tomato microarray have been putatively assigned to unigenes, and organised in functional classes using the MapMan ontology (Thimm  et al., 2004. Plant J. 37: 914–939). This ontology was initially developed for use with the ArabidopsisATH1 array, has a low level of redundancy, and can be combined with the MapMan software to provide a biologically structured overview of changes of transcripts, metabolites and enzyme activities. Use of this application is illustrated using three case studies with published or novel TOM1 array data sets for Solanaceousspecies. Comparison of previously reported data on transcript levels in potato leaves in the middle of the day and the middle of the night identified coordinated changes in the levels of transcripts of genes involved in various metabolic pathways and cellular events. Comparison with diurnal changes of gene expression in Arabidopsisrevealed common features, illustrating how MapMan can be used to compare responses in different organisms. Comparison of transcript levels in new experiments performed on the leaves of the cultivated tomato S. lycopersicumand the wild relative S. pennelliirevealed a general decrease of levels of transcripts of genes involved in terpene and, phenylpropanoid metabolism as well as chorismate biosynthesis in the crop compared to the wild relative. This matches the recently reported decrease of the levels of secondary metabolites in the latter. In the third case study, new expression array data for two genotypes deficient in TCA cycle enzymes is analysed to show that these genotypes have elevated levels of transcripts associated with photosynthesis. This in part explains the previously documented enhanced rates of photosynthesis in these genotypes. Since the SolanaceousMapMan is intended to be a community resource it will be regularly updated on improvements in tomato gene annotation and transcript profiling resources.

Various biochemical, chemical, and microspectroscopic methods have been developed throughout the years for the screening and identification of mutants with altered cell wall structure. However, these procedures fail to provide the insight into structural aspects of the cell wall polymers. In this paper, we present various methods for rapidly screening Arabidopsis cell wall mutants. The enzymatic fingerprinting procedures using high-performance anion-exchange-pulsed-amperometric detection liquid chromatography, fluorophore-assisted carbohydrate electrophoresis, and matrix-assisted laser-desorption ionization time of flight (MALDI-TOF) mass spectrometry (MS) were exemplified by the structural analysis of the hemicellulose xyloglucan. All three techniques are able to identify structural alterations of wall xyloglucans in mur1, mur2, and mur3, which in comparison with the wild type have side chain defects in their xyloglucan structure. The quickest analysis was provided by MALDI-TOF MS. Although MALDI-TOF MS per se is not quantitative, it is possible to reproducibly obtain relative abundance information of the various oligosaccharides present in the extract. The lack of absolute quantitation by MALDI-TOF MS was compensated for with a xyloglucan-specific endoglucanase and simple colorimetric assay. In view of the potential for mass screening using MALDI-TOF MS, a PERL-based program was developed to process the spectra obtained from MALDI-TOF MS automatically. Outliers can be identified very rapidly according to a set of defined parameters based on data collected from the wild-type plants. The methods presented here can easily be adopted for the analysis of other wall polysaccharides. MALDI-TOF MS offers a powerful tool to screen and identify cell wall mutants rapidly and efficiently and, more importantly, is able to give initial insights into the structural composition and/or modification that occurs in these mutants.

Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

Summary: Metabolomics, in particular gas chromatography–mass spectrometry (GC–MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology. Metabolite profiling has profound applications in discovering the mode of action of drugs or herbicides, and in unravelling the effect of altered gene expression on metabolism and organism performance in biotechnological applications. As such the technology needs to be available to many laboratories. For this, an open exchange of information is required, like that already achieved for transcript and protein data. One of the key-steps in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations from biological samples. Collections of mass spectra, which comprise frequently observed metabolites of either known or unknown exact chemical structure, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here we present GMD, The Golm Metabolome Database, an open access metabolome database, which should enable these processes. GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds. The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation. Availability: http://csbdb.mpimp-golm.mpg.de/gmd.html Contact: Steinhauser@mpimp-golm.mpg.de Supplementary information: http://csbdb.mpimp-golm.mpg.de/

Summary: The open access comprehensive systems-biology database (CSB.DB) presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this applications note, is a set of co-response databases that currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The database enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition, statistical tools are offered to the user, which allow validation and comparison of those co-responses that were discovered by gene queries performed on the currently available set of pre-selectable datasets. Availability: All co-response databases can be accessed through the CSB.DB Web server (http://csbdb.mpimp-golm.mpg.de/).