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Additional file 16: Figure S5. Cladogram of glutamine synthetase isoform in L. minor (Lminor), S. polyrhiza (Spipo), A. thaliana (AT), O. indica (OSINDICA) and B. distachyon (BD). The phylogentic relationships of glutamine synthetase from different species have been calculated under default parameters using phylogeny.fr.

Additional file 12: Figure S3. Distribution of top plant GO slim categories for L. minor, S. polyrhiza, Z. mays, and O. sative proteomes. GO slim categories were assigned to L. minor by InterProscan5. GO slim categories of S. polyrhiza were extracted from Phytozome10 and O. sativa and Z. mays from Plaza 3.0.

Additional file 9: Figure S2. Distribution of the number of exons per gene.

Additional file 5: Figure S1. Assembled scaffold length distribution of L. minor genome.

Additional file 4:Table S4. Statistics of transcriptome and whole genome assembly of L. minor..

Additional file 10: Table S8. BLAST results of L. minor GenBank genes vs L. minor 5500.

Additional file 8: Table S7. Illumina libraries statistics for transcriptome assembly.

Additional file 3: Table S3. Number of CEGMA hits for different genome assemblies.

Additional file 6: Table S5. Variant calling of L. minor (strain 5500) chloroplast genome vs. L. minor GenBank reference genome NC_01019.

Additional file 2: Table S2. Summary statistics of the L. minor genome assemblies.

Additional file 13: Table S10. Overview of gene ontology classification.

Additional file 17: Table S12. Blast hit results of L. minor glutamine synthetase and glutamate synthase genes.

Additional file 14: Table S11. Overview of the over and underrespresented GO terms for L. minor genes compared to S. polyrhiza genes and for L. minor and duckweed specific genes in L. minor genome. The number of tandem genes for each GO term are also included.

Additional file 1: Table S1. Illumina libraries statistics for genome assembly.

Additional file 7: Table S6. Summary of the masked and unmasked genome assembly.

Additional file 11: Table S9. Overview of OrthoMCL gene clusters for L. minor with S. polyrhiza, Z. mays and O. sativa.

When terrestrial environments get contaminated with long-lived gamma emitting radionuclides, plants that grow in these contaminated areas are exposed to gamma radiation during consecutive generations. Therefore it is important to evaluate the gamma induced stress response in plants in and between generations. The objective of this research is to reveal differences at the level of the antioxidative stress response between generations with a different radiation history. An experiment was conducted in which 7-days old Arabidopsis thaliana plants were exposed for 14 days to four different gamma dose rates: 22 mGy/h, 38 mGy/h, 86 mGy/h and 457 mGy/h. Two different plant groups were used: plants that were not exposed to gamma radiation before (P0) and plants that received the aforementioned gamma treatment during their previous generation (S1). Growth, the concentration of the antioxidants ascorbate and glutathione, a number of antioxidative enzyme activities and their gene transcript levels were analysed. A dose-rate dependent induction was seen for catalase (CAT) and guaiacol peroxidase (GPX) in the roots and for syringaldazine peroxidase (SPX) in the shoots. Differences between the two generations were observed for CAT and GPX in the roots, where a significantly higher activity of these reactive oxygen species (ROS) detoxifying enzymes was observed in the S1 generation. For SPX in the shoots, a dose dependent upregulation was observed in the PO generation. However, high SPX activities were present for all doses in the S1 generation. These differences in enzyme activity between generations for SPX and GPX and the involvement of these enzymes in cell wall biosynthesis, suggest an important role for cell wall strengthening in the response to gamma irradiation. (C) 2016 Elsevier Ltd. All rights reserved. This project was supported by the European project COMET (7th PCRD EURATOM Contract Number: Fission-2012-3.4.1-604794) (www.comet-radioecology.org) and the Belgian nuclear research centre (SCK CEN).

Background: Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. Results: The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein- coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. Conclusions: The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species. The authors thank the Research foundation-Flanders (FWO) (G.A040.11N) and the European Commission Contract Fission-2010-3.5.1-269672 Strategy for Allied Radioecology (http://www.star-radioecology.org) for financial support of this work. Belgian nuclear research institute (SCK.CEN) is further thanked for funding the PhD of AVH. HXC is supported by the German Research Foundation (SCH 951/18 1). The people from CALCUA at the University of Antwerp are acknowledged for assisting high performance computing (http://www.uantwerpen.be/calcua). The authors also thank L. Leus, ILVO, for estimating DNA genome size through flow cytometry.

The reactive oxygen species (ROS)-signaling pathway is very important in heavy metal toxicity. Induction of the antioxidative defense mechanism, comprising ROS-scavenging enzymes and metabolites, in plants after environmental uranium contamination has been insufficiently studied in the past. This study aimed to analyze oxidative stress related responses in Arabidopsis thaliana after uranium exposure. Seventeen-day-old seedlings were exposed to 0, 0.1, 1, 10 and 100 μM uranium for 3 days. After exposure to 100 μM uranium, a decrease in fresh weight for leaves and roots was observed, leaves colored anthocyanous and roots were stunted and yellow. To reveal the importance of oxidative stress in uranium toxicity, alterations in ROS-scavenging enzymes were studied at protein and transcriptional level. Superoxide dismutase (SOD) capacities increased in leaves and roots after exposure to 100 μM uranium but no differences were observed for catalase (CAT) capacities. Transcript levels of different SODs located at various cellular compartments were affected depending on the place of action. Gene expression of CAT in leaves and roots was also affected after uranium exposure. Results indicate that oxidative stress plays an important role in uranium toxicity but suggest that plant responses differ for leaves and roots.