Phototropism in Arabidopsis is mediated by the blue light receptor phototropin 1 (phot1), a plasma membrane-associated kinase. Here we examined which tissues are important for establishing phototropism and other phot1-mediated processes. Using targeted expression analysis of PHOT1, we excluded the hypocotyl apex as the site for light perception and showed that de-phosphorylation of the phot1-interacting protein NPH3 is tissue autonomous and occurs more prominently in the basal hypocotyl.

The plant hormone Jasmonic Acid was known to be involved in fiber initiation and elongation, but the molecular details were not fully elucidated. Here we show that a jasmonate ZIM-domain (JAZ) protein inhibits lint and fuzz fiber initiation by repressing the transcriptional activation of MYB-like and bHLH transcription factors and other genes in the JA signaling pathway.

Sporopollenin in the pollen wall is produced by the tapetum, but how genes encoding the required biosynthetic enzymes are regulated is unclear. Here we show that two transcription factors, MS188 and AMS, positively regulate the gene encoding CYP703A2, a cytochrome P450 required for sporopollenin biosynthesis.

Carotenoid biosynthesis in plants includes a series of desaturation/isomerisation reactions, catalysed by four independent enzymes; in bacteria these reactions are catalysed by one enzyme, the crtI like phytoene desaturase. Expressing crtI in plants confers resistance to bleaching herbicides and enhances provitamin A content, i.e. in Golden Rice. Here we introduced crtI into tomato mutants defective in two different steps in the carotenoid biosynthetic pathway to determine how the endogenous carotenoid pathway reacts to alterations in desaturation. Collectively our data provide insights into the regulatory mechanisms operating within the pathway and how multi-level metabolite changes can occur.

Apple fruit ripening is largely mediated by ethylene. Interference at the receptor level by an antagonist modifies both the transcriptional and metabolic patterns. Our correlation network analysis showed specific interactions between particular transcripts and fruit texture, aromatic VOCs and polyphenolic compounds. Gene de-repression and regulatory activations were linked to regulatory circuits that involved auxin, ethylene and transcription factors.

Plants respond to herbivore attack by mobilising specific chemical defences. In cereals, for example, induction of 1,4-benzoxazin-3-ones (BXs) has been hypothesised to be such a defensive response. Here, by profiling and manipulating the spatiotemporal induction of BXs, we show that BX induction is highly localised and long lasting and provides local protection against caterpillars.

Centromeric chromatin is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species, thus the evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. Here, we analyzed a diploid progenitor of tetraploid cotton species to elucidate the enrichment dynamics and targeting-preference alterations of centromeric retrotransposons; our results suggest that repeats can proliferate and spread between genomes after polyploidization.

Regulating stress-responsive genes is critical for adaptation to adverse growth conditions Here we show that a polyamine influx transporter contributes to the plant heat stress response, as polyamines stabilize heat stress-inducible mRNAs.

Phosphatidylglycerol (PG) is an indispensable lipid constituent of photosynthetic membranes. Here we identified the previously unknown phosphatidylglycerophosphate phosphatase that is required for the last step in PG biosynthesis.

Helitron transposons can capture gene fragments and move them around the genome and thus have played an important role in shaping eukaryotic genomes, but their mode of transposition was unclear. Here we used an automated computational tool that enabled the discovery of a large cache of previously overlooked Helitrons in many genomes. We propose a rolling-circle replication model that accounts for the different Helitron distributions found in current plant genomes. As many tandem array Helitrons locate preferentially to centromeres, we suggest that they might have contributed to the growth of plant centromeres.

Tricin, a flavone with human health benefits, is covalently linked to lignin in monocots. Here we developed a chemical degradative method to quantify lignin-integrated tricin. If methods to economically cleave tricin from lignin are developed, waste lignin streams from biomass processing could be used as an alternative source of tricin.

The development and update of genetic and genomic resources, involving new methods of data acquisition and analysis, is necessary even for such long established model organisms such as Arabidopsis thaliana. We present a transcriptome map of A. thaliana created using high-throughput RNA sequencing. It covers 79 organs and developmental stages; the analysis allowed the determination of global characteristics of the A. thaliana transcriptome and to add splice junctions and predicted genes to our current knowledge of the A. thaliana genome.

Microalgae are promising feedstocks for biofuels, but additional genomic tools are needed to fully dissect the cellular networks underlying production of oil and biomass. Here, using nitrate reductase as an example, we demonstrate CRISPR/Cas9-based genome editing for a model industrial microalga.