Summary: α‐dioxygenases (α‐DOXs) catalyze the primary oxygenation of fatty acids into a newly identified group of oxylipins. Here we show that expression of the Arabidopsis α‐DOX1 gene is induced in response to both incompatible and compatible bacterial infections. However, the level of α‐DOX1 mRNA and dioxygenase activity appears earlier and reaches higher values when infection promotes a hypersensitive reaction. Furthermore, whereas gene expression is confined to necrotic lesions during the hypersensitive response, it occurs throughout the chlorotic area during a compatible interaction. Accumulation of α‐DOX1 transcripts is impaired in SA‐compromised plants and induced by SA and by chemicals generating nitric oxide (NO), intracellular superoxide or singlet oxygen, three signals mediating host cell death. Transgenic plants with altered levels of α‐dioxygenase react like wild‐type plants to a compatible pathogen. In contrast, plants with reduced activity develop a more rapid and severe necrotic response than wild‐type plants to incompatible bacteria and paraquat treatment, respectively, and a milder response when α‐DOX1 is overproduced. Our results suggest that plant α‐dioxygenases are used to generate lipid‐derived molecules for a process that protects plant tissues from oxidative stress and cell death.

Summary: High‐throughput RNA sequencing (RNA‐seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage‐specific transcripts. As an example of variation of physico‐chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter‐laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

During evolution, plants have developed mechanisms to cope with and adapt to different types of stress, including microbial infection. Once the stress is sensed, signaling pathways are activated, leading to the induced expression of genes with different roles in defense. Mosses (Bryophytes) are non-vascular plants that diverged from flowering plants more than 450 million years ago, allowing comparative studies of the evolution of defense-related genes and defensive metabolites produced after microbial infection. The ancestral position among land plants, the sequenced genome and the feasibility of generating targeted knock-out mutants by homologous recombination has made the moss Physcomitrella patens an attractive model to perform functional studies of plant genes involved in stress responses. This paper reviews the current knowledge of inducible defense mechanisms in P. patens and compares them to those activated in flowering plants after pathogen assault, including the reinforcement of the cell wall, ROS production, programmed cell death, activation of defense genes and synthesis of secondary metabolites and defense hormones. The knowledge generated in P. patens together with comparative studies in flowering plants will help to identify key components in plant defense responses and to design novel strategies to enhance resistance to biotic stress.