Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation

Key message: Transcriptomic analysis resulted in the upregulation of the genes related to common defense mechanisms for black spot and the downregulation of the genes related to photosynthesis and cell wall modification for powdery mildew. Abstract: Plant pathogenic fungi successfully colonize their hosts by manipulating the host defense mechanisms, which is accompanied by major transcriptome changes in the host. To characterize compatible plant pathogen interactions at early stages of infection by the obligate biotrophic fungus Podosphaera pannosa, which causes powdery mildew, and the hemibiotrophic fungus Diplocarpon rosae, which causes black spot, we analyzed changes in the leaf transcriptome after the inoculation of detached rose leaves with each pathogen. In addition, we analyzed differences in the transcriptomic changes inflicted by both pathogens as a first step to characterize specific infection strategies. Transcriptomic changes were analyzed using next-generation sequencing based on the massive analysis of cDNA ends approach, which was validated using high-throughput qPCR. We identified a large number of differentially regulated genes. A common set of the differentially regulated genes comprised of pathogenesis-related (PR) genes, such as of PR10 homologs, chitinases and defense-related transcription factors, such as various WRKY genes, indicating a conserved but insufficient PTI [pathogen associated molecular pattern (PAMP) triggered immunity] reaction. Surprisingly, most of the differentially regulated genes were specific to the interactions with either P. pannosa or D. rosae. Specific regulation in response to D. rosae was detected for genes from the phenylpropanoid and flavonoid pathways and for individual PR genes, such as paralogs of PR1 and PR5, and other factors of the salicylic acid signaling pathway. Differently, inoculation with P. pannosa leads in addition to the general pathogen response to a downregulation of genes related to photosynthesis and cell wall modification. © 2019, The Author(s)

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily

The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period

Analyse wirtschaftlich wichtiger Merkmale in Zierpflanzen mit komplexen Genomen

Im Gegensatz zu Pflanzenarten die als Modelle für die Grundlagenforschung genutzt werden oder den wichtigsten landwirtschaftlichen Kulturpflanzen hat die Züchtungsforschung an Zierpflanzen mit einer Reihe von spezifischen Problemen zu kämpfen. Eines der Probleme ist die hohe Diversität an Zierpflanzenkulturen, die zur Folge hat, dass es, im Vergleich zu den landwirtschaftlichen Hauptkulturen, nur relative geringe Investitionen in Forschung und Entwicklung für die einzelne Kulturart gibt. Weitere Probleme entstehen durch Polyploidie, große Genome, lange Generationszeiten und schlechte Transformierbarkeit. Als Beispiel werden Arbeiten zur Resistenz an Rosen vorgestellt. In tetrasom spaltenden Nachkommenschaften mit Aufspaltung von Resistenz gegenüber einzelnen pathogenen Rassen eines Erregers ist die Markerentwicklung schwierig, da der Nachweis von Repulsionskopplungen sehr große Nachkommenschaften erfordert. In einem zweiten, alternativen Ansatz wurden in einem Panel von 96 überwiegend tetraploiden Rosensorten Assoziationsstudien zur Resistenz gegen verschiedene Pathogene und zu verschiedenen anderen Merkmalen durchgeführt. Als Markersysteme wurden hauptsächlich SNPs von einem Axiom SNP array sowie KASP Marker verwendet. Beispielhaft werden einzelne mit QTLs assoziierte Marker und erste Validierungsexperimente in unabhängigen Populationen sowie die Problematik der Dosisermittlung in tetraploiden Genotypen vorgestellt. Abschließend werden Ansätze und erste Ergebnisse zur Modifizierung von MLO-Genen in tetraploiden Rosen mit Hilfe von TALEN und CRISPR gezeigt

Inhibition of histone deacetylases permits lipopolysaccharide-mediated secretion of bioactive IL-1b via a caspase-1-independent mechanism

Histone deacetylase (HDAC) inhibitors (HDACi) are clinically approved anticancer drugs that have important immunemodulatory properties. We report the surprising finding that HDACi promote LPS-induced IL-1 beta processing and secretion in human and murine dendritic cells and murine macrophages. HDACi/LPS-induced IL-1 beta maturation and secretion kinetics differed completely from those observed upon inflammasome activation. Moreover, this pathway of IL-1 beta secretion was dependent on caspase-8 but was independent of the inflammasome components NACHT, LRR, and PYD domains-containing protein 3, apoptosis-associated speck-like protein containing a carboxyl-terminal caspase-recruitment domain, and caspase-1. Genetic studies excluded HDAC6 and HDAC10 as relevant HDAC targets in this pathway, whereas pharmacological inhibitor studies implicated the involvement of HDAC11. Treatment of mice with HDACi in a dextran sodium sulfate-induced colitis model resulted in a strong increase in intestinal IL-1 beta, confirming that this pathway is also operative in vivo. Thus, in addition to the conventional inflammasome-dependent IL-1 beta cleavage pathway, dendritic cells and macrophages are capable of generating, secreting, and processing bioactive IL-1 beta by a novel, caspase-8-dependent mechanism. Given the widespread interest in the therapeutic targeting of IL-1 beta, as well as the use of HDACi for anti-inflammatory applications, these findings have substantial clinical implications