The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

Background: Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.

One sentence summary: T6P can be targeted through genetic and chemical methods for crop yield 10 improvements in different environments through the effect of T6P on carbon allocation and 11 biosynthetic pathways 12Significant increases in global food security require improving crop yields in favourable and 13 poor conditions alike. However, it is challenging to increase both the crop yield potential and yield 14 resilience simultaneously, since the mechanisms that determine productivity and stress tolerance are 15 typically inversely related. Carbon allocation and use may be amenable to improving yields in a range 16 of conditions. The interaction between trehalose 6-phosphate (T6P) and SnRK1 (SNF1-related/AMPK 17 protein kinases) significantly affects the regulation of carbon allocation and utilisation in plants. 18Targeting T6P appropriately to certain cell types, tissue types, and developmental stages results in an 31 SUCROSE AND TREHALOSE: THE YIN AND YANG OF CROP IMPROVEMENT 32Plants are the only organisms that synthesise both non-reducing disaccharides, trehalose and 33 sucrose. The ubiquity of both pathways in plants has been known for less than 20 years and was a 34 major revelation for those working on carbon metabolism, as well as plant scientists in general, given 35 the range of processes affected by the trehalose pathway. Plant metabolism is highly regulated. Part 36 of this regulation is through trehalose 6-phosphate (T6P) signalling that regulates metabolism in the 37 light of carbon availability and reprograms metabolism between anabolic or catabolic pathways 38 depending on the carbohydrate status of the plant. This discovery is also significant for understanding 39 the regulation of growth and development by carbon supply. Furthermore, the trehalose pathway may 40 widely impact crop improvement. Crops are not yet optimised to maximize their biosynthetic pathways 41 for yield in sinks and growth recovery that are promoted by high T6P, and for mobilisation of reserves 42 and sugar transport which can enable resilience that are promoted by low T6P. 43Both the trehalose and sucrose biosynthesis pathways draw from a pool of core metabolites, 44 from which the carbon skeletons for all cellular components are also made (Paul et al. 2008 procedures to measure the abundance of T6P and trehalose (Lunn et al. 2006; Carillo et al. 2013; 51 Delatte et al. 2009;Mata et al. 2016). The capacity to synthesise trehalose in 52 plants began to become apparent as the associated plant genes were identified (Blazquez et al. 1998; 53 Vogel et al. 1998). Subsequent publication of the Arabidopsis genome showed an abundance of both 54 trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) gene families with 55 11 and 10 members respectively (Leyman et al. 2001). 56It is likely that T6P is a specific signal indicating sucrose abundance (Lunn et al. 2006; Nunes 57 et al. 2013a). T6P and sucrose levels are correlated in many tissues e.g. Arabidopsis and wheat 72TPSs have yet to be resolve...

Arbuscular mycorrhizal (AM) fungi are essential elements of soil fertility, plant nutrition and productivity, facilitating soil mineral nutrient uptake. Helianthus annuus is a non-model, widely cultivated species. Here we used an RNA-seq approach for evaluating gene expression variation at early and late stages of mycorrhizal establishment in sunflower roots colonized by the arbuscular fungus Rhizoglomus irregulare. mRNA was isolated from roots of plantlets at 4 and 16 days after inoculation with the fungus. cDNA libraries were built and sequenced with Illumina technology. Differential expression analysis was performed between control and inoculated plants. Overall 726 differentially expressed genes (DEGs) between inoculated and control plants were retrieved. The number of up-regulated DEGs greatly exceeded the number of down-regulated DEGs and this difference increased in later stages of colonization. Several DEGs were specifically involved in known mycorrhizal processes, such as membrane transport, cell wall shaping, and other. We also found previously unidentified mycorrhizal-induced transcripts. The most important DEGs were carefully described in order to hypothesize their roles in AM symbiosis. Our data add a valuable contribution for deciphering biological processes related to beneficial fungi and plant symbiosis, adding an Asteraceae, non-model species for future comparative functional genomics studies.