Project description:Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analysed the transcriptome of P. medicaginis across three phases of colonisation of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterisation of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.
Project description:As a broad group, hemibiotrophic pathogens cause significant losses within agriculture threatening the sustainability of food systems globally. The complex manner in which these microbes colonize their hosts, including an initial biotrophic phase of colonization followed by a biotrophic-to-necrotrophic switch (BNS) phase and ending with a necrotrophic mode of nutritional acquisition, renders their management more complex than pathogens which display a single nutritional strategy. Within model plant systems, typically each of these phases is characterized by both common and discrete transcriptional responses as the host modulates physiological processes in concert with changes in pathogen biology. Plant hormones also play an important role in these stages with classic models showing that salicylic acid accumulates during the biotrophic phase and jasmonic acid/ethylene responses occur during the necrotrophic phase. In this study, we use the interaction between the hemibiotroph Phytophthora medicaginis and the roots of its host Cicer arietinum (chickpea) to define the duration of the different life stages of P. medicaginis during the pathogenesis of chickpea. Using transcriptional profiling across all three stages of infection we demonstrate that chickpea displayed some similarities in response to P. medicaginis as has been previously documented in other model plant-pathogen hemibiotrophic interactions. However, our transcriptomic results suggest that chickpea does not conform to the phytohormone response model observed in leaf colonization, nor to that observed for roots of other plant species being colonised by soil-borne hemibiotrophs. We confirm these findings using targeted quantification of salicylic acid and jasmonic acid. The findings from this study demonstrate that a wider spectrum of plant species should be investigated in future to understand the physiological changes in plants during the different stages of colonization by hemibiotrophic soil-borne pathogens before we can better manage these economically important microbes in agronomically relevant conditions.
Project description:This genome-scale metabolic model (GEM) of Corynebacterium tuberculostearicum strain DSM 44922 (Taxon ID 38304) was initially built with CarveMe version 1.5.1 based on the genome assembly with NCBI accession GCF_013408445.1 and then underwent a series of careful semi-automatic and manual curation. It is the first model curated using the Python tool MCC for mass and charge curation.
Project description:We sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, the Banna Minipig Inbred Line (BMI). we conducted whole genome screening using next generation sequencing (NGS) technology and performed SNP calling using Sus Scrofa genome assembly Sscrofa11.1.
