Project description:To study the alteration pattern and defensive response mechanism triggered by herbivorous feeding stimuli under natural conditions, we built a biological model of the interrelationship between the Chinese pine (Pinus tabuliformis Carr.) and the Chinese pine caterpillar (Dendrolimus tabulaeformis Tsai et Liu) within their native habitat. We integrated proteomic and phosphoproteomic data, normalized the results, and combined them with bioinformatics to evaluate and analyze variations in phosphoproteomics in pine needles' response to the caterpillar's feeding stimulus. We systematically identified differentially significant phosphorylated proteins implicated in the pine's defense mechanism against caterpillar stress. Furthermore, we predicted upstream kinases of phosphorylation sites and their activities. Similarly, through an analysis of the Motif patterns of phosphorylated proteins, Mfuzz clustering of phosphorylation sites, kinase regulatory networks and functional modules of phosphorylated protein interaction networks in response to stress within pine, we can investigate the mechanisms behind resistance formation and regulation of caterpillar feeding incentives in pine. The identification results of partially phosphorylated proteins were additionally confirmed through PRM technology. Furthermore, genes upstream of differentially expressed proteins were validated through RT-qPCR detection.
Project description:The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes. This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using AgilentM-bM-^@M-^Ys web-based eArray software. Labeled target cRNA (complementary RNA) was generated using AgilentM-bM-^@M-^Ys Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of FloridaM-bM-^@M-^Ys Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.
