Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post infection with Xanthomonas oryzae pv. oryzae strain PXO99 , the goal is to understand the transcriptomic response of rice roots to colonization by bacterial pathogen
Project description:OsEDS1 is a key regulator of SA-mediated immunity in plants. The OsEDS1 knockout mutant (Oseds1) was characterized and shown to have increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), suggesting the positive role of OsEDS1 in regulating rice disease resistance. To identify differentially regulated downstream of Oseds1, we performed transcriptome deep sequencing (RNA-seq) of wild type (ZH11) and Oseds1 inoculated with Xanthomonas oryzae pv. Oryzae (PXO99A).
Project description:The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions and confirmed most of the annotated genes. Moreover, with high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons (uATGs) and upstream open reading frames (uORFs), which serves a remarkable insight into the A. oryzae transcriptome. We also were able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes or pathways that might involve in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae was much more complex than previously anticipated and the results might provide a blueprint for further study of A. oryzae transcriptome.
