Multi-dimensional interplay between Xanthomonas oryzae TALEs and the rice genome

本研究旨在通过生物学和生物信息学的交叉学科方法，从多个维度研究植物病原性黄单胞菌与寄主水稻的相互作用。该项目将重点关注X的关键毒力因子TALE（转录激活因子样效应子）。- 是的TALE作为植物细胞内的转录因子，诱导靶基因的表达。首先，将研究水稻中特定的TALE靶标在细菌毒力中的作用。其次，TAL盒的全基因组预测将与总RNA-seq数据相结合，不仅在蛋白质编码基因中，而且在非编码RNA中检测新的TALE靶标。第三，将以时间依赖性方式研究TALE介导的基因激活。虽然主要TALE靶标在感染后的前24-48小时内被激活，但差异表达基因的数量在24小时至48小时之间急剧增加。确定的二级TALE靶标组应归因于调节性TALE靶标的活性，例如，那些作为转录因子发挥作用的。解开这些网络将加深我们对整个感染过程的TALE的理解。最后，通过挑战X染色体，分析TALE在病原-宿主相互作用中的进化维度.用基因组编辑产生的抗性植物筛选菌株。对克服这些抗性的细菌的选择和分析将使人们深入了解TALE基因中可能发生的适应性变化。这将有助于制定培育具有持久抗性的植物的策略。该项目将进一步探索非常长的测序技术，以组装高度重复的X。分析基因组，并扩展成功的AnnoTALE生物信息学工具箱，用于研究TALE。

This proposal aims at studying the interaction between plant-pathogenic Xanthomonas oryzae bacteria and the host plant rice (Oryza sativa) in multiple dimensions by a interdisciplinary approach between biology and bioinformatics. The project will focus on TALEs (transcription activator-like effectors) which are key virulence factors of X. oryzae. TALEs function as transcription factors inside plant cells to induce expression of target genes. First, specific TALE targets in rice will be studied for their role in bacterial virulence. Second, genome-wide predictions of TAL-boxes will be combined with total RNA-seq data to detect novel TALE targets not only in protein-coding genes, but also in non-coding RNAs. Third, TALE-mediated gene activation will be studied in a time-dependent manner. While primary TALE targets are activated within the first 24-48 hours after infection, the number of differentially expressed genes increases dramatically between 24 h and 48 h. Defined sets of secondary TALE targets should be attributable to the activity of regulatory TALE targets, e.g., those that function as transcription factors. Unravelling these networks will deepen our understanding of TALEs on the whole infection process. Finally, the evolutionary dimension of TALEs in the pathogen - host interaction will be analyzed by challenging X. oryzae strains with resistant plants that have been generated by genome editing. Selection and analysis of bacteria that overcome these resistances will give insights into the adaptive changes that are possible in TALE genes. This will help to develop strategies for breeding plants with durable resistances. The project will further explore very long-read sequencing technologies to assemble the highly repetitive X. oryzae genomes and extend the successful AnnoTALE bioinformatics toolbox for studying TALEs.