Genome-wide mapping of the Galleria mellonella larvae transcription start sites during infection with the madurella mycetomatis pathogen
Using Low Quantity single strand CAGE (LQ-ssCAGE) we mapped the transcription start sites (TSS) and annotated the 5' end of the invertebrate Galleria mellonella which is upcoming and booming in the last years as an experimental model in infection disease and immunology research. The current genome annotation of this model lacks the annotation of the 5' end and TSS information. To map TSS under healthy and infection conditions, the G. mellonella larva was infected with the fungal pathogen Madurella mycetomatis  After 4, 30 and 52 hours of the infection, larvae were treated with itraconazole or ravuconazole. RNA-seq and LQ-ssCAGE libraries prepared and sequenced. The LQ-ssCAGE data was processed to identify CAGE transcription start site (CTSS), uni- and bi-directional clusters. LQ-ssCAGE enabled us to precisely identify (39,410) TSS and (249) active enhancers. We assigned genomic features to the resulting TSSs and enhancers. The majority of the TSS peaks are annotated as promoter regions while the enhancers were annotated as intergenic and genic. Furthermore, we confirmed the quality of TSS by promoter shapes and GC bias.  We identified a set of super-enhancers and predicted de-novo motifs. In this study we reported the first atlas of TSS and active enhancers of the G. mellonella. Overall design: To map and annotate the transcription start sits of the invertebrate Galleria mellonella larvae we prepared and sequenced LQ-ssCAGE (low quantity single strand CAGE) libraries (n=72). The resulting sequence tags are mapped against the reference genome for the Galleria mellonella. The CAGE tags are called using the mapped reads. Using statistical and clustering methods, TSS and active enhancers are identified and annotated again genomics regions.