Many species have evolved into diverse strains with phenotypic and genotypic variations that facilitate adaptation to different ecological niches and, in the case of pathogens, to different hosts. Whereas comparison of genome sequences reveals differences and similarities among strains, the consequences of genomic variations can be tracked by studying the functional output from the genome. RNA sequencing has been revolutionizing transcriptome analyses of both pro- and eukaryotes. However, the bioinformatics-based analysis is still lagging behind, and transcriptome features are often manually annotated, which is laborious and time-consuming. This is even more compounded for the analyses of multiple strains.
Here, a team led by researchers at the University of Würzburg and the University of Tübingen, Germany compared the primary transcriptomes of four isolates of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in humans, and provide genome-wide transcriptional start site (TSS) maps using a novel automated annotation method. Their comparative RNA–seq showed that most TSS are conserved in multiple strains, but they also observed SNP–dependent promoter usage. Furthermore, the researchers identified a novel minimal RNA–based CRISPR immune system as well as strain-specific small RNA repertoires. This automated, comparative TSS annotation will facilitate and improve transcriptome annotation for a wider range of organisms and provides insights into the contribution of transcriptome differences to phenotypic variation among closely related species.
- Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, et al. (2013) High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates. PLoS Genet 9(5), e1003495. [article]