Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling
Figure 4
Public RNA-seq datasets that lie in the Goldilocks Zone.
Ten strains with corresponding, publicly available RNA-seq data and phylogenetic distances in the Goldilocks Zone (Figure 3) have been identified. The maximum likelihood tree from a SSU rRNA alignment shows the relationships between these taxa. They fall into three clades, containing members of the families: Enterobacteriaceae and Xanthomonadaceae, and the genus: Pseudomonas. The nodes connecting taxa within the Goldilocks Zone are coloured gold, taxa that are too close are coloured red and those that are too divergent are coloured cyan. Each strain is annotated with gold boxes where there was stranded information, or if the majority of core mRNAs and ncRNAs (see Methods) were expressed (see Table S3 for the raw data).