Fig 1.
Percentage of species with depleted SD-like sequences.
The “Diwan Dataset” comprises the 284 prokaryotes studied by Diwan et al., but filtered for the subset (222) that demonstrably contains a perfect antiSD (CCUCCU) in the tail of the 16S rRNA (Amin et al., submitted). The “Control Dataset” comprises the 128 prokaryotes that lack a CCUCCU antiSD (Amin et al., submitted). The “Diwan high affinity codon shuffle” is the method used by Diwan et al. 2016 [8], and which uses high-affinity hexamers to define SD-like motifs. The “Complementary codon shuffle” is the method used here, using hexamers that are a 5-of-6 match to AGGAGG. The “Combined P-val” is the combination of the complementary codon shuffle with the codon usage metric. Depletion is scored at a p-value of 0.05. Results were not FDR corrected, because the distribution of p-values was not uniform.
Table 1.
Depletion of SD-like sequences from eukaryotes.
Table 2.
Hexamers used.
Table 3.
Codon usage of AGG.
Table 4.
Lack of correlation between depletion and strength of SD.
Fig 2.
Internal SD motifs are not depleted even when there is a downstream start codon.
Fig 3.
Evolution of ribosomal proteins S1 and S10 in organisms lacking an antiSD.
Each circle or dot on the arc of the graph is a query species. The relative dN/dS ratio (versus a control species, which is a close phylogenetic relative that has an antiSD) of the query species is shown by the size of the circle. A large circle indicates a large dN/dS, which indicates rapid directional evolution. Black dots/circles are control species that have an antiSD. Red dots/circles are species lacking an antiSD. Orange dots/circles are species lacking an antiSD, and in the “CFB” (Cytophaga-Flavobacterium-Bacteroides) phylum. In this phylum, species lacking antiSDs are relatively common, and SDs are rare. Empty circles are species where there is no annotated S1 (or, in B, no S10) ribosomal protein; this could mean the protein is present but not annotated, or it could mean the protein is entirely absent.