Figure 2

Basic features of the S. elongatus transcriptome. (a) Distribution of absolute transcript abundance per cell. Only transcripts with mean coverage of over two reads per nucleotide (corresponding to approximately 1 mRNA per 15 cells) are shown, and a total of 1,500 mRNA per cell is assumed [8, 9] (Materials and methods). (b) RNA sequencing versus RNA pol ChIP. Absolute transcription (RNA sequencing averaged over transcript) and absolute RNA pol occupancy (RNA pol ChIP averaged over transcript) are generally correlated (Pearson correlation, r = 0.65). The probability of getting a correlation as large by random chance (P-value) is 7.41e-169. (c) Distribution of ORFs per mRNA. Most mRNAs contain one to two ORFs. The extreme case is that of an operon composed primarily of ribosomal proteins that includes 31 ORFs and is 17,158 nucleotides in length. (d) Operon estimations based on RNA sequencing versus bioinformatic predictions. Comparison of RNA sequencing based operon determination and bioinformatic predictions from MicrobesOnline [12, 13]. (e) Distribution of mRNA lengths. The median mRNA length is 1,320 nucleotides, approximately twice the median size of an ORF (776 nucleotides) in S. elongatus.