(A) Example of dRNA-seq and ssRNA-seq profiles mapped onto the T. onnurineus NA1 genome. For TSS determination, total RNA samples were isolated from independent biological replicates of the mid-exponential growth phase cultures and two sequencing libraries were constructed, one from TEX treated (+TEX) and the other from untreated total RNA (−TEX). The expression levels of mRNA transcripts were obtained from ssRNA-seq, representing the genomic region between TON_1301 and TON_1310, in yeast peptone sulfur (YPS), MM1-CO (MMC), and MM1-Formate (MMF) media conditions. (B) TSS confirmation for TON_1301 and TON_1306 using the 5′ Rapid Amplification of cDNA Ends derivative method (5′tagRACE) and Sanger sequencing. Full-length gels are included in Supplementary Fig. S1. (C) Average normalized intensity of each position for maximum peak within ±200 nt from the identified TSSs. (D) A total of 1,082 TSSs were identified and classified according to their positions relative to adjacent ORFs. TSSs located from 300 bp upstream to 50 bp downstream of the start codon of the annotated ORF were classified as the primary (P) or secondary TSSs (S). The peaks found within the coding regions were assigned as the internal TSSs (I). TSSs located within the reverse strands and the annotated ORFs were classified as the antisense (A) and intergenic TSSs (N), respectively.