## 2 Results
### Novel sRNAs and Putative Targets  
Only very few sRNAs with known functions have been functionally characterized in _Streptomyces_. In _Streptomyces coelicolor_ A3(2), [PERSON] et al. [23] identified 63 ncRNAs including 29 _cis_-encoded antisense RNAs and confirmed expression for 11 of them which are now included in Rfam database (scr1601, scr2736, scr2952, scr3202, scr3920, scr4115, scr4389, scr4632, scr5676, scr6106, and scr6925) and in prevalence show growth-phase dependent expression. Of these ncRNAs, 5 out of 11 (scr1601, scr2736, scr2952, scr3920, and scr4115) were evolutionarily conserved in more than 50% of tested _Streptomyces_[23]. The Rfam database ([[http://rfam.xfam.org/](http://rfam.xfam.org/)]([http://rfam.xfam.org/](http://rfam.xfam.org/)), accessed on 15 February 2020) was first used to search for functional information and the degree of phylogenetic conservation of predicted _S. ambofacialen_sRNAs (Supplementary Table S8). Computational analysis predicted scr2736 homolog (sRNA #10) among the sRNAs, in addition to other conserved sRNAs including the bacterial small signal recognition particle RNA (SRP RNA) (sRNA #20), and 6C RNA (sRNA #24). 6C RNA is a class of ncRNA present in actinomycetes, which is characterized by a conserved RNA structure having two stem-loop structures each containing six or more cytosine residues. Transcription of the _S. coelicolor_ 6C RNA increases during sporulation [22]. In _Mycobacterium tuberculosis_, 6C sRNA regulates genes involved in various processes including DNA replication and protein secretion [41]. Extending our search to UTRs, we found scr1601, scr4115, scr4677, scr5239, and scr5676 homologs that were not predicted among sRNAs. This prediction also reveals conserved _cis_-acting regulatory elements including several riboswitches (S-adenosyl-methionine (SAM), glycine, flavin mononucleotide, thiamine pyrophosphate, cobalamin, cyclic di-AMP (_ydaO/yuaA_) riboswitches), _msiK_ RNA motif [42], _che1_ RNA motif [43], and the Group II catalytic intron D1-D4-7 (Supplementary Table S8). scr5239 is probably one of the currently best-characterized sRNAs in _Streptomyces coelicolor_[22; 23; 44]. scr5239 has two targets; it inhibits agarase DagA expression by direct base pairing to the _dagA_ mRNA coding region [45], and it represses translation of methionine synthase _metE_ mRNA by binding at the 5\({}^{\prime}\) end of its open-reading frame [46]. sRNA scr4677 is located in the intergenic region between anti-sigma factor SCO4677 gene and a putative regulatory protein gene SCO4676. scr4677 expression requires SCO4677 activity and scr4677 itself seems to affect the levels of SCO4676 mRNA [47]. Both SCO4676 and SCO4677 affect the production of the blue-pigmented antibiotic actinorhodin under specific growth conditions [47]. In intracistronic sequences of operons Rfam search predicted scr3202, in addition to other conserved _cis_-acting regulatory elements including _raiA_-hairpin RNA motif [43], _nrd_ RNA motif [43], Actico-_pnp_ RNA motif [43], group II catalytic intron, and cyclic di-AMP (_ydaO/yuaA_) and cobalamin riboswitches (Supplementary Table S8). Trying to understand the reason for the possible misclassification of scr1601, scr4115, scr4677, scr5239, scr5676, and scr3202 homologs in _S. ambofacialen_s we went back to timepoint predictions in search of possible prediction errors (Supplementary Figure S1). Only for two of them (scr5239, scr5676), we found predictions for both UTR and ncRNAs in different days and relevant signals corresponding to the expected ncRNAs length, so we decided to add them to the list of sRNA as sRNA #44 and sRNA #45. Starting from all 43 sRNA sequences (Supplementary Table S3) and from the 5 scrRNA sequences predicted in other ncRNAs (Supplementary Table S3), GLASSgo software [48; 49; 50] was used to analyze the degree of phylogenetic conservation of the predicted _S. ambofacialen_sRNAs.