*2.1. Analysis of N. edaphicum CCNP1411 Genome*

Total DNA has been isolated from *N*. *edaphicum* CCNP1411, and the whole genome sequence has been determined. Identified replicons of *N*. *edaphicum* CCNP1411 genome consist of the circular chromosome of 7,733,505 bps, and five circular plasmids (Table 1). Within the total size of 8,316,316 bps genome (chromosome and plasmids, Figure 2), we have distinguished, according to annotation, the total number of 6957 genes from which 6458 potentially code for proteins (CDSs), 415 are classified

as pseudo-genes and 84 are coding for non-translatable RNA molecules. Pseudo-genes can be divided into subcategories due to the shift in the coding frame (180), internal stop codons (77), incomplete sequence (228), or occurrence of multiple problems (63). Genes coding for functional RNAs consist of those encoding ribosomal (rRNA) (9), transporting (tRNA) (71) and regulatory noncoding (ncRNA) (4), all embedded on the chromosome. Out of total coding and pseudo-genes sequences (6873), the vast majority (5846) initiates with the ATG start codon, while GTG and TTG occur less frequently (561 and 217 times, respectively). The frequencies of stop codons were set out as follows: TAA (3455), TAG (1750), TGA (1526). Coding and pseudo-genes sequences are distributed almost equally on the leading and complementary strand, including 3408 and 3465 sequences, respectively.


**Table 1.** Composition and coverage of *N*. *edaphicum* CCNP1411 genome.

**Figure 2.** Map of the *N*. *edaphicum* CCNP1411 genome where chromosome (chr) and five plasmids (pNe\_1–5) are presented. The ORFs are indicated with grey arrows split into two rings outermost showing ORFs on direct strand and inner showing complementary strand ORFs. The middle circle shows GC content (black) and the innermost circle shows GC skew (green and purple). Genes for putative NRPS/PKS are marked on the chromosome in their proper position (red within a black circle), with closeup on NRPS in position 7,609,981–7,643,289 putatively coding for Ncp biosynthetic gene cluster.
