 the coverage obtained for the chromosome. Changes found in plasmids laid in intergenic regions or in genes encoding hypothetical or poor characterized proteins and were not taken into consideration for posterior analyzes. Chromosome and plasmid differences are listed in Supplementary_Table_2.

As shown in [Table 1](#tbl0005){ref-type="table"}, four non-synonymous substitutions were found in the ER79ag chromosome that were not present in our ZM4 strain: one of them (R676 M) was located within the ACT regulatory region of *spoT/relA,* a gene encoding a protein involved in the synthesis and degradation of the (p)ppGpp alarmone. Another mutation (S26 G) lies within in the gene encoding ClpP, a protease that, in association to the unfoldases ClpA and ClpX, degrades a wide variety of substrates and plays important roles in stress tolerance in many microorganisms \[[@bib0140]\] A third mutation (R399C) was located within in *rimO,* a gene encoding a methylthiotransferase of the 30S ribosomal protein S12 \[[@bib0145]\]. The last non-synonymous substitution (V313A) was located within a gene encoding a member of the HlyC/CorC family transporter protein (ZMO_RS01280). ER79ag also lost one of its plasmids (pZZM402).Table 1Mutations found in ER79ag and ER79ap. Comparison was made with the sequence of ZM4 clone sequenced in this work (ZM4\*). Positions listed here are the same that those in ZM4 reference sequence (NC_006526.2). **P_ZM4\*** position in ZM4\*; **P_ER79ag**, position in mutant ER79ag; **P_ER79ap**, position in mutant ER79ap; **P_CHANGE**, amino acid residues sequence change involved in the mutant protein.Table 1P_ZM4\*SUBST.P_ER79agLOCUS_TAGPROTEIN_IDPRODUCTP_CHANGEINTERGENIC_REGION76942C A76942ZMO_RS00360WP_012817506.1Bifunctional (p)ppGpp synthetase/guanosine-3\',5\'-bis(diphosphate) 3\'-pyrophosphohydrolase, **SpoT/RelA**R676M\_\_299718T C299718ZMO_RS01280WP_011240232.1**HlyC/CorC** family transporterV313A\_\_810750G A810750ZMO_RS03600WP_011240680.130S ribosomal protein S12 methylthiotransferase **RimO**R