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Background  Whilst being closely related to the model actinomycete  Streptomyces coelicolor  A3(2),  S. lividans  66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type  S. lividans  66, a derivative industrial strain, TK24, and  S. coelicolor  M145.    Results  The high coverage and specificity (detection of three nucleotide differences) of the new microarrays used has highlighted the macroscopic genomic differences between two  S. lividans  strains and  S. coelicolor . In a series of case studies we have validated the microarray and have identified subtle changes in genomic structure which occur in the Asp-activating adenylation domains of CDA non-ribosomal peptide synthetase genes which provides evidence of gene shuffling between these domains. We also identify single nucleotide sequence inter-species differences which exist in the actinorhodin biosynthetic gene cluster. As the glyoxylate bypass is non-functional in both  S. lividans  strains due to the absence of the gene encoding isocitrate lyase it is likely that the ethylmalonyl-CoA pathway functions as the alternative mechanism for the assimilation of C 2  compounds.    Conclusions  This study provides evidence for widespread genetic recombination, rather than it being focussed at 'hotspots', suggesting that the previously proposed 'archipelago model' of genomic differences between  S. coelicolor  and  S. lividans  is unduly simplistic. The two  S. lividans  strains investigated differ considerably in genetic complement, with TK24 lacking 175 more genes than its wild-type parent when compared to  S. coelicolor . Additionally, we confirm the presence of  bldB  in  S. lividans  and deduce that  S. lividans  66 and TK24, both deficient in the glyoxylate bypass, possess an alternative metabolic mechanism for the assimilation of C 2  compounds. Given that streptomycetes generally display high genetic instability it is envisaged that these high-density arrays will find application for rapid assessment of genome content (particularly amplifications/deletions) in mutational studies of  S. coelicolor  and related species.

bmc genomics

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization