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Background  Actinobacteria of the genus  Nocardia  usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some  Nocardia  genomes have been sequenced, and genome sequences have accumulated. Genome sizes of  Nocardia  strains are similar to those of  Streptomyces  strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative  Nocardia  species/strains based on domain organization and amino acid sequence homology.    Results  Draft genome sequences of  Nocardia asteroides  NBRC 15531 T ,  Nocardia otitidiscaviarum  IFM 11049,  Nocardia brasiliensis  NBRC 14402 T , and  N. brasiliensis  IFM 10847 were read and compared with published complete genome sequences of  Nocardia farcinica  IFM 10152,  Nocardia cyriacigeorgica  GUH-2, and  N. brasiliensis  HUJEG-1. Genome sizes are as follows:  N. farcinica , 6.0 Mb;  N. cyriacigeorgica , 6.2 Mb;  N. asteroides , 7.0 Mb;  N. otitidiscaviarum , 7.8 Mb; and  N. brasiliensis , 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4–11, 7–13, and 1–6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text.    Conclusion  We conclude the following: 1) genomes of  Nocardia  strains carry as many PKS-I and NRPS gene clusters as those of  Streptomyces  strains, 2) the number of PKS-I and NRPS gene clusters in  Nocardia  strains varies substantially depending on species, and  N. brasiliensis  strains carry the largest numbers of clusters among the species studied, 3) the seven  Nocardia  strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different  N. brasiliensis  strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the  N. brasiliensis  strains. Genome sequencing suggested that  Nocardia  strains are highly promising resources in the search of novel secondary metabolites.    Electronic supplementary material  The online version of this article (doi: 10.1186/1471-2164-15-323) contains supplementary material, which is available to authorized users.

bmc genomics

Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species