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Background    Corynebacterium glutamicum  is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some  C. glutamicum  strains are available, comprehensive comparative genome analyses of these species have not been done. Six wild type  C. glutamicum  strains were sequenced using next-generation sequencing technology in our study. Together with 20 previously reported strains, we present a comprehensive comparative analysis of  C. glutamicum  genomes.    Results  By average nucleotide identity (ANI) analysis, we show that 10 strains, which were previously classified either in the genus  Brevibacterium , or as some other species within the genus  Corynebacterium , should be reclassified as members of the species  C. glutamicum. C. glutamicum has  an open pan-genome with 2359 core genes. An additional NAD + /NADP +  specific glutamate dehydrogenase (GDH) gene ( gdh ) was identified in the glutamate synthesis pathway of some  C. glutamicum  strains. For analyzing variations related to amino acid production, we have developed an efficient pipeline that includes three major steps: multi locus sequence typing (MLST), phylogenomic analysis based on single nucleotide polymorphisms (SNPs), and a thorough comparison of all genomic variation amongst ancestral or closely related wild type strains. This combined approach can provide new perspectives on the industrial use of  C. glutamicum .    Conclusions  This is the first comprehensive comparative analysis of  C. glutamicum  genomes at the pan-genomic level. Whole genome comparison provides definitive evidence for classifying the members of this species. Identifying an aditional  gdh  gene in some  C. glutamicum  strains may accelerate further research on glutamate synthesis. Our proposed pipeline can provide a clear perspective, including the presumed ancestor, the strain breeding trajectory, and the genomic variations necessary to increase amino acid production in  C. glutamicum.Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3255-4) contains supplementary material, which is available to authorized users.

Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids