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Mycoplasma synoviae  is an important pathogen of poultry, causing significant economic losses in this industry. Analysis of the unique genes and shared genes among different  M. synoviae  strains and among related species is helpful for studying the molecular pathogenesis of  M. synoviae  and provides valuable molecular diagnostic targets to facilitate the identification of  M. synoviae  species. We selected a total of 46 strains, including six  M. synoviae  strains, from 25 major animal (including avian)  Mycoplasma  species/subspecies that had complete genome sequences and annotation information published in GenBank, and used them for comparative genomic analysis. After analysis, 16 common genes were found in the 46 strains. Thirteen single-copy core genes and the 16s rRNA genes were used for genetic evolutionary analysis.  M. synoviae  was found to have a distant evolutionary relationship not only with other arthritis-causing mycoplasmas, but also with another major avian pathogen,  Mycoplasma gallisepticum , that shares the major virulence factor  vlhA  with  M. synoviae . Subsequently, six unique coding genes were identified as shared among these  M. synoviae  strains that are absent in other species with published genome sequences. Two of the genes were found to be located in the genetically stable regions of the genomes of  M. synoviae  and were determined to be present in all  M. synoviae  isolated strains ( n  = 20) and  M. synoviae -positive clinical samples ( n  = 48) preserved in our laboratory. These two genes were used as molecular diagnostic targets for which SYBR green quantitative PCR detection methods were designed. The two quantitative PCR methods exhibited good reproducibility and high specificity when tested on positive plasmid controls and genomic DNA extracted from different  M. synoviae  strains, other major avian pathogenic bacteria/mycoplasmas, and low pathogenic Mycoplasma species. The detection limit for the two genes was 10 copies or less per reaction. The clinical sensitivity and specificity of the quantitative PCR methods were both 100% based on testing chicken hock joint samples with positive or negative  M. synoviae  infection. This research provides a foundation for the study of species-specific differences and molecular diagnosis of  M. synoviae .

Comparative Genomics of Mycoplasma synoviae and New Targets for Molecular Diagnostics