Similar differences in the deep tree nodes can be seen in the phylogenetic trees resulting from the concatenated alignments of the genes of each of the four groups and the trees

resulting from different combinations of the groups (Additional file 2: Figures S2–S4). However, as more genes are used to construct the trees, the clade and node structure of Proteasome inhibitor the trees becomes more consistent. Figure 3 MBA Based Phylogenetic Tree of 19 Ureaplasmas. The tree is based on the nucleotide sequence of the conserved domain of the mba (1–430 nt). Figure 4 Phylogenetic Tree of 19 Ureaplasma Strains Based on 82 Housekeeping Genes. ATCC type strains are labeled with tree letters (species) followed by a number (serovar). UUR = Ureaplasma urealyticum; UPA = Ureaplasma parvum; ntUPA3 = clinical isolate sequenced in 2000; 2033, 2608, 4155, and 4318 are clinical isolates of Ureaplasma urealyticum that cannot be serotyped. The tree is based on the concatenated alignment of 82 housekeeping genes 16 tRNA ligase genes, 12 DNA and RNA polymerase genes, 47 ribosomal protein genes, and the 7 urease subunit genes).

The non- informative positions were removed from the alignments. The removal of the non- nformative positions increased the bootstrap values. Recombination and integration of DNA All ureaplasma serovars contained one or more integrase-recombinase genes and some serovars contained transposases, or remnants of transposases, and some JNK-IN-8 molecular weight phage related proteins. Most of the recombinases were site-specific tyrosine recombinases, which are present also in other mycoplasmas and firmicutes. The highest number and variety of such genes was observed in serovar 2, and in general, UUR serovars had higher number of these

Demeclocycline genes than UPA serovars. However, insertion events represented only a small portion of the average 118 Kbp difference between the two species. A gene encoding a site-specific integrase-recombinase was adjacent to the phase variable locus of the MBA in 12 of the 14 serovars. This recombinase was likely involved in the rearrangements of the mba locus resulting in the variation of the C-terminal of this surface antigen. The presence of transposases suggested that foreign mobile DNA elements have been inserted in the genomes of ureaplasma serovars. Some of the transposases have truncations or unverified frameshifts indicating that the mobile element that they were part of was most likely no longer mobile. It was no surprise to find transposon related genes in serovar 9, which had acquired tetracycline resistance. The tetM gene was identified as part of a Tn916 transposon, based on the genes around it. Although tetracycline-resistant ureaplasma were probably less frequent when serovar 9 was isolated, now they comprise 25–35% of all patient isolates.