The removal of the non-informative positions increased the bootstrap values but did not affect the structure of the clades. The phylogenetic tree was generated with ClustalX 2.1 neighbor-joining bootstrap option. The gene content tree was generated using the information from the formed clusters of orthologous genes (COG) to generate a table with a serovar on each row and a COG in each column. The presence of a gene in a serovar for each COG was marked with the number 0–6 (0 = none, 1–6 = number of copies of the gene in the serovar). Singletons were added to the table
to increase the informative data. The core genome COGs (genes conserved in all 19 genomes) were removed from the dataset, since they are MLN2238 purchase non-informative. To be able to use ClustalX 2.1 to generate the tree the numbers were turned to letters: (0 = C, 1 = S, 2 = T, 3 = P, 4 = A, G = 5, N = 6).
The table was turned into a multifasta formatted file and loaded into ClustalX 2.1. The sequences did not need to be aligned with ClustalX 2.1, since they were already aligned. The tree was constructed using the bootstrap, neighbor joining method. The root for all trees is a poly-A sequence of similar size, since only the relationship within ureaplasmas was of interest. Acknowledgements The authors gratefully acknowledge BI 2536 order the assistance and contributions to this project by our J. Craig Venter Institute colleagues, Michael Montague, Elisabeth Caler, Sanjay Vashee, Mikkel Algire, Nacyra Assad-Garcia, Diana Radune, Jessica Hostetler, Scott Durkin, Jonathan Crabtree, and Jonathan Badger. Electronic supplementary material Additional file 1: Clinical isolates supplementary material. Contains information about the relatedness of the four sequenced urealyticum clinical isolates to the ATCC stains and genes
in their unique areas. (DOC 29 KB) Additional file 2: Figures S1-S5. Contains figures of additional phylogenetic trees. (DOC 1 MB) Additional file 3: Comparative Genomics Tables. Contains interactive tables of Thalidomide all gene clusters among the 19 ureaplasma genomes, % GC table, and a table of the genes from restriction modification systems in all 14 ATCC ureaplasma serovar strains. (XLS 3 MB) Additional file 4: Table S1. Contains anticodon table of tRNAs showing count of tRNAs used by human ureaplasmas. (DOC 63 KB) Additional file 5: All Genes Encoding Recombinase or Transposase Proteins in All 19 Ureaplasma Genomes. Contains a table of all genes in the 19 ureaplasma genomes that encode recombinase or transposase proteins. (XLS 26 KB) References 1. Shepard MC: The recovery of pleuropneumonia-like organisms from Negro men with and without nongonococcal urethritis. Am J Syph Gonor Vener Dis 1954, 38:113–124. 2. Shepard MC, Lunceford CD, Ford DK, Purcell RH, Taylor-Robinson D, Razin S, Black FT: Ureaplasma urealyticumgen. nov. sp. nov.: proposed nomenclature for the human T 7 (LCZ696 concentration T-strain) mycoplasmas. Int J Syst Bacteriol 1974, 24:160–171.CrossRef 3.