acanthamoebae'' has a 16S rRNA sequence that is 15% different and a 23S rRNA sequence that is 17% different from members of the Chlamydiaceae family. PAUP version 4.0 was used to create maximum parsimony and neighbor-joining phylogenetic trees.
They used the Clustal W program to align all of the 16S and 23S data that was collected. Sequence information for the 16S rRNA genes of these bacteria was collected from GenBank. They used Sequencher data analysis tools to accumulate 23S rRNA gene sequences from bacteria in all of the families within Chlamydiales. set out to determine the characteristics that specifically distinguish all the families in the order Chlamydiales, and in doing so proposed that the formation of the family Parachlamydiaceae. From this information, they proposed that the bacteria are likely a novel member of a genus in the family Chlamydiaceae. It had a sequence similarity of 70 to 75% when compared to bacteria from other phyla in the same domain. acanthamoebae'' has an 86 to 87% sequence similarity with bacteria in the Chlamydia genus. acanthamoebae'' rRNA sequences with the same bacteria used in the distance matrix. The maximum likelihood analysis compared the ''P. The maximum likelihood analysis was performed by comparing the rRNA sequence from Parachlamydia acanthamoebae to rRNA sequences from the entire ARB Project database. The ARB Project and the FastDNAml tool were used to perform maximum parsimony and maximum likelihood analyses.
A distance matrix was used to compare the attained 16S and 23S rRNA sequences with the 16S rRNA with other bacteria in the Chlamydia family as well as other bacteria from known phyla. They were able to amplify rRNA fragments that covered almost all of the rRNA operon using PCR. used a number of methods to analyze the phylogeny of Parachlamydia acanthamoebae.
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