Computational protocol: Isolation of Treponema DNA from Necrophagous Flies in a Natural Ecosystem

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Protocol publication

[…] Sequences were analyzed and edited using 4Peaks 1.8 (Griekspoor and Groothuis, nucleobytes.com) and SeaView 4.5.4 software (). Sequences were compared to respective orthologous sequences available in GenBank using the standard nucleotide (nt) BLAST search option (http://blast.ncbi.nlm.nih.gov/Blast.cgi) at the NCBI homepage.Phylogenetic tree reconstruction was conducted using 26 tp0548 sequences obtained from fly samples (accession numbers can be found under 2.6. or in ) and one of 28 identical sequences from LMNP baboon skin tissue isolates as well as TPA and TPE reference strain sequence data obtained from GenBank. Accession numbers of reference strain sequences are as follows: TPE str.: Gauthier [CP002376], and CDC-2 [CP002375]; TP str. F-B [CP003902]; TPA str.: Nichols [AE000520], Dallas 1 [CP003115], Chicago [CP001752], and Seattle 81-4 [CP003679]); T. p. subsp. endemicum str. Bosnia A [CP007548]. The accession number of a sequence of tp0548 of type “j”, which was obtained from a human, was not available. Data were copied from the respective publication () and the extension of these data to cover the full sequence (nt 40 to 344) that was obtained from the flies was added from unpublished data (DS). A maximum parsimony (MP) tree with gaps as fifth character and 1000 bootstrap replicates was constructed in SeaView. Tree visualization and editing was performed in FigTree 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Alignment data of sequences used in this study can be found in Fig. S3. […]

Pipeline specifications

Software tools SeaView, FigTree
Application Phylogenetics
Organisms Treponema pallidum, Drosophila melanogaster, Papio hamadryas, Hemisus marmoratus, Papio ursinus
Diseases Yaws