Data from: Cavernicola pilosa Barber (Hemiptera, Reduviidae, Triatominae) infected by Trypanosoma cruzi marinkellei Baker et al. (Kinetoplastida, Trypanosomatidae)
Data files
Jun 22, 2026 version files 251.61 KB
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gGAPDH.xml
32.41 KB
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README.md
3.46 KB
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SSU.xml
74.48 KB
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Supplementary_Material.pdf
141.26 KB
Abstract
This dataset consists of files used for phylogenetic reconstructions by Bayesian inference of some trypanosomatids species. It groups new sequences amplified from DNA extracted from the abdominal contents of Cavernicola pilosa (Hemiptera, Reduviidae, Triatominae) and others sequences available in Genbank. These analyses were performed to confirm the species of the detected trypanosomatid. After the analyses, the presence of Trypanosoma cruzi marinkellei was confirmed. In addition, the supplementary material compiles information on the protocols used in the polymerase chain reaction (PCR), such as primers and temperatures. It also includes the accession codes for the sequences deposited in GenBank and used in phylogenetic analyses.
Dataset DOI: 10.5061/dryad.z08kprrvh
Description of the data and file structure
The Supplementary Material file (Supplementary_Material.pdf) contains a table with the PCR protocols, as well as the primers used (Table 1), and a table with the GenBank accession codes for the sequences used in the phylogenetic analyses (Table 2).
The .xml files available in this dataset can be used for phylogenetic analyses in the Beast program (Drummond et al. 2012). After complete, the trees should be generated in the TreeAnnotator (BEAST package) with a burn-in of 25 % of the samples. The generated tree can be visualized in FigTree (Rambaut, 2018).
To produce the .xml files available in this dataset, sequences from some trypanosomatids should be grouped and aligned using the Muscle method in the Mega 11 program (TAMURA et al., 2021). The accession codes for the sequences used is available in Table 2 (Supplementary_Material.pdf). The resulting alignments should be submitted to the BEAUti program (from the BEAST package), with the Yule process prior and the GTR model of nucleotide substitutions with gamma distribution defined for both markers. For the SSU-rRNA analysis sampling should be performed over 100 million generations, while for gGAPDH over 300 million generations, for stabilization (ESS > 200).
References for the softwares used:
- DRUMMOND, A.J.; SUCHARD. M.A.; XIE, D.; RAMBAUT, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29, 1969-1973. https://doi.org/10.1093/molbev/mss075
- TAMURA K, STECHER G, AND KUMAR S (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38:3022-3027.
- RAMBAUT A. FigTree–tree figure drawing tool version v.1.4.4. Institute of Evolutionary Biology, University of Edinburgh: Edinburgh, 2018
Files and variables
File: Supplementary_Material.pdf
Description:
Table 1 - Primers, temperature conditions and time used in Polymerase Chain Reaction.
Table 2 - GenBank accession codes for Trypanosoma spp. sequences used in phylogenetic analyses.
File: gGAPDH.xml
Description:
File ready for phylogenetic reconstruction of Trypanosoma spp. based on glycosomal glyceraldehyde-phosphate dehydrogenase (gGAPDH) in the BEAST program.
File: SSU.xml
Description:
File ready for phylogenetic reconstruction of Trypanosoma spp. based on the small-subunit ribosomal RNA (SSU-rRNA) in the BEAST program.
Access information
Data was derived from the following sources:
- Hamilton et al. (2008): https://doi.org/10.1016/j.meegid.2007.09.003
- Noyes et al. (1999): https://doi.org/10.1016/s0020-7519(98)00167-2
- Borghesan et al. (2013): https://doi.org/10.1016/j.protis.2012.06.001
To obtain the sequences used in the phylogenetic analyses, the accession codes available in Table 2 (Supplementary_Material.pdf) must be entered into the search field on the GenBank website:
To produce the .xml files available in this dataset, sequences from some trypanosomatids should be grouped and aligned using the Muscle method in the Mega 11 program (TAMURA et al., 2021). The accession code for the sequences used is available in Table 2 (Supplementary_Material.pdf). The resulting alignments should be submitted to the BEAUti program (from the BEAST package), with the Yule process prior and the GTR model of nucleotide substitutions with gamma distribution defined for both markers. For the SSU-rRNA analysis sampling should be performed over 100 million generations, while for gGAPDH over 300 million generations, for stabilization (ESS > 200).
Phylogenetic analyses:
The .xml files available in this dataset can be used for phylogenetic analyses in the Beast program (Drummond et al. 2012). After complete, the trees should be generated in the TreeAnnotator (BEAST package) with a burn-in of 25% of the samples. The generated tree can be visualized in FigTree (Rambaut, 2018).
References for the softwares used:
- DRUMMOND, A.J.; SUCHARD. M.A.; XIE, D.; RAMBAUT, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29, 1969-1973. https://doi.org/10.1093/molbev/mss075
- TAMURA K, STECHER G, AND KUMAR S (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38:3022-3027.
- RAMBAUT A. FigTree–tree figure drawing tool version v.1.4.4. Institute of Evolutionary Biology, University of Edinburgh: Edinburgh, 2018