This repository contains open-source code, data, & text files.
Raw amplicon sequence files can be found at NCBI SRA BioProject ID PRJNA855478. Raw transcriptome sequence files can be found at NCBI SRA BioProject ID PRJNA854962. Assembled transcriptomes can be found on Zenodo.
Weinfurther, K.D., Stuckert, A.M.M., Muscarella, M.E., Peralta, A.L., Summers, K. Evidence for a Parabasalian Gut Symbiote in Egg-Feeding Poison Frog Tadpoles in Peru
- Aim: This study looks at the evolution of oophagy (egg-feeding) in the poison frog Ranitomeya imitator. We examine both gene expression and the microbiome in tadpole intestines from two congeneric species that are either facultative omnivores (Ranitomeya variabilis) or have evolved oophagy (Ranitomeya imitator).
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analyses: An R Markdown file that includes R script written by Ariane Peralta, Mario Muscarella, and Adam Stuckert containing functions used in analysis of gut microbiome bacterial and microeukaryotic communities and poison frog transcriptome of tadpole intestines.
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bin:
- MothurTools.R: An R script written by Mario Muscarella (Indiana University, now at University of Illinois) containing functions used in the analysis of community sequence data.
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data: Files associated with amplicon data sets.
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figures: Figures (of microbes-16S and 18S rRNA amplicons) generated according to R script located in R Markdown file.
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mothur: Files containing script for bioinformatic analysis of 16S rRNA and 18S rRNA gene sequences (Illumina MiSeq platform) using mothur pipeline.
K. Summers acknowledges funding from the National Geographic Society (Grant #WW-R015-17) and the National Science Foundation (DEB 1655336). M. Muscarella acknowledges funding from the National Science Foundation (OIA-1826801 Supplemental Award).
Dr. Adam Stuckert (website): Assistant Professor, University of Houston
Dr. Mario Muscarella (website): Assistant Professor, University of Alaska Fairbanks
Dr. Ariane Peralta (website): Associate Professor, Department of Biology, East Carolina University