Data from: Ecology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila
Data files
Aug 22, 2024 version files 8.40 MB
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Hanson_May19-2023.7z
8.40 MB
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README.md
2.12 KB
Abstract
Antimicrobial peptides are host-encoded immune effectors that combat pathogens and shape the microbiome in plants and animals. However, little is known about how the host antimicrobial peptide repertoire is adapted to its microbiome. Here we characterize the function and evolution of the Diptericin antimicrobial peptide family of Diptera. Using mutations affecting the two Diptericins (Dpt) of Drosophila melanogaster, we reveal the specific role of DptA for the pathogen Providencia rettgeri and DptB for the gut mutualist Acetobacter. Strikingly, presence of DptA- or DptB-like genes across Diptera correlates with the presence of Providencia and Acetobacter in their environment. Moreover, DptA- and DptB-like sequence predicts host resistance against infection by these bacteria across the genus Drosophila. Our study explains the evolutionary logic behind the bursts of rapid evolution of an antimicrobial peptide family and reveals how the host immune repertoire adapts to changing microbial environments.
README: Title of DatasetEcology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila
Fly infection experiment data alongside bioinformatic analyses (alignment, phylogeny, codon-based assessment of evolution) related to the evolution of the Diptera antimicrobial peptide family Diptericin, with a focus on Drosophila fruit flies.
Description of the data and file structure
The data are provided in folders that relate to the main figures as per the preprint version of the article. In this way, we hope the hierarchical structure of the folders is more intuitive to help readers find the specific data they are interested in related to a specific figure. The figures are titled per the preprint manuscript as this is the published text at time of writing. In the future, the supplementary figure naming format is likely to change from "Figure XsuppY", so we encourage users to view the latest version of the open access preprint to sort out any confusion.
see: https://doi.org/10.1101/2022.12.23.521774
Bioinformatic analyses were performed in Geneious, and we provide both the Geneious files (version R7 and later) to ensure ease of visualization. However we also have endeavoured to provide Nexus (.nex) or Genbank (.gb) files when possible to ensure users have access to data with their preferred software. User annotations to sequences we made in Geneious will not show up in .nexus files, and we cannot ensure that all software will read these annotations the same in GenBank files using other software.
Sharing/Access information
All data generated in this manuscript are free to access and re-use in future studies, and users are encouraged to cite with appropriate credit (specifically citation to the manuscript published in Science).
Code/Software
Statistics were run using a mix of R and Prism as was convenient for our purposes throughout the manuscript. The model for Figure 5 data was run in R and the output from our code is stored as a Text Document in the data folders pertaining to Figure 5 for full transparency.
Methods
The dataset was collected through wet lab experimentation and literature review, as described in the manuscript. In brief, bacterial infections were performed with immune mutant Drosophila flies. Immune evolution of fly defence genes was collected from previous studies and newly-published genomic data through sequence-based searches, and the host gene evolution was manually curated with a focus on specific residues of a priori interest.
Usage notes
The data are saved in excel file formats, csv file formats, and alignment and phylogeny data are provided in both Geneious proprietary software format, and either .nexus or .genbank as a non-proprietary alternative. Any Geneious files can be viewed with the free version of the software available from the company.