Data from: Genotype-by-environment interactions influence the composition of the Drosophila seminal proteome
- 1. University of Zurich
- 2. Syracuse University
Description
Ejaculate proteins are key mediators of post-mating sexual selection and sexual conflict, as they can influence both male fertilization success and female reproductive physiology. However, the extent and sources of genetic variation and condition dependence of the ejaculate proteome are largely unknown. Such knowledge could reveal the targets and mechanisms of post-mating selection and inform about the relative costs and allocation of different ejaculate components, each with its own potential fitness consequences. Here, we used liquid chromatography coupled with tandem mass spectrometry to characterize the whole-ejaculate protein composition across twelve isogenic lines of Drosophila melanogaster that were reared on a high- or low-quality diet. We discovered new proteins in the transferred ejaculate and inferred their origin in the male reproductive system. We further found that the ejaculate composition was mainly determined by genotype identity and genotype-specific responses to larval diet, with no clear overall diet effect. Nutrient restriction increased proteolytic protein activity and shifted the balance between reproductive function and RNA metabolism. Our results open new avenues for exploring the intricate role of genotypes and their environment in shaping ejaculate composition, or for studying the functional dynamics and evolutionary potential of the ejaculate in its multivariate complexity.
Notes
Usage notes
There are two supplementary table:
– "Table_S1_dataset": the datasets used in this study.
– "Table_S2_analysis_output": the output of the analysis.
There are 2 R-scripts:
– "code": the R-code used to produce the results of this study.
– "code_Fig.S4AC": a second R-code used to produce Fig. S4A, S4B and S4C.
The Mass Spectrometer data, which the analysis is based on:
– "raw_MS_file_TMT_A-E": The raw data as obtained using Proteome Discoverer v2.5 (Thermo Fisher Scientific), searching against the D. melanogaster protein database containing only the longest isoform for each protein (r6.32; Thurmond et al, 2019, n = 13,813 entries).
The thorax length data:
– "thorax_length": the thorax length of 35 focal males and standard females per isoline-treatment combination.
And 2 additional files used for the analysis:
– "bothContrasts": the proteins that were differentially expressed relative to diet or isoline prior to FDR correction (from Fig. 2 and Fig. S7C).
– "design": the design setup used to perform the ComBat normalization procedure.
There are 5 reference files:
– "20220418_semenComposition_reference_list": the FBgn_IDs reference list of all male ejaculate proteins (EJA) and female reproductive tract (FRT) proteins as of 18 April 2022.
o The SFPs were extracted from Wigby et al, 2020.
o The sperm proteins were extracted from McCullough et al, 2022.
o The FRT were extracted from McDonough-Goldstein et al, 2021.
– "EJA": the male ejaculate proteins extracted from "20220418_semenComposition_reference_list".
– "FRT": the FRT proteins extracted from "20220418_semenComposition_reference_list".
Two dataset are not uploaded here because they are part of original publications from other authors:
"FlyAtlas": Drosophila melanogaster expression atlas (FlyAtlas 2), as published by Leader et al, 2018.
– "mode_of_evolution_Patlar_2021": the mode of evolution (constrained, positive, relaxed) for the SFPs (but not SpPs) as published by Patlar et al, 2021.
Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711
Award Number: PP00P3_170669
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Additional details
Related works
- Is source of
- 10.5061/dryad.djh9w0w5m (DOI)