Data from: Variation in a microbial mutualist has transcriptional consequences for host-parasite interactions
Data files
May 20, 2026 version files 67.56 MB
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Dataset_S01.csv
9.52 MB
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Dataset_S02.csv
10.62 MB
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Dataset_S03.csv
46.32 MB
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Dataset_S04.csv
456.26 KB
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Dataset_S05.csv
366.54 KB
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Dataset_S06.csv
265.54 KB
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README.md
4.14 KB
Abstract
Strains of microbial symbionts often vary in their effect on their host. However, little is known about how the genetic variation in microbial symbiont populations impacts host interactions with other co-colonizing microbes. Here, we investigated how different strains of nitrogen-fixing rhizobial bacteria affect their host plant’s transcriptomic response to parasitic root-knot nematodes in the legume Medicago truncatula. Using dual RNA-seq of root organs harboring rhizobia or nematodes, we identified plant host, rhizobial, and nematode genes whose expression differed between parasite-infected and -uninfected plants and between plants inoculated with different rhizobial strains. At the site of host-parasite interactions (in nematode galls), hundreds of host genes and a few nematode genes differed in expression between host plants inoculated with different rhizobia strains. At the site of host-mutualist interactions (in rhizobia nodules), hundreds of host genes and a few rhizobial genes responded to parasite infection. The vast majority of parasite-induced changes in host gene expression depended on the resident rhizobia strain. The transcriptomic changes we observed suggest that microbial indirect genetic effects play an underappreciated role in structuring their host’s interactions with other co-colonizing microorganisms, which may be mediated by changes in host resource budgets, defense response, or developmental trajectories.
https://doi.org/10.5061/dryad.b8gtht7mp
We examined the transcriptional consequences of a host plant inoculated with different strains of rhizobia for host-parasite interactions with a parasitic nematode. We examined differential expression in different organs of the plant, including the organs where plant-rhizobia and plant-nematode interactions take place. We also used gene ontology overrepresentation analysis to infer the biological processes that may be associated with these transcriptional changes.
Description of the data and file structure
Dataset_S01.csv: Gene expression quantification
A comma-separated values file containing gene expression quantification data output from HTSeq-union for all genes in all organisms.
Dataset_S02.csv: Gene expression status
A comma-separated values file containing gene expression status for all genes in all organisms. Expression status is determined by a gene having >1 RPKM (reads per kilobase of gene length per million reads of an organism) in more than one sample of a given treatment. Column names are composed of the string “exp_” followed by an abbreviation of the organ type and the rhizobia strain treatment. The abbreviation “nodp” indicates nodules from hosts inoculated with nematodes, and the abbreviation “nodm” indicates nodules from hosts without nematode inoculation. “21” indicates rhizobial strain USDA1021 and “22” indicates rhizobial strain WSM1022. The abbreviation “gano” indicates the combination of galls and nodules, the abbreviation “garo” indicates the combination of galls and roots, and the abbreviation “noro” indicates the combination of nodules from hosts infected and roots.
Dataset_S03.csv: Differential expression analysis for Medicago truncatula
A comma-separated values file containing the results of all DESeq2 differential expression analyses for M. truncatula genes. Column names are composed of a prefix and a suffix separated by a period. Each prefix corresponds to one of the models detailed in Table S3. Suffixes are as follows: “baseMean” indicates the mean of normalized expression across all sample types; “ns_LFC” indicates the log fold change base 2 of the normalized expression across the contrast specified by the model in Table S3; “ns_SE” indicates the standard error of the log fold change estimate; “padj” indicates the p-value of the likelihood ratio test used to determine if the log fold change is significantly different from zero adjusted with false discovery rate correction. The final column, entitled NCR, indicates whether a gene is a nodule-specific cysteine-rich protein.
Dataset_S04.csv: Differential expression analysis for Ensifer meliloti
A comma-separated values file containing the results of all DESeq2 differential expression analyses for all E. meliloti genes. Column naming convention follows the same pattern as described in Dataset 3.
Dataset_S05.csv: Differential expression analysis for Meloidogyne hapla
A comma-separated values file containing the results of all DESeq2 differential expression analyses for all M. hapla genes. Column naming convention follows the same pattern as described in Dataset 3.
Dataset_S06.csv: Gene Ontology overrepresentation analysis
A comma-separated values file containing all Gene Ontology overrepresentation analysis results. These results are the output of the enrichGO function in the clusterprofiler R package.
Sharing/Access information
Links to other publicly accessible locations of the data:
Data was derived from the following sources:
- Raw read data was uploaded to the Sequence Read Archive under BioProjectID PRJNA1090526
Code/Software
All code is available at the GitHub address linked above, and all software specifications are outlined in the manuscript associated with this submission.