DOI: 10.5061/dryad.8cz8w9h3b
title: Data from: Parasite prevalence in a social host has colony-wide impacts on transcriptional activity and survival

description: Parasites pose significant challenges not only to individual hosts but
 also to entire social groups. We investigated the effects of parasitism by
 the cestode Anomotaenia brevis on colonies of its intermediate host, the
 ant Temnothorax nylanderi. We evaluated changes in worker and queen
 survival rates and transcriptional activity in the fat body of infected
 and uninfected workers, as well as in the parasite itself, in relation to
 infected worker prevalence and colony size. Cestode-infected workers are
 known to exhibit a significantly extended lifespan compared to uninfected
 workers. Here, we demonstrate that the survival rates of infected workers,
 uninfected queens, and uninfected workers decrease with increasing
 infected worker prevalence and increase with colony size. Transcriptomic
 analysis revealed stress-related signatures in all workers, regardless of
 infection status, as infection prevalence increased. Moreover, gene
 expression patterns, particularly in uninfected workers, were strongly
 influenced by colony size. The transcriptional activity of the parasitic
 cestode also shifted with infected worker prevalence, highlighting the
 complex dynamics of host-parasite interactions. These results demonstrate
 that parasites in social species impose colony-wide impacts that extend
 beyond infected individuals, even in the absence of direct cross-nestmate
 infection risks. Moreover, the consequences of parasitism can be modulated
 by colony size.
description: # Data from: Parasite prevalence in a social host has colony-wide impacts
 on transcriptional activity and survival Dataset DOI:
 [10.5061/dryad.8cz8w9h3b](10.5061/dryad.8cz8w9h3b) ## Description of the
 data and file structure **Transcriptomics data** RNA was extracted using
 the Qiagen RNeasy extraction kit, RNA extraction failed for a single
 sample from an uninfected colony (colony F; table S1). We sent the rest of
 the samples to Novogene (Cambridge, UK) for mRNA library preparation using
 a NEBNext Ultra RNA Library Prep Kit. For cestode samples, a SMARTer
 amplification step was performed to accommodate low RNA content. The
 libraries were sequenced on an Illumina Novaseq 6000 in paired-end 150 bp
 mode, yielding a minimum of 9 Gb per sample. RNA-seq data for four of the
 uninfected workers were also utilized in Sistermans et al. (2023), which
 were obtained using the same protocol.  We mapped the cestode RNA reads
 using STAR v 2.7.10b with default parameters (Dobin et al., 2013) onto a
 concatenated reference assembly, combining the cestode genome and the *T.
 nylanderi* genome assembly (Jongepier et al., 2022). This approach enabled
 us to filter out contaminant reads that mapped to the ant genome. We then
 constructed a gene count matrix using htseq-count (Zanini et al., 2022)
 with default parameters including the discarding of multiply mapped. For
 functional annotation, we BLASTed the longest CDS isoform of each gene
 against the non-redundant invertebrate database (retrieved august 10th
 2021) using BLAST diamond (Buchfink et al., 2014), and obtained Gene
 Ontology (GO) terms for these isoforms using eggNOG mapper against the
 eggNOG 5 database (Cantalapiedra et al., 2021). For the ant RNA libraries,
 we first removed contaminant sequences from *A. brevis, Homo sapiens*, and
 *Escherichia coli*, as well as adaptors and vectors using fastqscreen
 v0.14.0 (Wingett & Andrews, 2018). The remaining sequences were
 trimmed down to 120 bp using fastp (Chen et al., 2018) with an N-base
 cut-off of 15 and mapped against a genome assembly of *T. nylanderi*
 (Jongepier et al., 2022) with hisat2 v2.1.0 (Kim et al., 2015) using the
 "--downstream-transcriptome-assembly" parameter. We then
 obtained a genome-guided transcriptome assembly and gene count matrix with
 stringtie v1.3.6 (Pertea et al., 2015). Functional annotation was
 performed on the transcriptome assembly as described above for the
 cestode. **GTF annotation** We generated a reference genome assembly for
 the cestode *A. brevis*. We extracted high-molecular-weight DNA from a
 pool of 29 cestodes isolated from a single infected worker. An ultra-low
 input library was prepared and sequenced using a PacBio Sequel II system.
 HiFi reads were called using DeepConsensus v1.2.0 (Baid et al., 2023) and
 assembled using Flye v2.9.2 (Kolmogorov et al., 2019), with the option
 "*--pacbio-raw*" to address sequence diversity within the
 sample, as well as options "*-i 4", "--no-alt-contigs"
 and "--scaffold*." The resultant assembly was deposited in the
 NCBI database under accession number JAUOZQ01. The assembly was
 annotated with BRAKER v3.0.3 (Brůna et al., 2021) in native mode using *A.
 brevis* RNA-seq data—from this study, Sistermans et al., 2023, and Stoldt
 et al., 2021—and from all nuclear protein sequences of the Cyclophyllid
 family available on NCBI (accessed on August 13, 2023). **Survival
 analysis** Re-analysis of data from Beros et al. 2021. ### Files and
 variables #### File: infected_degscript.R **Description:**  R
 transcriptomics script for infected ants #### File: uninfected_degscript.R
 **Description:** R transcriptomics script for uninfected ants #### File:
 parrate_gene_count_matrix.csv **Description:** Gene count matrix for all
 ants, the first column names all the gene names, all other columns are the
 gene counts for each sample (sample names are in the first row) #### File:
 readfile_combined.csv **Description:** Readfile containing metadata for
 all ants. column 1: sample name, column 2: proportion of infected ants in
 the colony from which the sample was taken, column 3: colony ID, column 4:
 colony size in number of total adult ants disregarding the queen, column
 5: number of cestodes the ant contains, column 6: whether the RNA was
 isolated in 2020 (a) or 2022 (b), column 7: whether the ant was infected
 or not with the cestode. #### File: readfile_infected.csv
 **Description:** Readfile containing metadata for infected ants. Column 1:
 sample name, column 2: proportion of infected ants in the colony from
 which the sample was taken, column 3: colony ID, column 4: colony size in
 number of total adult ants disregarding the queen, column 5: number of
 cestodes the ant contains #### File: parrate_transcript_count_matrix.csv
 **Description:** Transcript count matrix all ants. First column contains
 all transcript names, every other column transcript counts of
 corresponding transcripts (sample names are in the first row). #### File:
 readfile_uninfected.csv **Description:** Readfile containing metadata for
 uninfected ants.  Column 1: sample name, column 2: proportion of infected
 ants, column 3: colony ID, column 4: colony size, column 5: whether the
 RNA was isolated in 2020 (a) or 2022 (b). #### File:
 GO_genelevel_filtered.tsv **Description:** GO terms of all ant genes ####
 File: eggnog_output.tsv **Description:** Eggnog output for ants including
 GO terms #### File: BLAST_output_complete.tsv **Description:** BLAST
 output for all ant genes #### File: cestode_degscript_complete.R
 **Description:** R transcriptomics script for infected cestodes.  ####
 File: GO_terms.tsv **Description:** GO terms for all cestode genes ####
 File: BLAST_output.tsv **Description:** BLAST output for all cestode genes
 #### File: readfile_cestodes.csv **Description:** Readfile containing
 metadata for all cestodes. Column 1: sample name, column 2: proportion of
 infected ants in the colony from which the sample was taken, column 3:
 colony ID, column 4: colony size in number of total adult ants
 disregarding the queen, column 5: number of cestodes sequenced in the
 sample. #### File: cestode_gene_count_matrix.csv **Description:** Gene
 count matrix for all cestode genes. First column contains all transcript
 names, every other column gene counts of the corresponding transcripts
 (sample names are in the first row). #### File:
 MM_v50qswcl.emapper.annotations.tsv **Description:** Eggnog output for
 cestodes including GO terms #### File: colony_all.csv **Description:**
 Colony information for the survival analysis (derived from Beros et al.
 2021). Column 1: Colony ID, column 2: number of infected ants in the
 colony, column 3: total number of workers. #### File: demo_data.csv
 **Description:** Survival data for the survival analysis (derived from
 Beros et al. 2021). Column 1: colony ID of the sample, column 2: whether
 the ant is infected (infected), freshly emerged from pupa (callow),
 uninfected adult (old), or a queen (queen) by the time of the first
 observation, column 3: Age of death of the ant in days, column 4: whether
 the ant is alive at the end of the experiment (0) or dead (1) #### File:
 Script_survival_analysis.R **Description:** R script survival analysis
 #### File: JAUOZQ01.1.annotation_BRAKER3-v1.0.gtf **Description:** GTF
 annotation for *Anomotaenia brevis* genome ## Code/software All data was
 analysed using R (version 4.3.2 for the transcriptomics analysis and
 version 4.2.3 for the survival analysis). Most other files were thus also
 opened on R. The exception was the GTF file containing the annotation
 which was used for the pre-processing of raw reads of* Anomotaenia
 brevis*.  ## Access information Other publicly accessible locations of the
 data: * Raw RNA seq reads are found on NCBI under BioProject
 ID PRJNA1246159 Survival data was derived from: * Beros, S., Lenhart, A.,
 Scharf, I., Negroni, M. A., Menzel, F., & Foitzik, S. (2021). Extreme
 lifespan extension in tapeworm-infected ant workers. *Royal Society Open
 Science*, *8*(5).
 [https://doi.org/10.1098/rsos.202118](https://doi.org/10.1098/rsos.202118)