Data for: Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila
Data files
Nov 09, 2026 version files 6.63 GB
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datasets.tar.gz
32.36 MB
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ncbi_dataset.tar.gz
1.04 GB
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outputs.tar.gz
5.56 GB
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README.md
18.61 KB
Abstract
This dataset supports the study of these horizontal gene transfer (HGT) in the genome of the dark-winged fungus gnat Bradysia coprophila, as presented in our manuscript “Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila”. It includes input genome data and intermediate outputs used for HGT detection, as well as in the downstream bioinformatic characterization of these genes, and experimental data generated via genetic complementation assays in Drosophila melanogaster and Saccharomyces cerevisiae. These data can be reused to reproduce our HGT and functional inferences or search for inter-metazoan HGT in other dipteran genomes. No ethical or legal restrictions apply to the data.
Dataset DOI: 10.5061/dryad.5dv41nsmx
Description of the data and file structure
ncbi_dataset.tar.gz
Description: Input genome sequences obtained from NCBI, along with available or BRAKER3-generated annotation data. All genome data are contained in subdirectories within the /data/ directory.
GCF_014529535.2
Latest RefSeq annotation for Bradysia coprophila, accessed May 26, 2026. longest_isoform.fasta contains the longest extracted protein isoform for each gene.
GCF_019649055.1
Paramacrobiotus metropolitanus annotation, accessed July 5, 2026.
GCF_002217175.1
Folsomia candida annotation, accessed July 5, 2026.
GCA_965233325.1
Bradysia impatiens genome, accessed May 27, 2026, with a custom BRAKER3 annotation and downstream CD-HIT clustering results.
Files include:
Galaxy13-[BRAKER3 on dataset 1 and 2_ GTF Annotation].gtf: raw BRAKER3 annotationbraker.gtf: filtered annotationcds.faa,protein.faa, andlongest_isoform.faa: extracted FASTA files
GCA_965233655.1
Lycoriella ingenua genome, accessed May 28, 2026, with a custom BRAKER3 annotation and downstream CD-HIT clustering results.
Files include:
Galaxy11-[BRAKER3 on dataset 2 and 4_ GTF Annotation].gtf: raw BRAKER3 annotationbraker.gtf: filtered annotationcds.faa,protein.faa, andlongest_isoform.faa: extracted FASTA files
GCA_016920775.1
Bradysia odoriphaga genome annotation, accessed June 1, 2026.
GCA_029228625.1
Pseudolycoriella hygida genome annotation, accessed June 1, 2026.
datasets.tar.gz
Description: Input data used in the analyses.
Pseudolycoriella_hygida_data
Supplementary data from Trinca and Monesi et al. (2023), DOI: 10.1016/j.isci.2023.106449, used as input for proteome and carbohydrate-active enzyme analyses.
These data are not included in this repository and must be downloaded from the source publication.
RNA_seq
B. coprophila transcriptomic data obtained from the RefSeq FTP site associated with the reference genome annotation.
phylogenetic_trees
Literature-derived lineage trees used to construct the concatenated arthropod phylogeny in Figure 2A. Sources were:
- Misof et al. (2014) for Hexapoda (https://www.science.org/doi/10.1126/science.1257570)
- Howard et al. (2020) for Chelicerata (10.1016/j.asd.2020.100997)
- Bernot et al. (2023) for Pancrustacea (https://academic.oup.com/mbe/article/40/8/msad175/7239260)
- Fernández et al. (2015) for Myriapoda (https://www.biorxiv.org/content/10.1101/030973v1)
- Wiegmann et al. (2011) for Diptera (https://www.pnas.org/doi/10.1073/pnas.1012675108).
Newick trees were obtained directly from the publication for Bernot et al.; with permission from TimeTree.org for Misof et al., Howard et al., and Fernández et al.; and by using Treemble v1.6.2 to extract the tree from Figure S3 of Wiegmann et al. These data are not included in this repository and must be downloaded from the source publication.
annotated_genomes_ncbi_5_27_26.tsv
RefSeq- or GenBank-annotated genome accessions and associated metadata as of May 27, 2026.
go-basic.obo
Gene Ontology (GO) term-name mapping, accessed July 7, 2026; file modified June 26, 2026.
GCF_014529535.2-RS_2026_02_gene_ontology.gaf
B. coprophila Gene Ontology assignments obtained from the RefSeq annotation FTP site on July 7, 2026.
.txt files
iTOL annotation-template files used for gene-tree visualization.
GCF_014529535.1_BU_Bcop_v1_genomic.gff and GCF_014529535.1_BU_Bcop_v1_protein.faa
Annotation files from the previous B. coprophila RefSeq annotation, accessed July 7, 2026.
outputs.tar.gz
Description: Output files and intermediate data generated by the analyses.
diamond_clustered_results_split_edited.tar.gz
Directory containing DIAMOND results for B. coprophila proteins searched against the clustered NR database, using one protein isoform per protein-coding gene. Each .tsv file is named according to the accession of the query protein.
Column headers correspond to standard DIAMOND output fields described in the DIAMOND documentation.
per_protein_diamond_data.tsv
HGT analysis data for all protein-coding genes.
DIAMOND_htgs.fasta
FASTA file containing protein sequences of DIAMOND-inferred horizontally transferred genes (HTGs).
annotated_dipteran_genomes_6_7_2026.tsv
Tabular data containing dipteran genome accessions and associated metadata used for the Diptera-wide analysis. Not all available genomes were analyzed; some Drosophila and Anopheles genomes were excluded to reduce redundancy.
Column headers correspond to standard NCBI Datasets outputs described in the NCBI Datasets genome documentation, except for the taxid, family, and family_taxid fields, which were added to capture taxonomic information.
diptera_wide_screen
Directory containing per-protein ancestry annotations across 53 non-sciarid dipteran genomes. Rhagoletis zephyria was excluded from the final analysis because of likely contamination (DOI: 10.1016/j.ijpara.2024.07.001).
Columns are:
accession:genome_accession;protein_accessionn_non_diptera: number of non-dipteran DIAMOND hitsn_out_fam_diptera: number of dipteran hits outside the family of the queryAI: alien indexsciname: scientific name of the top hit outside the family of the querytype: annotation category as described in the Supplementary Information Methods
SI_table_1.tsv
Per-genome results of the DIAMOND screen for HTGs.
DIAMOND_htgs.fasta
FASTA file containing all DIAMOND-identified HTG protein sequences.
connected_components.pickle
Pickle file containing a Python dictionary mapping cluster IDs to the HTGs contained within each cluster. Used for gene-tree construction.
connected_components_reps.pickle
Pickle file containing a Python dictionary mapping cluster IDs to their representative sequences. Used for gene-tree construction.
sciarid_diamond_search.tsv
DIAMOND search results for B. coprophila HTGs searched against a combined database of sciarid proteins. Columns correspond to standard DIAMOND output fields; species indicates the species associated with each hit.
phylogenetic_dataset
Directory containing intermediate files and outputs from gene-tree inference for DIAMOND-identified putative HTGs. Each subdirectory is named according to a unique cluster identifier matching the corresponding identifier in iTOL.
Files include:
seqs.fasta: unaligned protein sequences selected for phylogenetic inferenceMSA.fasta: MUSCLE multiple-sequence alignmenttrimmed_MSA_sub_seq.fasta: alignment trimmed to the region overlapping the top non-sciarid hittrimAl_MSA_sub_seq.fasta: alignment further trimmed to 60% column occupancy- Files beginning with
rev_aa: standard IQ-TREE output files rev_aa.treefile: maximum-likelihood tree selected for analysis and visualization.txtfiles: annotation files for use in iTOL
manual_inspection_table.tsv
Table used to assist with manual inspection of gene-tree topologies.
SI_inspection_bradysia_6_23_2026.tsv
Results of manual gene-tree inspection, used as input for Table S5.
SI_tables/SI_table_9_convergent_transfers.tsv
Recipients of convergent transfers, tabulated by the number of HTG sciarid clades.
sister_automated_per_clade.tsv
Automated analysis of the phylogenetic sisters of HTG clades.
sister_automated_per_sequence.tsv
Closest non-sciarid phylogenetic relatives for individual HTGs, with one HTG per row. Used as input for Table S5.
hgts.fasta
FASTA file containing 1,517 tree-confirmed HTGs.
ONT_reads.csv
Number of Oxford Nanopore Technologies (ONT) reads mapped to each gene (rows) for each SRA accession (columns).
vmean_read_length.csv
Mean ONT read length overlapping each gene, with ancestry annotations.
read_depth_per_gene.csv
Mean ONT read depth per gene, with ancestry annotations.
nucleotide_composition_stats.csv
Codon usage (Measurement Independent of Length and Composition; MILC), GC content, and GC3 content for each protein-coding gene in B. coprophila and Folsomia candida, with B. coprophila used as the reference for MILC values. Gene type is indicated in the tree_HTG column.
final_concatenated_arthropod_order.nwk, final_concatenated_arthropod_order_collapsed_diptera.nwk, and arthropod_tree_for_paper.nwk
Lineage trees of arthropod orders used for Figure 2B, derived by concatenating phylogenies from previously published studies. The latter two trees are collapsed within Diptera. arthropod_tree_for_paper.nwk is additionally annotated with the numbers and percentages of HTGs based on their top non-sciarid DIAMOND hits.
itol_arthropod_donor_annotation_file.txt
iTOL annotation file specifying circle sizes for the arthropod lineage tree in Figure 2B.
homologs_in_other_sciarids_per_gene.tsv
Gene-tree-based inference of HTG homolog presence in sciarid genomes other than B. coprophila, with one HTG protein accession per row.
*_v_coprophila_reciprocal_best_blast_results.csv
Results of reciprocal best DIAMOND-hit searches between B. coprophila and other sciarids. Each row contains a pair of corresponding protein accessions from B. coprophila and another sciarid species.
genomic_clusters.csv
Adjacently clustered HTGs. Each of the 199 clusters is assigned a unique numeric identifier in the cluster_number column.
sra_accessions.tsv
Run accessions and sample descriptors for previously published SRA RNA-Seq datasets.
mean_tpms.tsv
Mean transcripts-per-million (TPM) expression values for all B. coprophila genes, pooled across all datasets available through RefSeq.
htgs_mean_tissue_stage_concat_tpms.tsv
Mean TPM expression values for B. coprophila genes, pooled by sex, developmental stage, and tissue type.
salivary_counts.csv, developmental_counts.csv, irradiation_counts.csv, and associated *_meta.csv files
Raw RNA-Seq read counts and metadata used as input for DESeq2 analyses.
deseq2larval.csv, deseq2irradiated.csv, and deseq2salivary.csv
DESeq2 differential-expression results filtered to include only upregulated HTGs.
pairwise_dnds.csv
Pairwise dN/dS values for reciprocal best DIAMOND hits between B. coprophila and B. impatiens.
pairwise_copro_impatiens_dnds
Directory containing protein alignments, codon alignments, and PAML M0 outputs used for pairwise dN/dS estimation between B. coprophila and B. impatiens. Subdirectories are named according to B. coprophila protein accessions.
sciarid_species_tree
Directory containing outputs from the sciarid species-tree analysis, including:
BUSCO_outputs: BUSCO orthology-search outputs for sciarids and relatives.BUSCO_alignment_iqtree: IQ-TREE analyses of the resulting supermatrix.MCMC_runs: two independent MCMC calibration runs. The first MCMC run was selected for the analyses presented in the manuscript.
PROKKA_06122024
Directory containing Prokka-generated protein predictions from the putative B. coprophila endosymbiont genome.
endosymbiont_dmnd.tsv
DIAMOND search results for the putative endosymbiont genome annotation, using HTGs as queries.
bradysia_endosymbiont_blast_top_hits.csv
DIAMOND tabular output from searches of the putative B. coprophila endosymbiont genome for matches to B. coprophila HTGs.
Columns correspond to standard DIAMOND output fields, except for fields beginning with top_NR, which describe the top non-sciarid hits in the NR database. Results are restricted to the highest-bitscore hit per B. coprophila HGT query (qseqid).
GCA_965233685.1_liftoff
Liftoff-generated annotation of the B. coprophila genome assembly GCA_965233685.1.
GCA_965233685.1_liftoff_comparison.tsv
Results of Liftoff annotation transfer for HTGs from the RefSeq genome to the B. coprophila genome assembly GCA_965233685.1. Used as input for Table S3.
collembola_pident_comparison.csv
DIAMOND percent-identity comparisons to the top collembolan hit for each B. coprophila protein accession. Tree_collembola: indicates whether the HTG was confirmed as being of collembolan origin through manual gene-tree inspection. Tree_collembola was compared with type == dipt in the manuscript.
pairwise_folsomia_alignments_intron
Intermediate files and outputs from analyses of intron-position conservation between two-step HTGs and their Folsomia candida homologs. The analysis includes 34 selected genes as well as glyoxylate-shunt and beta-lactam genes. Each directory is named according to its B. coprophila HTG accession.
Files include:
ali_prot.fasta: amino-acid alignment.codon_ali.fasta: codon alignment.alignment_with_exon_boundaries.txt: final alignment in which the final nucleotide position of each exon is denoted by a lowercase letter; asterisks indicate the final position of an exon in either sequence, and caret symbols indicate conserved intron positions inferred from a shared final nucleotide of an exon.
folsomia_conserved_introns.csv
Summary of conserved intron positions between two-step-origin HTGs and their F. candida candida homologs.
pairwise_paramacrobiotus_alignments_intron
Intermediate files and outputs from analyses of intron-position conservation between two-step HTGs and the tardigrade Paramacrobiotus metropolitanus for the beta-lactam gene cluster.
deeploc_results.csv
DeepLoc2 functional predictions for the longest isoform of each B. coprophila protein-coding gene.
Columns include:
Localization: predicted localization label or labels, separated by|when multiple predictions are present.Signals: predicted signal motif or motifs, when detected.- Remaining columns: localization probabilities for each cellular location.
hgt_deeploc_results.csv
DeepLoc2 results filtered to include only HTGs.
localization_enrichment_stats.csv
Fisher's exact-test enrichment statistics comparing DeepLoc2 localization predictions for HTGs and non-HTGs.
hgt_go_terms.csv
Gene Ontology molecular-function and biological-process assignments for each HTG. Multiple GO terms are separated by semicolons. Assignments were derived from RefSeq.
molecular_function_enrichment.tsv and biological_process_enrichment.tsv
Fisher's exact-test enrichment statistics for Gene Ontology terms. padj contains Benjamini-Hochberg-adjusted P values.
predicted_cazymes.csv, confirmed_cazys.csv, and p_hygida_proteome.csv
Carbohydrate-active enzyme (CAZyme) annotations and proteome-expression data for HTGs, derived from Trinca and Monesi et al. (2023), DOI: 10.1016/j.isci.2023.106449.
new_vs_old.tsv
Results of a DIAMOND search in which proteins from the previous B. coprophila annotation (GCF_014529535.1) were used as queries against the new annotation (GCF_014529535.2).
interproscan
Directory containing raw InterProScan outputs for all proteins in the B. coprophila reference annotation, using the longest protein isoform per gene.
interproscan_htgs_counts.tsv
Counts of HTGs assigned to each InterProScan domain.
per_protein_manual_annotation.tsv
Results of manual curation of predicted HTG functions using InterProScan.
carbohydrate_catabolism.tsv
HTGs assigned putative carbohydrate-catabolism functions based on manual curation of InterProScan results and Trinca and Monesi et al. (2023), DOI: 10.1016/j.isci.2023.106449.
biosynthesis.tsv, tryptophan_kynurenine.tsv, and dna_repair.tsv
Tables containing ancestry assignments and functional predictions for dipteran-ancestry genes and HTGs highlighted in the Supplementary Information.
drosophila_experimental_data
Directory containing source data for Drosophila transgenic experiments across five data sheets.
`cyanide_data - time_to_paralysis.csvandcyanide_data - number_of_flies_recovered.csv contain data on the time to 100% fly recovery and the number of flies recovered overnight, respectively, following cyanide-fumigation experiments. Each row represents one biological replicate (Vial`) of a Sex × Genotype combination.
`ArsMeth_ArsenicToxicityExpt.csvandH2O2_stress_tests - cumulative_daily_deaths.csv contain cumulative daily mortality data following dietary supplementation with sodium arsenite and hydrogen peroxide, respectively. Each row represents one biological replicate (Repeat) of a Genotype × Sex × Treatment combination. Day N` columns indicate the cumulative number of dead flies observed N days after initiation of the experiment.
yeast_experimental_data
OD600 yeast-growth data for bna1, bna6, and bna5 complementation assays. Each row represents a time point, and columns correspond to replicates of each growth-condition × genotype combination, as extracted using the yeast_complementation_growth_curves.ipynb script in the accompanying GitHub repository.
The data sheet containing bna1 and bna6 measurements have been blank-corrected. Blank correction for bna5 is performed by the corresponding analysis code.
Code/software
All .txt/.fasta files can be viewed in a text editor, and .tsv or .csv files can be viewed in Google Sheets or Microsoft excel. Newick files for phylogenetic trees and associated iTOL annotation text files for phylogenies can be visualized in iTOL (https://itol.embl.de/). Plotting and data visualization scripts are provided in the accompanying GitHub repository.