Data and code from: Diversity and spatial segregation of TRP channels in the closest relatives of animals
Data files
Sep 17, 2026 version files 427.52 MB
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AlphaFold_models.zip
3.38 MB
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Bioinformatics.zip
392.48 KB
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Raw_Images_Fig2.zip
423.75 MB
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README.md
11.24 KB
Abstract
The following submission contains raw and supporting data for the manuscript "Diversity and Spatial Segregation of TRP Channels in the Closest Relatives of Animals". Sensory systems, built around specialized cell types, are central to how animals perceive and respond to their environment. However, the evolutionary origin of these systems remains unclear. In this work, we examine transient receptor potential (TRP) channels, important for animal sensation, across choanoflagellates and the other close relatives of animals. We find a rich repertoire present, with large choanoflagellate expansions in two different families. Furthermore, in the choanoflagellate model, Salpingoeca rosetta, we find channels from different families form discrete microdomains within the feeding collar complex. The datasets available here contain sequences and files used in bioinformatic analyses, the parameters, commands, and scripts used, and raw imaging files generated.
Dataset DOI: 10.5061/dryad.d7wm37qh8
Description of the data and file structure
This dataset contains data and code used in the preparation and needed to replicate the results found in 'Diversity and Spatial Segregation of TRP Channels in the Closest Relatives of Animals' by Mannsåker, et. al. This includes all sequences used in the study, alignments, sequence similarity network analyses, and trees generated. The dataset also includes all parameters and commands used in various software and scripts used for identifying and compiling the transmembrane domain regions analyzed. It also contains .cif files for channels modeled with AlphaFold and detailed tables describing annotations of all putative channels analyzed and listing the publicly available sources of the data used. The dataset also contains raw image files (.oir) for all data presented in Figure 2 of the manuscript.
Files and variables
File: Bioinformatics.zip
Description: This file contains multiple files:
'Parameters and Commands used in Bioinformatic Analyses.pdf' is a listing of all parameters and commands used in the analysis. This includes information on PSI-BLAST search used to generate datasets, Hidden Markov Models generated and used, Sequence Similarity Networks, and phylogenetic analysis.
'srTRPA2_peptide_sequence_corrected.fasta' is the corrected peptide sequence for srTRPA2 which was generated by targeted sequencing.
'srTRPA2_TMD_sequenced_cDNA.ab1' is the raw sequencing results for the central regions of srTRPA2.
'Dataset_S4_TRP_model.hmm' is a custom Hidden Markov Model used for searching for the transmembrane domain of TRP channels. Parameters used for construction are described in 'Parameters and Commands used in Bioinformatic Analyses.pdf'.
'S6_Choano_TRP_annotation_V2.xlsx' is a searchable table of all TRP annotations generated and used in the study. One tab contains a table for choanoflagellate channels (Choanoflagellate_TRP_channels) and one tab contains a table for other non-animal holozoan channels (Non-choanozoan_TRP_channels). Descriptions of columns are also available as a Readme tab in the workbook. The columns in order are:
| Column header | Description |
|---|---|
| Sequence name | Names as listed in source files. (Note that "_" has been replaced with "-") |
| Clade | What major holozoan clade the species belong to. |
| Species | Scientific name of species |
| Type | Whether the sequence is derived from a genome, complete transcript, or incomplete transcript |
| SSN cluster | Annotation based on SSN alone |
| Phylogenetic branch | Annotation based on phylogenetic placement in TMD-focused tree |
| Classification | Manual annotation into one of the TRP channel families based on phylogeny and sequence similarity |
| WD40 | 1 if the domain PF00400.38 was detected, 0 if not |
| Ion_trans | 1 if the domain PF00520.37 was detected, 0 if not |
| LSDAT_euk | 1 if the domain PF18139.7 was detected, 0 if not |
| NUDIX | 1 if the domain PF00293.34 was detected, 0 if not |
| Ank | 1 if the domain PF00023.36 was detected, 0 if not |
| Isochorismatase | 1 if the domain PF00857.26 was detected, 0 if not |
| TRPP ECD | 1 if the domain TRPP extracellular domain was detected, 0 if not. A custom HMM was used |
| TM_domains | Number of transmembrane domain predicted by deepTMHMM |
'S6_Choano_TRP_annotation_v2.csv' a plain text file version of the table of TRP annotations for sequences from different choanoflagellate species. Columns are the same as listed above. File is semicolon-delimited.
'S6_Choano_TRP_annotation_v2_Non_Choano.csv' a plain text file version of the table of TRP annotations for sequences from non-choanoflagellate, non-animal holozoan species. Columns are the same as listed above. File is semicolon-delimited.
'Dataset_S7_TRPP_ECD.hmm' is a custom Hidden Markov Model used for searching for the extracellular domain of TRPP channels. Parameters used for construction are described in 'Parameters and Commands used in Bioinformatic Analyses.pdf'
'S9_Sequence_origin_table.xlsx'. and a table containing the publicly available sources for the sequences analyzed. It is organized in the following columns:
| Column header | Description |
|---|---|
| Group | Phylum for the organisms |
| Species | Species within each phylum |
| Type | Whether the data is derived from genomic or transcriptomic sequencing |
| Source | The publication or depository from which raw data is available |
| Name of the File Downloaded | The specific name of the file used |
'S9_Sequence_origin_table.csv' is a plain text file version of the table of sources for sequences used in the study. The columns are the same as listed above. File is semicolon-delimited.
The folder named 'Scripts' contains the Python scripts used to generate and compile the TMD50 sequences (transmembrane domain with 50 flanking amino acids) used in the analysis.
File: Raw_Images_Fig2.zip
Description: This folder contains the raw images used to generate Figure 2. For Figure 2A; 'Fig2_1d_TRPA2.oir', 'Fig2_1d_TRPC.oir', and 'Fig2_1d_TRPV.oir' were used for the 1dpt panels (left), and 'Fig2_5d_TRPA2.oir', 'Fig2_5d_TRPC.oir', and 'Fig2_5d_TRPV.oir' were used for the 5dpt panels (right). For Figure 2B, 'Fig2_TRPA1.oir' is a 5dpt image of a cell expressing only TRPA1 (left panel), and 'Fig2_TRPA2-SG_TRPA1-mCh.oir' is a representative image of a cell co-expressing TRPA2 tagged with StayGold and TRPA1 labeled with mCherry (right panel). Imaging was performed using an Olympus FV3000RS confocal microscope using FLUOVIEW acquisition software (Olympus). Metadata is embedded in the individual files.
File: AlphaFold_models.zip
Description: This folder contains files for the AlphaFold models of tetrameric channels generated for the Salpingoeca rosetta channels, srTRPA1, srTRPA2, srTRPC, srTRPV, and srTRPML. Models were generated from full length sequences from '20260805_All_choano_candidate_TRPs_full_sequences.fasta' and srTRPA2 sequence was corrected based on 'srTRPA2_peptide_sequence_corrected.fasta'.
Supplemental File: Sequence_files_and_ortholog_search.zip
Hosted on Zenodo.
Description: This folder contains files related to the search and annotation of the putative TRP channels in various choanoflagellate and other non-animal holozoan species. It is separated into two folders, one that contains data relevant to the search within choanoflagellates ('Data_choano_ortholog_search') and one that contains data relevant to the search of non-choanoflagellate-non-animal holozoans ('Data_non_choano-ortholog_search'). Detailed descriptions of each file are listed below;
The folder 'Data_choano_ortholog_search' contains all files related to analysis of the choanoflagellate TRP channels;
'20260805_All_choano_candidate_TRPs_full_sequences.fasta' is a FASTA file of all full-length sequences from initial search.
'20260805_All_TRPs_phylogeny_TMD50.fasta' is a FASTA file of the trimmed sequences, containing the transmembrane domain and 50 flanking amino acids.
'20260805_All_TRPs_phylogeny_TMD50_MSA.fasta' is the alignment of the TMD50 trimmed sequences using MAFFT (multiple alignment using fast Fourier transform), following default parameters.
'20260805_All_TRPs_phylogeny_TMD50_MSA.fasta.treefile' is the treefile of the alignment constructed using IQ-tree. The integrated ModelFinder algorithm was used to select substitution model. 1000 bootstrapping replicates.
'20260805_choano_TRP_phylogeny_annotated.pdf' is a high resolution visualization of the tree generated in iTOL.
'20260805_All_choano_SSN_edges.tsv' contains the results of the sequence similarity network analysis (SSN). Full length sequences were used as query in an all-against-all BLAST search. Edges with an E-value less than 10^-20 were selected.
'20260805_Missing_entries_from_SSN_choano.txt' is a .txt file of the missing entries from the SSN.
'All_choano_TRP_channel_full_Sequences_pfam_results.tbl' is a list of all pfam domain predictions used for the annotation of predicted channels. The Pfam-A set of HMMs was used to search for WD40, Ion_transport, LSDAT_euk (SLOG), NUDIX, Ankryn, and Isochorismatase domains in all sequences. The custom HHM (Dataset S7) was used to search for the extracellular domains of TRPP family channels.
The folder 'Data_non_choano-ortholog_search' contains all files related to the analysis of non-choanoflagellate, non-animal holozoan TRP channels;
'20260807_SSN_non-choano_all_sequences.fasta' is a FASTA file of all full-length putative TRP channels from non-choanoflagellate, non-animal holozoans following initial search.
'20260807_Non-choano_candidate_TRPs_and_all_TMD50.fasta'is a FASTA file of the trimmed sequences, containing the transmembrane domain and 50 flanking amino acids.
'20260807_Non-choano_candidate_TRPs_and_all_MSA.fasta' contains the alignment of the TMD50 trimmed sequences using MAFFT (multiple alignment using fast Fourier transform), following default parameters.
'20260807_Non-choano_candidate_TRPs_and_all_MSA.fasta.treefile' is the treefile of the alignment constructed using IQ-tree. The integrated ModelFinder algorithm was used to select substitution model. 1000 bootstrapping replicates.
'20260805_non-choano_TRP_phylogeny_annotated.pdf' is a high resolution visualization of the tree generated in iTOL.
'20260807_SSN_non-choano_edges.tsv' Full length sequences were used as query in an all-against-all BLAST search. Edges with an E-value less than 10^-20 were selected.
'20260807_missing_from_SSN_non-choano.txt' is a .txt file of the missing entries from the SSN.
Access information
Sources for all publicly accessible data are listed in file 'S9_Sequence_origin_table.xlsx'.