Materials for rattlesnake chemoreceptor gene expression
Data files
May 12, 2025 version files 12.90 MB
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README.md
4.35 KB
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supp02_Deseq2_results.xlsx
8.15 MB
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supp03_combined_trees_aligned.txt
3.73 MB
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supp04_selection_stats.xlsx
1.02 MB
Abstract
Predatory species who hunt for their prey rely on a suite of integrated characters, including sensory traits which are also used for non-predatory behaviors. Linking the evolution of sensory traits to specific selection pressures therefore requires a deep understanding of the underlying genetics and molecular mechanisms producing these complex phenotypes. However, this relationship remains poorly understood for complex sensory systems that consist of proteins encoded by large gene families. The chemosensory repertoire of rattlesnakes includes hundreds of type-2 vomeronasal receptors (V2Rs) and olfactory receptors (ORs), representing the two largest gene families found in the genome. To investigate the biological importance of this chemoreceptor diversity, we assessed gene expression in the eastern diamondback rattlesnake (Crotalus adamanteus) and identified sex- and age-biased genes. We found V2R expression in the vomeronasal epithelium was limited to juvenile snakes, suggesting the sensory programming of this tissue may be correlated with early life development. In the olfactory epithelium, we found subtle expression biases which were more indicative of life history rather than development. We also found transcriptional evidence for dosage compensation of sex-linked genes and trait integration in the expression of transcription factors (TFs). We overlay our molecular characterizations in C. adamanteus onto updated OR and V2R phylogenies, providing a genetic road map for future research on these receptors. Finally, we investigated the deeper macroevolutionary context of the most highly expressed V2R gene spanning the rise of tetrapods and estimated the strength of positive selection for individual amino acid residues in the predicted protein structure. We hypothesize that this gene may have evolved as a conserved signaling subunit to ensure consistent G-protein coupled receptor (GPCR) functionality, potentially relaxing signaling constraints on other V2R paralogs and promoting ligand binding specificity.
https://doi.org/10.5061/dryad.cfxpnvxhm
Description of the data and file structure
Supplemental information to accompany Hogan et al., 2025 "Life history and chromosome organization determine chemoreceptor gene expression in rattlesnakes". Article published in the Journal of Heredity.
Files and variables
File: supp04_selection_stats.xlsx
Description: Statistical tests and results for interpreting gene sequences. Tab labels and contents: "TM domain info" = trans-membrane alignment positions for C. adamanteus OR and V2R gene alignment and for the multi-species conserved V2R alignment; "FEL raw" = HyPhy FEL selection test results for C. adamanteus ORs followed by V2Rs; "FEL Extra vs Intra vs TM" = proportional z-test results comparing protein domain distribution of selected sites detected by FEL for C. adamanteus ORs followed by V2Rs; "MEME raw" = HyPhy MEME selection test results for C. adamanteus ORs followed by V2Rs; "MEME Extra vs Intra vs TM" = proportional z-test results comparing protein domain distribution of selected sites detected by MEME for C. adamanteus ORs followed by V2Rs; "all EBF>100" = lists of Estimated Bayes Factor scores > 100 reported from MEME for C. adamanteus ORs, V2Rs, and for the multi-species analysis on a conserved V2R; "Chrm ancestral recon" = percent breakdowns of chromosome ancestral gene tree reconstructions calculated for C. adamanteus ORs and V2Rs; "Chrm vs selection" = data (left) and stats results (right) using another z-test to compare the chromosomal distribution of significantly selected sites detected using MEME for C. adamanteus ORs followed by V2Rs below;
Variables
- Significant z-test results in this spreadsheet will be shown with red text in a yellow cell
- Cell colors = colors were added to cells in this spreadsheet to facilitate reading and to distinguish tests performed on ORs and tests performed on V2Rs. We designated green to OR data, and blue to V2R data. For the slides reporting proportional tests, we color coded extracellular tests with light red, and intracellular tests with light blue.
- NA = represents amino acid sites which had no known protein domain or function.
- nuc = nucleotiode
- AA = amino acid
- Extracellular = outside of cell
- Intracellular = cytoplasmic region inside of cell
- TM = trans membrane
- alpha = value used to represent non-synonymonous mutations
- beta = value used to represent synonymonous mutations
- LRT = Log ratio test result
- q - and q + = selection test parameter generated by MEME
- EBF = estimated Bayes factor
- LogL = result of the log L test performed by HyPhy
- Interaction site = an amino acid or codon position which has the specific proteomic functionality
File: supp03_combined_trees_aligned.txt
Description: Three consecutive Nexus alignments, ordered *C. adamanteus *ORs first, *C. adamanteus * V2Rs second, and multi-species conserved V2R alignment third.
File: supp02_Deseq2_results.xlsx
Description: Results from our differential gene expression tests using Deseq2 in R. Tab labels and contents: "Olfactory AGE" = Full Deseq2 results of C. adamanteus olfactory epithelium RNA aligned to whole genome comparing juvenile and adult rattlesnakes; "Olfactory SEX" = Full Deseq2 results of C. adamanteus olfactory epithelium RNA aligned to whole genome comparing male and female rattlesnakes; "Vomeronasal AGE" = Full Deseq2 results of C. adamanteus vomeronasal epithelium RNA aligned to whole genome comparing juvenile and adult rattlesnakes; "Vomeronasal SEX" = Full Deseq2
Variables
- Gene_cds_id = column containing the gene ID reported in the genome.
- baseMean = the mean expression value used by Deseq2 to calculate differential expression.
- log2FoldChange = the main differential expression result, reported as positive or negative by Deseq2 based on direction of bias.
- lfcSE = standard error reported by Deseq2
- stat = test statistic value used internally by Deseq2 for calculating differential expression.
- pvalue = p value reported by Deseq2 prior to adjusting for over dispersion.
- padj = adjusted p value reported by Deseq2, which we utilized for statistical cutoffs in our analyses.