Daniel Winston Bellott

Supplementary Information for:

Rapid expansion and specialization of the TAS2R bitter taste receptor family in amphibians

Kathleen W Higgins, Akihiro Itoigawa, Yasuka Toda, Daniel W Bellott, Rachel Anderson, Roberto Márquez, Jing-Ke Weng

PLoS genetics 21, e1011533 (2025)

Figures:

S1 Fig: (PDF)

The comparison of intact TAS2R gene counts between this study and recent literature Policarpo et al.

S2 Fig: (PDF)

Correlation between genome size (c-value) and number of TAS2Rs identified in genomes for different taxa.

S3 Fig: (PDF)

Four best-fitting regime shift configurations inferred by l1 ou, accounting for roughly 97% of pBIC weight.

S4 Fig: (PDF)

Comparison of different ways of defining TAS2R clusters.

S5 Fig: (PDF)

Additional features of TAS2R gene loci in genomes.

S6 Fig: (PDF)

Distance of TAS2R gene loci to either end of chromosome separately analyzed by qualities of genome assembly.

S7 Fig: (PDF)

Barplots showing the percent of various regions identified as being repeat elements using RepeatMasker and RepeatModeler.

S8 Fig: (PDF)

Comparison between TAS2R repertoires of closely related species, based on the tree in Fig 2, as described for Fig 3A.

S9 Fig: (PDF)

Proportion of cluster and singleton TAS2Rs that are “copy-number-constrained orthologs” (CNCOs).

S10 Fig: (PDF)

Conserved singleton TAS2R locus from two distantly related fish, the sablefish (Anoplopoma fimbria, left) and the mangrove rivulus (Kryptolebias marmoratus, right).

S11 Fig: (PDF)

Diagram relating the location of TAS2Rs in a phylogenetic tree to their location along the chromosome.

S12 Fig: (PDF)

Number of TAS2Rs detected with FPKM > 0.01 per tissue per animal.

S13 Fig: (PDF)

Percent of expressed receptors that are unique to exactly one tissue, by tissue and by species.

S14 Fig: (PDF)

Heatmap of tissue expression across amphibian tissues with hierarchical clustering applied to the tissue samples.

S15 Fig: (PDF)

Relationships between TAS2R phylogeny (based on the amino acid alignment) and mRNA expression.

S16 Fig: (PDF)

Agonist screenings of eighteen amphibian TAS2Rs. Eighteen amphibian TAS2Rs were assayed using luminescence-based functional assays with 28 substances (see S4 Table).

S17 Fig: (PDF)

Relationships between TAS2R phylogeny (based on the nucleic acid alignment) and mRNA expression.

S18 Fig: (PDF)

Relationships between TAS2R phylogeny (based on the amino acid alignment) and mRNA expression including multi-mapped reads.

S19 Fig: (PDF)

Correlations between the human TAS2R positions and quality scores of genome assemblies.

S20 Fig: (PDF)

Correlations between the zebrafish TAS2R positions and quality scores of genome assemblies.

S21 Fig: (PDF)

Comparisons between TAS2R gene loci and qualities of genome assembly in humans and zebrafish.

S22 Fig: (PDF)

Principal component analysis comparing TAS2R expression levels across tissues.

S23 Fig: (PDF)

Cellular responses of no-receptor control in the functional assay.

Tables:

S1 Table: (PDF)

Percent of genomic regions identified as repeat elements of various kinds in amphibians.

S2 Table: (PDF)

Percent of genomic regions identified as repeat elements of various kinds in nonamphibians.

S3 Table: (PDF)

Orthologous loci (TAS2R clusters and singletons) identified using conserved neighboring BUSCO genes.

S4 Table: (PDF)

Compounds used in functional assay.

S5 Table: (PDF)

The comparison of intact TAS2Rs in an axolotl genome assembly between gene mining methods.

S6 Table: (PDF)

The list of species whose names were replaced by close relatives in our analysis.

S7 Table: (PDF)

Fit parameters for various phylogenetic generalized least squares models, assuming covariance between phylogeny and traits under an OU model.

Data:

S1 Data: (XLS)

The list of TAS2R genes discovered in our pipeline.

S2 Data: (CSV)

Summary data for 661 species analyzed in this study.

S3 Data: (TXT)

Gene tree file underlying Fig 2.

S4 Data: (TXT)

Gene tree file underlying S13 Fig.