Research ArticleEVOLUTIONARY BIOLOGY

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

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Science Advances  31 Jul 2019:
Vol. 5, no. 7, eaax0396
DOI: 10.1126/sciadv.aax0396
  • Fig. 1 Conservation of WOM expression signatures across mammals.

    (A) RNA-seq was performed on six species, representing three mammalian lineages: Carnivora, Rodentia, and Primates. Species color scheme used is kept consistent across all figures and is as follows: light green, dog; orange, mouse; brown, rat; dark gray, marmoset; light blue, macaque; fuchsia, human. Ma, million years; Hsap, H. sapiens; Mmul, M. mulatta; Cjac, C. jacchus; Rnor, R. norvegicus; Mmus, M. musculus; Cfam, C. familiaris. (B) PCA of the expression levels for the 9725 “one-to-one” orthologs. Percentages of the variance explained by the PCs are indicated in parentheses. PC1 separates rodents from primates, PC2 separates Old World from New World primates and hominins, and PC3 separates dog from the other five species. (C) Heatmap of the expression levels of the canonical markers of the main cell populations present in the WOM samples. RNA expression levels are represented on a log10 scale of normalized counts (NC) plus one (0, not expressed; 5, highly expressed). There is conservation of expression among all species. mOSNs, mature OSNs; iOSNs, immature OSNs; GBCs, globose basal cells; HBCs, horizontal basal cells; SUSs, sustentacular cells. No CHL1 ortholog was annotated in the rat genome version analyzed (black squares).

  • Fig. 2 Gene expression profiles of nasal chemosensory receptors in mammals.

    (A and B) Unrooted phylogenetic tree and mean expression levels for all TAAR (A) and MS4A (B) receptor orthologs in the six species. Bars indicate the mean contribution (%) of each receptor to the total gene expression within each family and per species. Red branches indicate pseudo and truncated OR genes. Black branches indicate intact OR genes. (C) Heatmap of the expression pattern for markers of Gucy2D+ (GC-D+) and Gucy1b2+ OSNs in mammals. RNA expression levels are represented on a log10 (x + 1) scale of normalized counts (0, not expressed; 4, highly expressed). Black squares indicate, for a given species, genes where no orthologs were found annotated in the genome version analyzed. TRPC2 is a pseudogene in human and macaque, and GUCY1B2 is a pseudogene in human. (D to I) Distribution of mean expression values for each of the OR genes in the WOM of dog (D), mouse (E), rat (F), marmoset (G), macaque (H), and human (I). Genes are displayed in descending order of their mean expression values [log10 (x + 1) normalized counts]. Error bars represent the SEM from three to four individuals. Insets: circular plots show the percentages of intact and pseudo plus truncated ORs expressed (≥ 1 normalized counts) or not expressed (< 1 normalized counts) in at least one individual. Under the x axis, the total number of ORs within each species and the position of the last OR plotted (arrow) are noted.

  • Fig. 3 Abundance for all OR-expressing OSN subtypes across mammalian evolution.

    Unrooted phylogenetic trees containing the mean expression levels for all OR genes from the orders Rodentia and Primates separately and for all six species. Bars indicate the mean contribution (%) of each receptor to the total gene expression within each receptor family and per species. Red branches indicate pseudo and truncated OR genes. Black branches indicate intact OR genes.

  • Fig. 4 Ligand biases for highly conserved OR-expressing OSN subtypes across mammalian evolution.

    (A) Heatmap of the expression pattern for the ORs populating the highly conserved 73 OGGs across all species. Two clusters were identified (arrows): cluster 1 containing highly abundant ORs across all species and cluster 2 containing highly abundant ORs only in one or a subset of species. Normalized percentage values of expression are represented on a relative abundance scale (−2, lowly abundant; +2, highly abundant). OGGs containing human and/or mouse deorphaned ORs are indicated by orange and fuchsia circles, respectively. Mouse ORs activated by SMCs and human ORs activated by KFOs are indicated by cyan or dark green circles, respectively. Class I and class II ORs are indicated by the OGG1- and OGG2- prefixes, respectively. (B) Odorants recognized by the deorphaned mouse (left column and within orange rectangles) and human (right column and within fuchsia rectangles) ORs. In some, but not all cases, ligands for the same OR have similar structures. In one of three OGGs (OGG2-288) containing both deorphaned mouse and human ORs, the ligands are different in structure and perceived odors. (C) Percentage of odorants, according to their chemical class, activating mouse and/or human ORs.

  • Fig. 5 Sensory profile and detection of ecologically relevant odorants by highly abundant ORs/OSN subtypes in mouse and humans.

    (A) The sensory profiles (spider plot) of the odorants detected exclusively by either mouse or human ORs above the 90th percentile of expression (Venn diagram) are vastly overlapping and significantly positively correlated (rs = 0.6019, P = 0.0227). (B) PCA of the 696 physicochemical descriptors of odorants detected exclusively by either mouse or human ORs above the 90th percentile of expression [see bottom left in (A)]. Percentages of the variance explained by the PCs are indicated in parentheses. The mouse- and human-specific odorants greatly overlap in the odor space. (C and D) Distribution of mean normalized counts represented on a log10 (x + 1) scale expression values for each of the OR genes in the human (C) and mouse (D) WOM. OR genes detecting at least one human KFO or a mouse SMC are indicated according to their expression percentile (fuchsia/orange, above the 90th percentile; black, below the 90th percentile). Known OR-ligand pairs playing a role in olfactory perception, hedonics, or behavior are indicated below the x axis. Error bars represent SEM from three sample replicates. Binomial test using Wilson-Brown method to calculate the confidence interval, two-tail. (E and F) The mean expression levels of ORs detecting human KFOs are 2.4 times higher in humans (E) but not in mouse (F). Unpaired t test with Welch’s correction, two-tail, ***P ≤ 0.001; ns, not significant (P ≥ 0.05). (G and H) The mean expression levels of ORs detecting mouse SMCs are 2.7 times higher in mouse (G) but not in humans (H). Unpaired t test with Welch’s correction, two-tail, ***P ≤ 0.01; ns, P ≥ 0.05.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/7/eaax0396/DC1

    Fig. S1. Conservation of the WOM expression signatures across mammals.

    Fig. S2. OR gene expression in mammals.

    Fig. S3. Abundance and ligand biases for highly conserved canonical/OR-expressing OSN subtypes across mammalian evolution.

    Fig. S4. The muscone human OR, OR5AN1, is also weakly activated by the KFO β-ionone.

    Fig. S5. Distribution of mouse and human OR genes that detect exclusively other odorants.

    Data file S1. Sample information, accession numbers, RNA-seq quality metrics, and gene expression estimates.

    Data file S2. Differential expression analysis for all pairwise comparisons between the 9785 dog, mouse, rat, marmoset, macaque, and human.

    Data file S3. Expression estimates for the OR repertoires of dog, mouse, rat, marmoset, macaque, and human.

    Data file S4. Composition of the highly conserved 73 OGGs across mammals.

    Data file S5. Expression estimates of the most and least abundant ORs or OSN subtypes.

  • Supplementary Materials

    The PDF file includes:

    • Fig. S1. Conservation of the WOM expression signatures across mammals.
    • Fig. S2. OR gene expression in mammals.
    • Fig. S3. Abundance and ligand biases for highly conserved canonical/OR-expressing OSN subtypes across mammalian evolution.
    • Fig. S4. The muscone human OR, OR5AN1, is also weakly activated by the KFO β-ionone.
    • Fig. S5. Distribution of mouse and human OR genes that detect exclusively other odorants.
    • Legends for data files S1 to S5

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    Other Supplementary Material for this manuscript includes the following:

    • Data file S1 (Microsoft Excel format). Sample information, accession numbers, RNA-seq quality metrics, and gene expression estimates.
    • Data file S2 (Microsoft Excel format). Differential expression analysis for all pairwise comparisons between the 9785 dog, mouse, rat, marmoset, macaque, and human.
    • Data file S3 (Microsoft Excel format). Expression estimates for the OR repertoires of dog, mouse, rat, marmoset, macaque, and human.
    • Data file S4 (Microsoft Excel format). Composition of the highly conserved 73 OGGs across mammals.
    • Data file S5 (Microsoft Excel format). Expression estimates of the most and least abundant ORs or OSN subtypes.

    Files in this Data Supplement:

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