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Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation

Citation

Twomey, Evan; Johnson, James; Castroviejo-Fisher, Santiago; Van Bocxlaer, Ines (2020), Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation, Dryad, Dataset, https://doi.org/10.5061/dryad.wpzgmsbj2

Abstract

The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog Ranitomeya sirensis is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.

Methods

See manuscript for details on data collection methods.

Usage Notes

Supplementary tables.zip -- Supplementary tables S1-S7
deseq2_results_skin.csv -- Full DEseq2 results for skin tissue
deseq2_results_liver.csv -- Full DEseq2 results for liver tissue
CYP_full_alignment.fasta -- Protein alignment underlying Figure S7
cyp3A_alignment.fasta -- Protein alignment underlying Figure 4
liver_annotation.gtf -- Annotation track for liver transcriptome assembly
liver_assembly.fasta -- Liver transcriptome assembly
reflectance.csv -- Spectral reflectance data underlying Figure 1A
sirensis_CYP_amino_acid.fasta -- CYPs found in Ranitomeya sirensis, aa sequence
sirensis_CYP_mRNA.fasta -- CYPs found in Ranitomeya sirensis, mRNA sequence
sirensis_carotenoid_concentrations.csv - Carotenoid concentration data underlying Figures 1C, S2, and S3
skin_annotation.gtf -- Annotation track for skin transcriptome assembly
skin_assembly.fasta -- Skin transcriptome assembly

Funding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Award: 88881.067967/2014-01

Fonds Wetenschappelijk Onderzoek, Award: G0D6618N

Vrije Universiteit Brussel, Award: Strategic Research Programme - SRP30