DOI: 10.5061/dryad.18931zd5c
title: Data from: A molecular mechanism for bright color variation in parrots

description: Parrots produce stunning plumage colors through unique pigments called
 psittacofulvins. However, the mechanism underlying their ability to
 generate a spectrum of vibrant yellows, reds, and greens remains
 enigmatic. Here, we uncover a unifying chemical basis for a wide range of
 parrot plumage colors, which result from the selective deposition of red
 aldehyde- and yellow carboxyl-containing psittacofulvin molecules in
 developing feathers. Through genetic mapping, biochemical assays, and
 single-cell genomics, we identified a critical player in this process, the
 aldehyde dehydrogenase ALDH3A2, which oxidizes aldehyde psittacofulvins
 into carboxyl forms in late-differentiating keratinocytes during feather
 development. The simplicity of the underlying molecular mechanism — in
 which a single enzyme influences the balance of red and yellow pigments —
 offers an explanation for the exceptional evolutionary lability of parrot
 coloration.
description: # Data from: A molecular mechanism for bright color variation in parrots
 [https://doi.org/10.5061/dryad.18931zd5c](https://doi.org/10.5061/dryad.18931zd5c) Here we provide supporting files associated with the genome reference and annotation. ## Description of the data and file structure **We provide the genomic data in the following files:** 1. A fasta file with the dusky lory reference genome (dusky_lori_draft_genome.fa). This genome was produced using Pacific Biosciences (PacBio) HiFi sequencing reads. Contig assembly was carried out with *Hifiasm* and contigs were scaffolded into a pseudochromosome assembly using the homology-based scaffolding algorithm of *RagTag *and the budgerigar *bMelUnd1* genome assembly as reference (GCF_012275295.1). 2. A gff file with the annotation of the dusky lory reference genome (annotation_dusky_lory.gff). Gene annotation was performed using iterative runs of *MAKER *(please see the Supplementary Methods of the publoication for additional details). **We provide the Raman spectroscopy data in the following file:** Raman_spectra_psittacofulvins_from_various_species.xlsx. This excel spreadsheet contains Raman spectra from each region of each measured species in numeric format. Data were batch treated as follows: Cosmic rays were removed, spectra were cropped to remove regiond corresponding to Raleigh scattering, and background was subtracted. **We provide the chemical data in the following files:**  All the datafiles from HPLC/MS analyses are in the Bruker compass native format. The .d file format is the native raw data format of the Bruker acquisition software for LC/MS analyses. To open the files with the .d extension, we recommend using Bruker's DataAnalysis software. To download the software a user must first register at bruker.com (my bruker -&gt;register)[[https://sso.bruker.com/auth/realms/bruker/login-actions/registration?client_id=aem-bruker.com&tab_id=-rTFVcu1eA0](https://sso.bruker.com/auth/realms/bruker/login-actions/registration?client_id=aem-bruker.com&tab_id=-rTFVcu1eA0)]. Following that a section to download mass-spectrometry software unlocks (bruker.com -&gt; services & support -&gt; software support & upgrades -&gt; mass spectrometry [here a user needs to be signed in] -&gt; software solutions -&gt; DataAnalysis) [[https://www.bruker.com/protected/en/services/software-downloads/mass-spectrometry/software-solutions.html](https://www.bruker.com/protected/en/services/software-downloads/mass-spectrometry/software-solutions.html)]. This is the direct link to download the software (user needs to be signed in on bruker.com) [[https://www.bruker.com/protected/en/services/software-downloads/mass-spectrometry/software-solutions/_jcr_content/root/sections/section_795158518/sectionpar/twocolumns_copy/contentpar-2/maintenancewrapper/content/externaldownload_cop_1204623677.external.zip/BDAL/LSMS/DataAnalysis/6.0/6.0.536.33/dataanalysis-sfx-6.0.536.33-ISO.zip](https://www.bruker.com/protected/en/services/software-downloads/mass-spectrometry/software-solutions/_jcr_content/root/sections/section_795158518/sectionpar/twocolumns_copy/contentpar-2/maintenancewrapper/content/externaldownload_cop_1204623677.external.zip/BDAL/LSMS/DataAnalysis/6.0/6.0.536.33/dataanalysis-sfx-6.0.536.33-ISO.zip)]. Even though the software requires a paid license to offer all the functionalities, viewing and exporting in various formats is available in unlicensed versions of the DataAnalysis software. Alternatively, the files can also be opened using the opensource program ProteoWizard ([https://proteowizard.sourceforge.io/](https://proteowizard.sourceforge.io/)). However, the full compatibility using this software is not guaranteed. Species.zip -Psittac2_AM1-r_C30-APCI_FA_Pos_01_RA2_1_5402.d PDA and MS data of psittacofulvins extracted from red feather of Ara macao separated on C30 column with APCI ionisation in positive mode -Psittac2_AM1-y_C30-APCI_FA_Pos_01_RA3_1_5406.d PDA and MS data of psittacofulvins extracted from yellow feather of Ara macao separated on C30 column with APCI ionisation in positive mode -Psittac2_LP-r_C30-APCI_FA_Pos_01_RA5_1_5408.d PDA and MS data of psittacofulvins extracted from red feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode -Psittac2_LP-y_C30-APCI_FA_Pos_01_RA8_1_5412.d PDA and MS data of psittacofulvins extracted from yellow feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode -Psittac3_ARR2-g_C30-APCI_FA_Pos_01_RB3_1_5666.d PDA and MS data of psittacofulvins extracted from green feather of Agapornis rosiecollis separated on C30 column with APCI ionisation in positive mode -Psittac3_ARR2-r_C30-APCI_FA_Pos_01_RC1_1_5676.d PDA and MS data of psittacofulvins extracted from red feather of Agapornis rosiecollis separated on C30 column with APCI ionisation in positive mode -Psittac3_G-p_C30-APCI_FA_Pos_02_RA6_1_5657.d PDA and MS data of psittacofulvins extracted from pink feather of Eolophus reseicapilla separated on C30 column with APCI ionisation in positive mode -Psittac3_MU-g_C30-APCI_FA_Pos_01_RA5_1_5655.d PDA and MS data of psittacofulvins extracted from green feather of Melopsittacus undulatus separated on C30 column with APCI ionisation in positive mode -Psittac3_MU-y_C30-APCI_FA_Pos_01_RA4_1_5654.d PDA and MS data of psittacofulvins extracted from yellow feather of Melopsittacus undulatus separated on C30 column with APCI ionisation in positive mode -Psittac3_NH-r_C30-APCI_FA_Pos_01_RA3_1_5653.d PDA and MS data of psittacofulvins extracted from red feather of Nymphicus hollandicus separated on C30 column with APCI ionisation in positive mode -Psittac3_NH-y_C30-APCI_FA_Pos_01_RA2_1_5652.d PDA and MS data of psittacofulvins extracted from yellow feather of Nymphicus hollandicus separated on C30 column with APCI ionisation in positive mode -Psittac3_PF-r_C30-APCI_FA_Pos_01_RA7_1_5660.d PDA and MS data of psittacofulvins extracted from yellow feather of Psittrichas fulgidus separated on C30 column with APCI ionisation in positive mode -Psittac4_NK-g_C30-APCI_FA_Pos_01_RE5_1_5788.d PDA and MS data of psittacofulvins extracted from green feather of Nestor notabilis separated on C30 column with APCI ionisation in positive mode -Psittac4_NK-gyo_C30-APCI_FA_Pos_01_RE4_1_5787.d PDA and MS data of psittacofulvins extracted from green-yellow-orange feather of Nestor notabilis separated on C30 column with APCI ionisation in positive mode -Psittac4_NK-gyo_PhHex-ESI_FA_Pos_01_RE4_1_5795.d PDA and MS data of psittacofulvins extracted from green-yellow-orange feather of Nestor notabilis separated on Phenyl-hexyl column with ESI ionisation in positive mode -Psittac4_NK-r_C30-APCI_FA_Pos_01_RE2_1_5785.d PDA and MS data of psittacofulvins extracted from red feather of Nestor notabilis separated on C30 column with APCI ionisation in positive mode -Psittac4_NK-y_C30-APCI_FA_Pos_01_RE3_1_5786.d PDA and MS data of psittacofulvins extracted from yellow feather of Nestor notabilis separated on C30 column with APCI ionisation in positive mode Pseudeos fuscata.zip \- Psittac5_LP-y_C30-APCI_FA_Pos_01_RA7_1_6453.d PDA and MS data of psittacofulvins extracted from yellow feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode \- Psittac5_LP-AM002-1-y_C30-APCI_FA_Pos_01_RA5_1_6451.d PDA and MS data of psittacofulvins extracted from yellow feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode \- Psittac5_LP-AM002-2-y_C30-APCI_FA_Pos_01_RA6_1_6452.d PDA and MS data of psittacofulvins extracted from yellow feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode \- Psittac5_LP-VER0076-r_C30-APCI_FA_Pos_01_RA3_1_6449.d PDA and MS data of psittacofulvins extracted from red feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode \- Psittac5_LP-VER1-r_C30-APCI_FA_Pos_01_RA4_1_6450.d PDA and MS data of psittacofulvins extracted from red feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode \- Psittac5_LOR41-r_C30-APCI_FA_Pos_01_RA2_1_6448.d PDA and MS data of psittacofulvins extracted from red feather of Pseudeos fuscata separated on C30 column with APCI ionisation in positive mode MS2 - psittacofulvins.zip \- Psittac2_AM1-r_C30-APCI-MS2_FA_Pos_01_RA2_1_5403.d MS/MS fragmentation data of psittacofulvins extracted from red feather of Ara macao separated on C30 column with APCI ionisation in positive mode \- Psittac2_test_ARA-Y-MS2_Pyr_PFP_FA_Pos_01_RA3_1_5398.d MS/MS fragmentation data of psittacofulvins extracted from yellow feather of Agapornis rosiecollis separated on Pentafluorphenyl column with APCI ionisation in positive mode \- Psittac5_LOR41-r_PhHex-APCI-MS2-al_FA_Pos_01_RA2_1_6444.d MS/MS fragmentation data of aldehyde psittacofulvins extracted from red feather of Pseudeos fuscata separated on Phenyl-hexyl column with APCI ionisation in positive mode \- Psittac5_LOR41-r_PhHex-APCI-MS2-ac_FA_Pos_01_RA2_1_6443.d MS/MS fragmentation data of carboxyl psittacofulvins extracted from red feather of Pseudeos fuscata separated on Phenyl-hexyl column with APCI ionisation in positive mode Yeast.zip \- Psittac6_blank_PhHex-APCI_FA_Pos_01_RA1_1_6549.d PDA and MS data of control blank separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_WE1_PhHex-APCI_FA_Pos_01_RA4_1_6551.d PDA and MS data of WE yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_WP1_PhHex-APCI_FA_Pos_01_RA3_1_6550.d PDA and MS data of WP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_HE1_PhHex-APCI_FA_Pos_01_RA5_1_6552.d PDA and MS data of HE yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_HP1_PhHex-APCI_FA_Pos_01_RA6_1_6553.d PDA and MS data of HP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_HP1_PhHex-APCI-MS2_FA_Pos_01_RA5_1_6560.d MS/MS fragmentation data of HP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_ALE1_PhHex-APCI_FA_Pos_01_RB1_1_6556.d PDA and MS data of ALE yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_ALP1_PhHex-APCI_FA_Pos_01_RB2_1_6557.d PDA and MS data of ALP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_ASE1_PhHex-APCI_FA_Pos_01_RA7_1_6554.d PDA and MS data of ASE yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_ASP1_PhHex-APCI_FA_Pos_01_RA8_1_6555.d PDA and MS data of ASP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_blank_PhHex-APCI_FA_Pos_02_RA1_1_6558.d PDA and MS data of control blank separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_blank_PhHex-ESI_Neg_Pos_01_RA1_1_6565.d PDA and MS data of control blank separated on Phenyl-Hexyl column with ESI ionisation in negative mode \- Psittac6_ALP1_PhHex-ESI_FA_Neg_01_RB2_1_6566.d PDA and MS data of ALP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in negative mode \- Psittac6_ALP1_PhHex-ESI_FA_Pos_01_RB2_1_6564.d PDA and MS data of ALP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in positive mode \- Psittac6_ALP1_PhHex-APCI_FA_Neg_01_RB2_1_6562.d PDA and MS data of ALP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in negative mode -Psittac6_ALP1_PhHex-APCI_FA_Neg_01_RB2_1_6563.d PDA and MS data of ALP yeast extracts separated on Phenyl-Hexyl column with APCI ionisation in negative mode In the above mentioned filenames yeast strains have been abbreviated as follows: WT ← WE WT + PKS ← WP Δhfd1 ← HE Δhfd1 + PKS ← HP Δhfd1 + ALDH3A2 ← ALE Δhfd1 + ALDH3A2 + PKS ← ALP Δhfd1 + ALDH3A2-488aa ← ASE Δhfd1 + ALDH3A2-488aa + PKS ← ASP MS-Peak 2.zip \- Psittac7_HP2-p2a_PHex-ESI-MS2-245_FA_Pos_01_RA3_1_7299.d MS/MS fragmentation data from peak 2a extracted in yeast sample HP separated on Phenyl-Hexyl column with ESI ionisation in positive mode \- Psittac7_HP2-p2b_PHex-ESI-MS2-231_FA_Pos_01_RA4_1_7313.d MS/MS fragmentation data from peak 2b extracted in yeast sample HP separated on Phenyl-Hexyl column with ESI ionisation in positive mode ## Sharing/Access information PacBio reads used for genome assembly, and Iso-seq and RNA-seq data for genome annotationare available in NCBI SRA under BioProject PRJNA986688.