Red and yellow parrot feathers

https://www.science.org/content/article/why-are-parrots-so-colorful-study-points-simple-chemical-tweak
There is a link to the research article in this news piece, but it may not be open access.  It is a pretty amazing molecular genetic analysis coming out of an ecology and evolution group of researchers.  They utilized genomic sequence, long read RNA Seq, single cell RNA Seq, and regulatory sequences involved in gene expression in feather cells.
They identified the causative gene for turning red feathers yellow, and the possible causative mutation that is segregating in one species that is responsible for the recessive red feather expression.  The difference in expression levels for the gene are not that great, but there is a larger difference in single cell types.  The enzyme is expressed in all cells, but has higher expression in the yellow feathers.  This increase in expression is enough to convert enough red pigment to yellow to make yellow feathers.
The only issue that I see in this paper is that they may not have the causative mutation.  They mapped the causative gene because there were 3 SNP (single nucleotide polymorphisms) found to be significant.  They mapped to possibly a small region of the genome flanking the ALDH3A2 gene, but two of the SNPs were on one contig and 1 SNP was on another containing the gene.  This means that there are issues with not having continuous sequence in this region.  It could be repetitive sequence or issues with genome assembly.  What they needed to do was long read genomic sequencing of the region to obtain the continuous sequence in order to determine if they were dealing with something like a retroviral insertion or some other assembly issue.  The causative mutation may exist in the missing sequence between the two contigs.
In my own experience we have the recessive white allele at the C locus in chickens.  This mutation turns out to be due to a retroviral insertion in an intron of the Tyrosinase gene that causes differential splicing in epidermal cells, but normal splicing in other tissues.  When you assemble a genome out of short reads using a reference genome if the reference genome (in our case it was Red Junglefowl that did not have recessive white) you get two contigs cleanly separated from each other with the retroviral insertion sequence missing.  These researchers may be having issues with something similar.
Ron Okimoto
Ron Okimoto