Haplotype-specific expression of the sepiapterin reductase (SPR) gene based on RNA-seq data from throat skin collected from outside of the main color patch for a Uta stansburiana: Yellow throat-color morph (all-yellow throat phenotype)
The focal tissue was throat skin just outside of the main colored region, which was typically white in color, but which sometimes had a very faint amount of the color found in the main color patch. RNA was extracted using a New England Biolabs Monarch Total RNA Miniprep kit.  Libraries were prepared with a KAPA (Roche) stranded mRNA-Seq Kit with unique dual indexes.  The sequence data was cleaned with HTStream and mapped with STAR to the Uta stansburiana orange-morph genome that was modified as follows.  The sequence for the SPR coding sequence, untranslated regions (UTRs), and the divergent region upstream of the SPR gene were deleted from the orange-morph reference genome.  Then an orange (O) and blue (B) haplotype were added as separate contigs, each of which included the divergent upstream region, the 5' UTR, and most of the first exon of the SPR gene.The bam file includes the data for the O and B-haplotypes that were added in as separate contigs.  The expression of the SPR gene was compared between the O and B-haplotypes in a region including the 5' UTR, and most of the first exon of the SPR gene.  For this individual, the O and B-haplotypes were not the haplotypes of this individual lizard, but the B-haplotype sequence came from the blue-morph reference genome and the O-haplotype sequence came from the orange-morph reference genome. The expression of the SPR gene was quantified in the region from 10302-11002 bp in the blue haplotype and from 7306-8006 bp in the orange haplotype.