Comparing coding regions of melanin production pathway between
colour morphs
A total of 15 coding regions of genes known to be involved in the
melanin production pathway were compared between genomes (Table S2).
Coding sequences were extracted with blasr (Chaisson & Tesler,
2012) and seqtk (Li, 2012) from grey morph assembly and utilized
as a reference to identify similar regions on the brown morph genome.
Sequences were inspected for start and stop codons to ensure
completeness as well as for synonymous and non-synonymous mutations
after alignment with MUSCLE (Edgar, 2004). We then utilized
NCBI’s blast to collect similar sequences (>95%
similarity) to phylogenetically contextualize any observed variation
between morphs. Phylogenetic analyses were performed in MEGA11 (Tamura,
Stecher, & Kumar, 2021) with a Maximum Likelihood approach. We
estimated nucleotide substitution model, which was then inserted as a
parameter in the ML tree construction. The bootstrap consensus was
inferred with 10000 replicates, and trees to initiate the algorithm were
obtained aby applying Neighbor-Join and BioNJ algorithms, utilizing all
sites, prior to selecting the topology with superior log likelihood
value and with complete deletion. Lastly, we estimated Nei’ s
evolutionary distances between and within putative copies.