Skin colouration in many aquaculture species is an important trait, particularly where rare colour phenotypes have high economic value. The wild-type skin phenotype of barramundi (Lates calcarifer) is typically silver and slightly darker dorsally. However, golden (xanthic) variants are very rarely but occasionally oserved. These golden variants are of interest to not only the aquarium trade, but also to aquaculture as golden barramundi exhibit lower levels of “greyness” in their flesh – a characteristic that often is a negative consumer attribute. The genetic basis of the golden variant is unknown. To understand the possible genetic and molecular mechanisms underlying this phenotype, we analyzed the transcriptomic differences between the golden and wild type colour variants.
RNA was extracted from the dorsal fin of 5 wild type (WT) and 5 golden (G) barramundi. Pair-end sequencing was undertaken on an Illumina NovaSeq S4 Lane, 300 cycles, yielding 150 bp reads. The average raw reads for the WT were 115,181,698 and 104,918,905 for the G samples. Raw reads were analyzed, cleaned, and mapped to the L. calcarifer genome. DEseq analysis revealed 2,409 Differentially Expressed Genes (DEG) between colour variants, with 58.57% of DEG being upregulated and 41.39% being downregulated (Figure 1A).
Gene Ontology (GO) analysis revealed that the circadian cycle, tyrosine metabolism, xanthophore associated genes and melanogenesis were within the top pathways that differed between WT and G. Additionally, analysis of normalized counts of selected genes was conducted, alongside the protein-protein interaction network between DEG. From this, a direct link between melanogenesis, the circadian cycle, and xanthophore associated genes was established, with genes known to be involved in melanogenesis and to produce proteins present in melanocyte melanosomes, playing a critical role in linking those processes. Thus it appears that these genes are implicated in the colouration of the golden variant.