Genome-Wide Comparative Analyses of Pigmentation Genes in Four Fish Species Provides Insights on Fish Skin Color Patterning
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Lei Jia, Na Zhao, Xiaoxu He, Kangkang Peng, Kefeng Liu, Bo Zhang
Although it is well known that vertebrates universally use the chromatophore to control their body color patterns, the difference of chromatophore types within vertebrates were observed: mammals have one single chromatophore type while fish could possess six types of chromatophores. To better understand the molecular mechanisms underlying the chromatophore diversity in fish, the genomic resources and data of four fish species, Cynoglossus semilaevis, Danio rerio(zebrafish), Oreochromis niloticus and Paralichthys olivaceus, including whole-genome sequence, annotation, and transcription data, were exploited. A total of 61 pigmentation-related genes were identified in all studied species and classified into six groups including the Mcr gene family group, which plays the most important role in melanocortin system. The numbers of each pigmentation-related gene family members are similar across all four species, except Mc3r gene is only found in zebrafish genome. Comparative analysis of pigmentation-related genes structures and phylogenetic analysis provide a clear orthologous relationship for all Mcr genes. For Danio rerio and Cynoglossus semilaevis, using the skin samples from different developmental stages, the transcriptome analyses revealeda diverse expression pattern across all pigmentation-related genes and Dbh and Hbxd3a genes highly co-expressed with multiple pigmentation-related genes. The STRING analysis of pigmentation-related proteins in zebrafish demonstrates that five proteins, corticotrophin releasing hormone, oxytocin-like protein, opioid receptor (delta), prepronociceptin α and β have strong interactions with pigmentation-related proteins. This work provides a better understanding of compositions of pigmentation-related genes in four fish species and provides insights on the far-reaching genetic mechanism of chromatophore-controlled pigmentation.
Pigmentation Genes, Genome-Wide, Fish, Color Patterning