Transcriptome Analysis Of Skin And Scale Of Different Colors Of Cyprinus Carpio Var.Koi

Cyprinus carpio var.Koi is one of the artificially bred varieties of carp(Cyprinus carpio)and is a valuable ornamental fish.Its body color is based on white,accompanied by red patches.Erythrophores(predominantly red)and iridopphores(predominantly white)were distributed on the skin and scales of the body surface,which determine the body color of red and white.In order to investigate the genetic mechanism of red body color and white body color in koi carp,we collected two colors of skin of red and white koi and two kinds of scales.We performed comparative transcriptomics study using RNA-seq method.According to the differential gene analysis between skin and scales,the numbers of expressed genes in skin and scales was 30,005 and 30,384 respectively.The overall gene expression levels of skin and scale were significantly different.The global expression level of the scale is higher than the skin.A total of 4,042 and 3,787 genes were found to be up-regulated in the skin and scales,respectively.The GO enrichment showed that the up-regulated genes in the scales were significantly enriched in biological processes related to immune and the development of scales.The up-regulated genes in the skin are significantly enriched in the biological processes associated with the morphogenesis of the skin and appendages and immune regulation,and these enriched biological processes are compatible with the specific functions of the skin.We performed GO enrichment analysis of the total differentially expressed genes between red scale and white scale.The 223 up-regulated genes in red scale were significantly enriched in neural cell differentiation,and retinoic acid metabolism,pigment cell regulation,and sex determination were related.Neuronal cell differentiation,retinoic acid metabolism and regulation of pigment cells,these results provide strong support for the theory that pigment cells originate from nerve sheath cells.In many sex dimorphic fish,there are obvious differences in the body color of the two sexes,and the male body color is generally brighter.The question how these sex-determining genes control body color remains to be further explored.The 195up-regulated genes in white scales were significantly enriched in biological processes related to growth regulation,cell migration,and muscle cell function.These results suggest that red pigment cells and iridescent cells may have different migratory abilities.Combine the results of the differential genetic analysis of the Koi red skin and white skin before with the results of the differential genetic analysis of the Koi red scale and white scale,the consistent GO Term showed that the consistent biological process in two different tissues of the same color was “lipid storage”and “regulation of lipid catabolic process”.This may be because carotenoids are lipid-soluble pigments,and the storage and metabolism of fat facilitate the absorption and metabolism of carotenoids.In the enrichment of up-regulated genes in white skin and up-regulated genes in white scales,the most abundant biological process is striated muscle development,suggesting that the chromophore crystals in iridescent cells may have strong activity.Compared with the differential genes of red and white,red and white scales,22 genes with the same pattern of expression in the skin and scales were screened,including the genes related to retinoic acid metabolism(cyp2ae1,box1 and opsin5)and transport proteins(Slc2a11b,bscl2 and tmem130),and nerve cell-specific expression genes(syt11b and nell2b).Beta-carotene oxygenase(box1)is a key enzyme that converts ?-?-carotene to retinal molecules,and box1 genes are specifically expressed in red skin and red scales.Opsin5 is a member of the opsin gene family.By combining retinal with rhodopsin,opsin5 is a photoreceptor molecule in both visual and non-visual animals.A Pacbio full-length transcriptome analysis software,ISO-Analysis,was developed.ISO-Analysis analyzes Pacbio Iso-sequencing reads to identify full-length transcripts,align transcripts to genomes,cluster transcripts and identify alternative splicing isoforms.Cpared with the widely used full-length transcript analysis software SMRT-link,ISO-Analysis can obtain more full-length transcripts,and align more transcripts to genomes.We applied this software to analyze the Iso-sequencing reads of common carp and identified the full-length sequences of ten candidate color-related genes.