Transcriptome profiling between Carassius auratus red var. and Autotetraploid Carassius auratus

Three biological replicates were used for Carassius auratus red var. and Autotetraploid Carassius auratus (4nRR, 4n = 200, RRRR) skin transcriptome analysis, and they were sourced from the same individuals previously analyzed for carotenoid composition. The concentration and quality of extracted total skin RNA were judged by NanoDrop-2000 spectrophotometer and agarose (1.0%) gel electrophoresis. The cDNA was synthesized from the high-quality RNA of each biological replicate. Six paired-end libraries (three for RCC and three for 4nRR) were constructed using a TruSeqTM RNA library prep kit (Illumina, San Diego, CA, USA). Subsequent steps involved end-repair, 3-end adenylation, adapter ligation, and enrichment. The clean data were assessed using the FastQC v0.11.9 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then aligned to the 4nRR reference sequence (unpublished) using the STAR software. The quantified and normalized transcription levels of genes were achieved by the Stringtie software and the Deseq2 R package (version 1.26.0). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) were implemented using the clusterProfiler R package (version 3.14.0).