Full-length transcriptome sequencing integrated with RNA-Seq reads identify pigment genes in goldfish (Carassius auratus) (III)

The goldfish (carassius auratus) is a valuable ornamental fish with the most diverse pheotypes, which is originally demoesticated from wild grey cruician carp in China over 1,000 yeas ago. Red color skin is the first trait fixed in goldfish and distinguished from its ancestor. However, the genomic resources about the speices is limited when performing the study, which heavely hampers our understanding of the genetic basis of the diverse phenotypes. To quickly provide a large amount of genomic resources and decipher the possible mechanism underlying diverse color skin in goldfish, We performed a large scale of transcriptome sequencing on 13 tissues and 4 typical color skins through combinng PacBio long-read sequencing and Illumina short-read sequencing. A full-length transcriptome with 137,674 transcripts was generated with mean length and N50 length of 2,956 bp and 4,017 bp, respectively. A total of 108,122 (78.53%) novel isoforms from known genes and 17,622 novel genes were identified compared to the annotation of recently published goldfish reference genome. Moreover, 59,014 alternative splicing events were present in 15,380 genes. A total of 162 differentially expressed genes (DEGs) were identified among the four different color skins, which were mainly involved in the pathways of Melanogenesis, Tyrosine metabolism, Riboflavin metabolism, Folate biosynthesis, and alpha-Linolenic acid metabolism. Fourteen DEGs may have function in pigmentation, including Melanophilin genes, solute carrier family 2 member 11 and solute carrier family 2 member 9. In conclusion, the genomic resources provided in study significantly improved the gene annotation of the published referecne genome and enhanced the understanding of the goldfish pigmentation pathways and will finally facilitate future studies on genetic basis of goldfish diverse phenotypes.