Abstract：The transcriptome of mature gonads was constructed and sequenced in long -tailed gold strain of goldfish Carassius auratus by Lllumina RNA sequencing .Through sequencing ,61769892 clean data in‐cluding 6 .18G bp were obtained in the ovary with an average error rate of 0 .03% ,and 69557514 clean data including 6 .96G bp in testis with an average error rate 0 .03% .The terminal GC content for library was 51 .15% in the left ovary and 51 .2% in the right ovary ,and 48 .91% in the left testis and 49 .44% in the right testis .The two libraries represented a total of 170245 transcripts ,with 80591 unigenes .As deter‐mined by the multiple databases ,functional annotation of 51364 unigenes was obtained ,accounting for 63 .73% of the total .All of the unigenes were found to be functional by classification of GO software ,and unigenes involved in cell process ,cell and binding occupied major proportion in the secondary classifica‐tion .There were 17347 SSR markers and 363416 SNP markers throughout the transcriptomic data .The gene expression differences between the two transcriptome revealed that 6317 genes expressed differentially in male and female samples .The findings provided basic data for the gene cloning and screening of the goldfish ,as well laid the foundation for clarifying the molecular mechanism of gonadal differentiation and development .
