Identification and comparative analysis of piRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus)

It has been shown that piRNA is the largest class of small non-coding RNA in germline cells of animals which plays key roles in transposons regulation and transcriptional activities. In the present study, piRNAs from two small RNA libraries including ovary and testis of Nile tilapia were identified and characterized. By length and k-mer based small RNA prediction algorithm, 279,059 and 583,230 small RNA reads were confirmed as piRNA from ovary and testis, respectively. The identified piRNAs showed evolutionarily conserved characterization, such as uridine bias in the 5′ ends. The 142,961 and 296,775 piRNAs from ovary and testis were mapped to the draft assembly of the tilapia genome, respectively. Both ovary and testis piRNAs were enriched from linkage (LG)6 and LG7. Meanwhile, the even distribution of +strand and −strand suggested the Ping–pong pathway (a double-displacement reaction of +strand and −strand) hypothesis. These piRNAs were derived from the upstream −2 kb and downstream +2 kb as well as gene regions which suggested a regulatory function on transcription activities. In gene regions, abundant piRNAs were derived from 5′UTR, 3′UTR and CDS. Furthermore, we characterized the differentially expressed piRNAs between ovary and testis. In total, 1979 and 2453 piRNAs were significantly higher and lower expressed in ovary compared to that in testis, respectively. Thereinto, the most concentrated up-regulate and down-regulate piRNAs were both from serine/threonine–protein kinase PIM genes of different transcripts. These findings will be helpful to facilitate studies on the piRNAs regulation on genes during gonad development of teleosts.