Abstract
Piwi-interacting RNAs (piRNAs) belong to a recently discovered class of small non-coding RNAs whose best-understood function is repressing transposable element activity. Most piRNA studies have been conducted on model organisms and little is known about piRNA expression and function in mollusks. We performed high-throughput sequencing of small RNAs extracted from the mantle, adductor muscle, gill, and ovary tissues of the pearl oyster, Pinctada fucata. RNA species with sequences of approximately 30 nt were widely expressed in all tissues. Uridine at the 5′ terminal and protection from β-elimination at the 3′ terminal suggested that these were putative piRNAs. A total of 18.0 million putative piRNAs were assigned to 2.8 million unique piRNAs, and 35,848 piRNA clusters were identified. Mapping to the reference genome showed that 25% of the unique piRNAs mapped to multiple tandem loci on the scaffold. Expression patterns of the piRNA clusters were similar within the somatic tissues, but differed significantly between the somatic and gonadal tissues. These findings suggest that in pearl oysters piRNAs have important and novel functions beyond those in the germ line.
Highlights
To date, hundreds of pearl formation related genes have been identified[8,9,10,11,12], but knowledge regarding small RNA function in the pearl oyster is limited
22.6 million reads were mapped to the pearl oyster reference genome (Step 3)
The results showed no difference in the expression patterns of Piwi-interacting RNAs (piRNAs) clusters among the somatic tissues
Summary
Sequencing of putative piRNAs from somatic and gonadal tissues of pearl oysters. Eight small-. We examined the expression patterns of small RNAs in the mantle (Ma), adductor muscle (Ad), gill (Gi), and ovary (Go) tissues of pearl oysters. Mapping of the putative piRNAs to the reference genome of the pearl oyster revealed that they were encoded in multiple loci, with tandem patterns on the genome Their expression patterns were notably different in somatic and gonadal tissues. These results provide useful information for further research on piRNA in pearl oysters, and on the functions and molecular regulatory mechanisms of small RNAs in mollusks. Putative piRNAs partially generated from repeats shared characteristic features with piRNAs identified in other organisms, and were strongly expressed in somatic and gonadal tissues, with different expression patterns. Further studies are needed to determine whether piRNAs play a critical role in epigenetic silencing through DNA/chromatin methylation, similar to their germline homologs in mollusks[48]
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