Functional analysis of small RNAs in pearl oyster, Pinctada fucata

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During the doctoral studying in the University of Tokyo, I do research about the small RNA species, expression, and their functional analysis in Pinctada fucata, more specifically on (1) classification, identification, expression and target prediction of miRNAs, and (2) piRNA identification, expression and biogenesis analysis in the somatic and gonad tissues. A total of 228 miRNAs, including 186 known and 42 novel miRNAs, were identified in P. fucata. Furthermore, 105 biomineralization-related genes with complete sequences from Pinctada genus were used for miRNAs target prediction. In piRNA analysis, we firstly found that piRNAs were ubiquitously expressed in somatic and gonad tissues in P. fucata. The expression patterns and characteristics of piRNAs were demonstrated, which reveal a fascinating and unanticipated dimension of P. fucata biology. The key piRNA biogenesis factors in P. fucata, including PIWI, AGO, Zucchini and HEN, were identified using transcriptomic analysis. We also knockdown the highest expressed piRNA0001 by locked-nucleic-acid modified oligonucleotide (LNA) to research its function in P. fucata. The characterization and identification of small RNAs will help to further understand the mechanism of small RNA biogenesis and its function in P. fucata. In summary, during this period I published 6 papers (4 as first authors and 2 as co-authors) in high-indexed journals, and presented the research work at 14th International Symposium on Biomineralization (2017), JSFS (2017, 2018 and 2019), International Symposium on Aquatic Metagenomics.