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Identification and Characterization of miRNAs and Their Predicted mRNAs in the Larval Development of Pearl Oyster Pinctada fucata

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Abstract

As an important economic shellfish, the pearl oyster, Pinctada fucata, and its larvae are an ideal model for studying molecular mechanisms of larval development in invertebrates. Larval development directly affects the quantity and quality of pearl oysters. MicroRNAs (miRNAs) may play important roles in development, but the effects of miRNA expression on P. fucata early development remain unknown. In this study, miRNA and mRNA transcriptomics of seven different P. fucata developmental stages were analyzed using Illumina RNA sequencing. A total of 329 miRNAs, including 87 known miRNAs and 242 novel miRNAs, and 33,550 unigenes, including 26,333 known genes and 7217 predicted new genes, were identified in these stages. A cluster analysis showed that the difference in the numbers of miRNAs was greatest between fertilized eggs and trochophores. In addition, the integrated mRNA transcriptome was used to predict target genes for differentially expressed miRNAs between adjacent developmental stages, and the target genes were subjected to a gene ontology enrichment analysis. Using the gene ontology annotation, 100 different expressed genes and 95 differentially expressed miRNAs were identified as part of larval development regulation. Real-time PCR was used to identify eight mRNAs and three miRNAs related to larval development. The present findings will be helpful for further clarifying the regulatory mechanisms of miRNA in invertebrate larval development.

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Data Availability

miRNAseq and RNAseq data have been deposited to the sequence read archive (SRA) with accession numbers SRR15315621–SRR15315641 and SRR15310576–SRR15310596, respectively. The datasets used and analyzed during the current study are also available from the corresponding author on reasonable request.

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Funding

This work was supported by the National Key R&D Program of China (2018YFD0901406), the National Natural Science Foundation of China (31873042), the Guangxi Key R&D Program (2018AB52002), the Guangxi Natural Science Foundation Program (2021GXNSFAA075008), the and Guangxi Key Laboratory of Marine Biodiversity Conservation Program (2021ZB02).

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  1. Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People’s Republic of China

    Jian Chen, Ziqin Zhai, Lili Lu, Suping Li, Dan Guo, Lirong Bai & Dahui Yu

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  1. Jian Chen
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  2. Ziqin Zhai
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  3. Lili Lu
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Contributions

Jian Chen and Dahui Yu contributed to the study conception and design. Material preparation, data collection, and analysis were performed by Jian Chen, Ziqin Zhai, Lili Lu, Suping Li, and Lirong Bai. The first draft of the manuscript was written by Jian Chen, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Chen, J., Zhai, Z., Lu, L. et al. Identification and Characterization of miRNAs and Their Predicted mRNAs in the Larval Development of Pearl Oyster Pinctada fucata. Mar Biotechnol 24, 303–319 (2022). https://doi.org/10.1007/s10126-022-10105-3

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