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MiRNA-mRNA Integration Analysis Reveals the Regulatory Roles of MiRNAs in Shell Pigmentation of the Manila clam (Ruditapes philippinarum)

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Abstract

The shell color of the Manila clam (Ruditapes philippinarum) is an economically important trait. We used high-throughput sequencing and transcriptome analysis to study the molecular mechanisms that underlie shell color formation and regulation in this species. We constructed small RNA libraries from mantle tissues from four shell color strains of Manila clam, subjected them to high-throughput sequencing. Notably, the results suggested that a number of pigment-associated genes including Mitf, HERC2, were negatively regulated by nvi-miR-2a, tgu-miR-133-3p, respectively. They might be involved in melanin formation via the activation of the melanogenesis pathway. And aae-miR-71-5p and dme-miR-7-5p linked to shell formation-related genes such as Calmodulin and IMSP3 were considered to participate in the calcium signaling pathway. We then used quantitative PCR to verify the candidate miRNAs and target genes in different shell color groups. Our results indicated that miR-7, miR-71, and miR-133 may regulate target mRNAs to participate in shell color pigmentation. These results provide the foundation to further characterize miRNA effects on the regulation of shell color and have significant implications for the breeding of new varieties of clams.

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Availability of Data and Materials

All the sequencing reads were deposited in the NCBI Short Read Archive database (http://www.ncbi.nlm.nih.gov/sra/) and are retrievable under the accession numbers SAMN19340242, SAMN19340243, SAMN19340244, SAMN19340245, SAMN19340246, SAMN19340247, SAMN19340248, SAMN19340249, SAMN19340250, SAMN19340251, SAMN19340252, and SAMN19340253. The R. philippinarum assembly was deposited with the accession number SUB9727219 under PRJNA732722. The transcriptome sequence data for the R. philippinarum genome were deposited in the NCBI Sequence Read Archive under the accession numbers SUB5380483.

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Acknowledgements

This work was supported by the Chinese Ministry of Science and Technology through the National Key Research and Development Program of China (2018YFD0901400, 2019YFD0900704) and supported by China Agriculture Research System of MOF and MARA. The Project is sponsored by “Liaoning BaiQianWan Talents Program” and Intercollegiate jointtraining program of colleges and universities in Liaoning Province. The work was supported by the Outstanding Chinese and Foreign Youth Exchange Program of China Association for Science and Technology (CAST), 2019.

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  1. Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China

    Qiaoyue Xu, Hongtao Nie, Zhihui Yin, Yanming Zhang, Zhongming Huo & Xiwu Yan

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  1. Qiaoyue Xu
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Xu, Q., Nie, H., Yin, Z. et al. MiRNA-mRNA Integration Analysis Reveals the Regulatory Roles of MiRNAs in Shell Pigmentation of the Manila clam (Ruditapes philippinarum). Mar Biotechnol 23, 976–993 (2021). https://doi.org/10.1007/s10126-021-10080-1

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