Integrated mRNA and Small RNA Sequencing Reveals Regulatory Expression of Larval Metamorphosis of the Razor Clam
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ORIGINAL ARTICLE
Integrated mRNA and Small RNA Sequencing Reveals Regulatory Expression of Larval Metamorphosis of the Razor Clam Donghong Niu 1,2,3 & Beibei Li 1 & Shumei Xie 1 & Zhiguo Dong 3 & Jiale Li 1,3 Received: 31 May 2020 / Accepted: 25 August 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The razor clam, Sinonovacula constricta, is an important economic marine shellfish, and its larval development involves obvious morphological and physiological changes. MicroRNA plays a key role in the physiological changes of the organism through regulating targeted mRNA. This study performed miRNA–mRNA sequencing for eight different developmental stages of S. constricta using Illumina sequencing. A total of 2156 miRNAs were obtained, including 2069 known miRNAs and 87 novel miRNAs. In addition, target genes were predicted for key miRNAs differentially expressed between adjacent development samples by integrating the mRNA transcriptome. Further analysis revealed that the differentially expressed genes were enriched in complement activation, alternative pathways, translation, and negative regulation of monocyte molecular protein-1 production. KEGG pathway annotation showed significant enrichment in the regulation of the ribosome, phagosome, tuberculosis and fluid shear stress, and atherosclerosis. Ten mRNAs and ten miRNAs that are related to larval metamorphosis were identified using real-time PCR. Furthermore, the double luciferase experiment validated the negative regulatory relationship between miR-133 and peroxisome proliferator-activated receptor-γ (PPAR-γ). These results indicated that the target genes regulated by these differentially expressed miRNAs may play an important regulatory role in the metamorphosis development of S. constricta. Keywords Sinonovacula constricta . Developmental transcriptome . Metamorphosis . MicroRNA
Introduction The early larval development of shellfish is a major feature that affects individual survival rate, population number (Vogeler et al. 2019), spatial distribution, and resource supplementation (Rey et al. 2019). Thus, the genetics and the regulatory mechanisms of larval metamorphosis in shellfish Donghong Niu and Beibei Li contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10126-020-09993-0) contains supplementary material, which is available to authorized users. * Jiale Li [email protected] 1
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
2
Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
3
Co-innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
have been extensively investigated. Genetic and environmental factors such as gene expression (Okazaki and Shizuri 2000), genomic variation (Henry et al. 2010), hormonal regulation (Applebaum et al. 2012), nu
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