Mol. Nature 490, 49–54 (2012). Notch signaling pathway was identified in WS vs BS, which had been reported to regulate shell pigmentation in both C. gigas17 and Meretrix meretrix42. Request a miranda free trial license. It is good software, robust, but sometimes is rather "optimistic". 53 out of 144 miRNAs are abundant in four libraries, and 14 out of 144 miRNAs are rarely expressed (Supplementary Table S2). Biotechnol. Mar. https://doi.org/10.1038/s41598-020-77181-0, DOI: https://doi.org/10.1038/s41598-020-77181-0, Frontiers in Genetics Shells in NS family show pigmentation strip, while the shells in other three families represent solid pigmentation distribution16. ADS The abundance of all the miRNAs was normalized and calculated by TPM method. Article The nominal significant results were validated in an independent sample (cohort B, 72 vs 75) by real-time quantitative polymerase chain reaction (PCR). Mapped small RNA tags were used to look for known miRNA from miRBase 21.0 (ftp://mirbase.org/pub/mirbase/). PLoS ONE 5, e15224 (2010). PubMed PLoS ONE 10, e0145257 (2015). „Miranda IM“ vereint alle gängigen Kurznachrichtendienste („Instant Messenger“) unter einem Dach; hierzu zählen etwa ICQ, MSN, Yahoo, Google Talk oder AIM. 21, 634–642 (2019). Identification of conserved and novel microRNAs in the Pacific Oyster Crassostrea gigas by deep sequencing. Bioinformatics 21, 3787–3793 (2005). While the solid pigmentation represented one color in a shell, which could be black, white or yellow. And lgi-miR-317 was reported to express at the body pigmentation stage in silkworm larvae44. Approximately 38 miRNA families were represented in each library (Supplementary Table S2). Article The total rRNA proportion was only 1.7% (996,313/56,576,919), indicating high quality of the sample. So four miRNAs were suggested to involve in shell pigmentation. Williams, S. T. Molluscan shell colour. Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A. goseq: Gene Ontology testing for RNA-seq datasets. Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. CAS Article For example, the small RNA libraries analysis of pigmented and non-pigmented skin suggests a functional relevance of miRNA in the modulation of pigmentation processes in alpaca11, goat12 and fish10,13. The y-axis represents the numbers of small RNA identified in each library, the x-axis represents the length of small RNA. The Tyrosinase-like protein 3 (LOC105324831) and Tyrosinase-like protein 2 (LOC105344040), reported as the key enzyme to regulate melanin synthesis, were negatively regulated by lgi-miR-96b and lgi-miR-315, respectively. Emerging evidence indicated that miRNAs may have important roles in pigmentation. PubMed Hierarchical clustering of differentially expressed miRNAs among four shell colors variants of Crassostrea gigas. Predicting the target gene of miRNA was performed by miRanda30. Article CAS All of the measurements were made in triplicate. MiRNA with lower expression level is in blue and higher expression in red. Cell Sci. The results of Gene Ontology enrichment analysis on the up and down regulated circRNAs with identified target genes were shown in Fig. Langmead, B. 17, 364–374 (2015). Rep. 8, 1436. https://doi.org/10.1038/s41598-018-19950-6 (2018). volume 10, Article number: 20238 (2020) Biggar, K. K., Kornfeld, S. F., Maistrovski, Y. Article J. Investig. J. Mol. Stat. Feng, D. D., Li, Q. Methods 9, 357–359 (2012). There was larger number of DE miRNAs when NS was compared with other three samples (WS, BS, GS). In all four libraries, miRNAs with TPM ≥ 1000 were classified as abundant while those with TPM < 1 were classified as rare. 2, 919–929 (2001). Julia, S. R., Paulina, G. M. & Wlodzimierz, J. K. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer. Friedlander, M. R., Mackowiak, S. D., Li, N., Chen, W. & Rajewsky, N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. However, the miRNAs profiles in mantle of four shell color variants have not been characterized, and their association with shell pigmentation remains to be discovered. Sci. You are using a browser version with limited support for CSS. Ann. Both miR-34 and miR-124 have been detected to influence migration of retinal pigment epithelium40,41. To make every unique small RNA mapped to only one annotation, we summarized all alignments and annotations following the priority rule: known miRNA > rRNA > snRNA > snoRNA > repeat > gene > novel miRNA. PLoS ONE 9, e104371 (2014). The miRanda software was initially designed to predict miRNA target genes in D. melanogaster (Enright 2003, John 2004). The function enrichment analysis further confirmed the miRNAs played a role in shell pigmentation. With the discovery of RNA interference (RNAi) and related phenomena, … The complete dataset of raw data was deposited into NCBI`s Sequence Read Archive under the accession number PRJNA628161. CAS Genome Biol. The screened miRNAs were further verified by luciferase assay, viral protein expression assay and virus replication assay. Guo, B. Y., Zhang, Q., Wang, H. Y., Chang, P. & Tao, K. KCNQ1OT1 promotes melanoma growth and metastasis. Ophthalmol. A total 91 novel miRNAs were identified, most of them represented rare expression, which suggested they are hard to be identified. 16, 54–62 (2014). This algorithm consists of three basic phases: (1) identification of a sequence that may be bound to miRNA; (2) calculation of the free energy for predicted miRNA–mRNA duplexes; and (3) detection of evolutionary conservation among D. melanogaster, D. … The prepared libraries were sequenced on an Illumina Hiseq 2500 platform at Novogene (Tianjing, China) and 50 bp single-end reads were generated. Lorsque la simulation est lancée, l'évolution du programme est directement affichée sur le programme Scratch facilitant ainsi la mise au point. Esteller, M. Non-coding RNAs in human disease. Rev. Biotechnol. Chen, X. J., Bai, Z. Y. Auf diese Weise können sie ihre Kontakte plattformübergreifend verwalten und mit ihnen kommunzieren. All miRNA families only had 1 to 2 members, of which three families have two members, mir-1994 (lgi-mir-1994a, lgi-mir-1994b), mir-216 (lgi-mir-216a, lgi-mir-216b), mir-10 (lgi-mir-10, lgi-mir-100). Interactive editors are directly integrated into the application. At first, the 47 DE miRNAs was input to miRanda software to predict the target genes, which resulted in 77,721 miRNA-target pairs. A total of 114 miRNAs were identified to be with > 1 TPM in each library. Before prediction, the lncRNAs were filtered based the homology. CAS A total of 870 DE genes were identified as the target gene, and there were 322, 304, 313, 126, 127 and 124 DE genes identified as putative target from WS vs NS, GS vs NS, BS vs NS, BS vs WS, GS vs WS and BS vs GS comparisons, respectively (Supplementary Table S3). Genome Biol. The identification and characteristics of immune-related MicroRNAs in haemocytes of oyster Crassostrea gigas. Author : Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, Huiyan Sun, Garry Wong Software Plugins für Miranda IM. ADS Miranda NG is a successor of a popular multi-protocol instant messaging client for Windows - Miranda IM. Xu, F. et al. Liu, S. P. et al. Based on KEGG pathway analysis, theses targeted genes mainly involved in the ECM-receptor interaction and Notch signaling pathway, which have been reported in mantle transcriptome analysis. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. 133, 201–209 (2013). Mar. By using miRanda software, circRNA-miRNA predictive interaction network was built based on the prediction and analysis of miRNA binding sites and the correlations between circRNA and miRNA that were ranked as previously described . Values are shown as mean ± SD (n = 3), *, P < 0.05, **, P < 0.01. Methods: In this study, we established a broad-spectrum anti-IAV miRNA screening method using miRanda software. At present, the studies on molecular mechanism related to the pigmentation processes have mainly focused on mRNAs, little information is available on the roles of miRNAs in shell pigmentation15. The miRNA-mRNA networks for transcription and phosphorylation were analyzed. Wir bieten dir die Software, die du suchst - schnell & sicher! Identification of Wolbachia -responsive microRNAs in the two-spotted spider mite, Tetranychus urticae. Z., Cai, T., Olyarchuk, J. G. & Wei, L. P. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Google Scholar. & Li, J. L. The mantle exosome and microRNAs of Hyriopsis cumingii involved in nacre color formation. Furthermore, a total of four miRNAs and their target mRNAs were predicted to involve in synthesis of melanin, carotenoid or tetrapyrrole. Nat. Cite this article. Salmena, L., Poliseno, L., Tay, Y., Kats, L. & Pandolfi, P. P. A ceRNA hypothesis: The rosetta stone of a hidden RNA language?. PubMed Central 5). Gene ontology distribution of the target genes for all differentially expressed miRNAs among four shell colors variants of Crassostrea gigas. This comprehensive database of miRNAs could provide a valuable resource for studying function of miRNAs in mantle of C. gigas, as well as contributes to better understanding the molecular mechanism of shell pigmentation. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. R Bioconductor, 8, 1–25 (2012). BMC Bioinform. Reliable and abundant sRNAs database in mantle of C. gigas was produced for downstream miRNA analysis by high-throughput sequencing. High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response. Six previously reported pigmentation related genes in oyster were predicted to be targets by 37 miRNAs (Supplementary Table S5). The large proportion of a eukaryotic genome is transcribed to produce a huge array of RNA molecules differing in protein-coding capability, size, and abundance1. Left mantle was dissected and immediately stored by liquid nitrogen for RNA extraction. D.F. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. PubMed The KEGG enrichment pathways of target genes of differentially expressed micrRNAs in WS vs BS comparison. 1, the majority of the sRNAs sequenced were 21–23 nt in length, and the most frequent length of sRNA was 22 nt. Article PLoS ONE 9, e88397 (2014). Ultimately, 59 highly correlated miRNA-mRNA pairs were formed. Scientific Reports PubMed Central STEM robots simulation : download miranda, read manual A total number of 30, 27, 26, 6, 8 and 9 DE miRNAs were respectively detected from the comparison of WS vs NS, GS vs NS, BS vs NS, BS vs WS, GS vs WS and BS vs GS. Rev. PubMed Central This study was supported by Grants from National Natural Science Foundation of China (31972789 and 31772843), Shandong Province (2017LZGC009), and the Ocean University of China-Auburn University Joint Research Center for Aquaculture and Environmental Science. Storey, J. D. The positive false discovery rate: A Bayesian interpretation and the q-value. Author : Yunji Xiu, Guangpeng Jiang, Shun Zhou, Jing Diao, Hongjun Liu, Baofeng Su, Chao Li The total sRNA tags were mapped to the oyster genome databases by Bowtie23 without mismatch to analyze their expression and distribution on the reference. Sci. Nat. In mollusca, the fabulous and diverse shell colors are generally believed to be determined by presence of biological pigments of melanin, carotenoid and tetrapyrrole14. 5, R1 (2003). & Storey, K. B. MicroRNA regulation in extreme environments: differential expression of microRNAs in the intertidal snail Littorina littorea during extended periods of freezing and anoxia. Gaiti, F. et al. Zhao, X. L., Yu, H., Kong, L. F., Liu, S. K. & Li, Q. https://doi.org/10.1038/s41598-018-19950-6, http://creativecommons.org/licenses/by/4.0/, https://doi.org/10.1038/s41598-020-77181-0, Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. The functional role of such DE miRNAs is the focus of future investigation. J. Inheritance of shell pigmentation in Pacific oyster Crassostrea gigas. CAS The lncRNA database sequenced from the same four families was used to predict miRNAs targets by miRanda30. PubMed Google Scholar. Article DE miRNAs represent differential expression pattern in NS sample (Fig. Jong, H. J. Bartel, D. P. MicroRNAs: Genomics, biogenesis, mechanism, and function. did the experiment, analyzed the data and drafted the manuscript. Article MathSciNet In the interacting network, lgi-miR-317 seemed to play a central role and down-regulated the expression level of peroxidase (LOC105324712) in WS vs NS comparison. All clean reads were mapped to RepeatMasker, Rfam database to remove reads originating from protein-coding genes, repeat sequences, rRNA, small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA). Through successive family selection and breeding, four shell color strains of C. gigas (white, WS; golden, GS; black, BS and partially pigmented, NS) have been developed to improve the commercial values. Biotechnol. GO analysis revealed that the primary function of these miRNAs was to regulate transcription and phosphorylation. 11, 1–12 (2010). By aligning the sRNAs to all known animal miRNA precursors, 2360 (14,718,092 total reads) unique sequences were identified as potentially conserved miRNA in oyster mantle. ADS Both ECM-receptor interaction and Notch signaling pathway were significantly enriched in WS vs NS comparison (Fig. CAS Genes Dev. By integrating miRNA and mRNA expression profiles, a total of 870 genes were predicted as targets of differentially expressed miRNAs, mainly involving in biomineralization and pigmentation through functional enrichment. In mouse melanocytes, miR-193 has been detected to downregulate after stimulating the product, processing, and transport of melanosomes39. Reverse transcription of miRNA was carried out using the cDNA Synthesis Kit (TaKaRa, China). A total of 47 miRNAs exhibited differential expression patterns from six pair-wise comparisons. The authors declare no competing interests. Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China, Dandan Feng, Qi Li, Hong Yu, Shikai Liu & Lingfeng Kong, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China, Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, USA, You can also search for this author in MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). Miranda NG 0.95.13 Deutsch: Miranda NG ist ein kostenloser Multi-Messenger für Facebook, Skype, ICQ und Co. Enright, A. J. et al. BMC Genomics 13, 555–555 (2012). Miranda software is one of the great classics in miRNA target prediction. METHODS: miRNA sequencing was performed using the peripheral blood of patients with MDD and matched controls (cohort A, 10 vs 10). Sci Rep 10, 20238 (2020). Cell 136, 629–641 (2009). Google Scholar. PubMed Central 13, 140–140 (2012). (b) The lncRNA–miRNA–mRNA interaction network in NS vs WS comparison. miRanda software for microRNA target prediction (not including conservation analysis) siRNAs can function as miRNAs. Figure 1 depicts the flowchart in the present study. For target prediction, miRanda software 44 has been integrated. 92, 1039–1058 (2017). Feng, D. D., Li, Q., Yu, H., Zhao, X. L. & Kong, L. F. Comparative transcriptome analysis of the Pacific Oyster Crassostrea gigas characterized by shell colors: Identification of genetic bases potentially involved in pigmentation. The length distribution of sRNAs was represented in Fig. Biotechnol. These DE-miRNAs and their targets might further be used as molecular markers to screen for shell color variant of oyster. Most of these identified miRNA families in C. gigas are also conserved in other molluscan species, such as Pinctada martensii37, Littorina littorea38, Haliotis discus hannai34 and Pinctada fucata33. The pigmentation strip is generally black or a mixture of black and other colors. CAS Beliebteste Plugins. A total of 15 DE miRNAs are shared by WS vs NS, GS vs NS and BS vs NS comparisons, including ten conserved miRNA of lgi-miR-96b, lgi-miR-745b, lgi-miR-34, lgi-miR-317, lgi-miR-315, lgi-miR-2c, lgi-miR-281-3p, lgi-miR-193, lgi-miR-153 and lgi-miR-124. The novel miRNAs were predicted using software miREvo25 and mirdeep226. The results of qRT-PCR analysis showed that the expression patterns of these miRNAs were consistent with the deep sequencing results (Fig. Search for your favorite gene/miRNA and view their targets. 1), which is characteristic of sRNAs from metazoans11,35. 5a). The miR-153 was reported to act as a ceRNA with the lncRNA KCNQ1OTQ to depress the expression of receptor tyrosine kinase to inhibit melanogenesis45. Vis. Wienholds, E. et al. PubMed There were 12 out of 17 downregulated circRNAs had target microRNAs. Sci. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. 2003 17(4): 438- 442 Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. Using qRT-PCR, the expression level of lgi-miRNA-317, peroxidase (LOC_105324712, XM_011423866) and its potential cis-acting lincRNA (TCONS_00951105) was studied, lgi-miRNA-317 showed opposite expression with XM_011423866 and TCONS_00951105 in WS vs NS comparison18. 2), which is consistent with the pronounced phenotypic difference between NS and any of other three. And four DE miRNAs (lgi-miR-315, lgi-miR-96b, lgi-miR-317 and lgi-miR-153) were closely associated with shell pigmentation. The miRNA of PTM < 1000 and transcripts of RPKM < 10 was filtered. The Gene ontology (GO) distribution of the predicted targets is shown (Fig. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Zhou, Z. et al. PubMed Very light on system resources and extremely fast. After alignment and additional sequence analysis, a total of 144 candidate miRNAs from mantle libraries were identified, including 53 known miRNAs and 91 novel miRNAs (Supplementary Table S2). (2021). H.Y., S.L., L.K. ADS Gene 666, 32–43 (2018). Nature 433, 769–773 (2005). Z. Transcriptome analysis of shell color-related genes in the Clam Meretrix meretrix. The total RNA was extracted from mantle of each individual using Trizol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. By integrating with DE mRNAs assemblies and lncRNAs profiles from same four shell color oyster families, the target mRNAs and lncRNAs of DE miRNAs were identified and the ceRNA networks were constructed. Then, clean reads of 18–35 bp length were chosen to do all the downstream analyses. Q.L. 31, 2013–2035 (2003). 32, 2367–2382 (2015). The whole expression of DE miRNAs was shown in the Hierarchical clustering heatmap (Fig. When the simulation is launched, the progress of the program is directly displayed on the Scratch program … Then we selected the miRNA-target pairs, when a miRNA and its target gene were negatively correlated.