Identification And Characteristic Analysis Of MicroRNAs In Four Red Algae

MicroRNAs (miRNAs) are endogenous, small non-coding RNAs of about 21 nt in length that having typical precursor secontary stem-loop structures. They block the post-transcriptional expression of target gene by cleavage degradation or translational inhibition of targeted mRNA. Researches demonstrate that miRNA play an important role in regulating the growth and development, metabolism, cell differentiation and apoptosis, stress response and so on, which is the hotspot in life sciences currently. As a class of earlier evolutionary red algae with simple biological structure, large and diverse groups, they not only have economic and industrial value, but some also a variety of biological functions, such as medicine, health care and so on. Tens of thousands of miRNAs have been reported in animals and plants, but the related studies on the lower plants are rarely reported, much less their functions. Amount of miRNAs have been identified and analyzed by high-through sequencing combined with bioinformatics in four red algae (Chondrus crispus, Eucheuma denticulatum Porphyridium purpureum and Galdieria sulphuraria) in this paper, which will be essential for enriching algae miRNA data, supplying a gap of study on miRNAs in the four red algae, and conducting a further research on some unique function of them.The main results and their significances are as follows:1. A total of 645 miRNAs with 562 conserved miRNAs and 83 novel miRNAs from 596 families have been identified by next generation deep sequencing techonlogy and bioinformatics in four red algae.2. Characterization of these miRNAs has been analyzed by statistical softwares and bioinformatics in four red algae. The main miRNAs investigations consist of their quantity, length, base bias, secondary structure, family conservation, targets regulation and so on. The identifying data are creditable primarily based on the results above.3. Part of miRNAs has been validated by northern blot and stem-loop qRT-PCR. The validation results indicate further that the miRNAs identified in the four red algae should be credible.4. Tens of thousands of target genes and targets have been predicted based on psRobot and TargetFinder, and cleavage are the major inhibition type between miRNAs and their targets based on psRNATarget in four red algae. These results will establish foundation for some unqiue miRNAs express and further research on their regulation mechanisms.5. Variety of target genes predicted in four red algae have diverse functions based on Gene Ontology. Majority of them could be classified into biological processes, molecular functions and cellular components, which also reflect the functional diversity of miRNAs in four red algae. Some potentially enriched, specially, functional candidated target genes in red algae will be the key factors to reveal some imporatant character and function in the future.6. PPAR signaling pathway, porphyrin and chlorophyll metabolism, FcyR-mediated phagocytosis and RNA transport are the significant enrichment of the metabolic pathways for the four red algae by KEGG pathway analysis with relevant target genes involved in. The study will lay a foundation for researching the metabolic pathways and showing their roles in the red algae life activities.7. miRNA-target genes interaction networks based on Cytoscape software, and miRNAs comparative analysis among the four red algae based on statistic calculation will be future perspectives for further study from overall and individual aspects. Moreover, the evolutionary research on miRNA gene family will be the new direction for algae in the future.