Project description:Eucheuma denticulatum or commonly known as "Spinosum", is an economically important red alga that naturally grows on coral reefs with moderately strong currents in tropical and sub-tropical areas. This species is the primary source of iota-carrageenan which has high demands in the food, pharmaceutical and manufacturing industries, and as such it has been widely cultivated. The increasing global demand for carrageenan has led to extensive commercial cultivation of carrageenophytes mainly in the tropics. The carrageenophyte seaweeds including E. denticulatum are indigenous to Sabah, Malaysia. To enrich the information on the genes involved in carrageenan biosynthesis, RNA sequencing has been performed and transcriptomic dataset has been generated using Illumina HiSeq™ 2000 sequencer. The raw data and transcriptomic data have been deposited in NCBI database with the accession number PRJNA477734. These data will provide valuable resources for functional genomics annotation and investigation of mechanisms underlying the regulations of genes in this algal species.
Project description:Eucheuma denticulatum, an economically and industrially important red alga, is a valuable marine resource. Although microRNAs (miRNAs) play an essential role in gene post-transcriptional regulation, no research has been conducted to identify and characterize miRNAs in E. denticulatum. In this study, we identified 134 miRNAs (133 conserved miRNAs and one novel miRNA) from 2,997,135 small-RNA reads by high-throughput sequencing combined with bioinformatics analysis. BLAST searching against miRBase uncovered 126 potential miRNA families. A conservation and diversity analysis of predicted miRNA families in different plant species was performed by comparative alignment and homology searching. A total of 4 and 13 randomly selected miRNAs were respectively validated by northern blotting and stem-loop reverse transcription PCR, thereby demonstrating the reliability of the miRNA sequencing data. Altogether, 871 potential target genes were predicted using psRobot and TargetFinder. Target genes classification and enrichment were conducted based on Gene Ontology analysis. The functions of target gene products and associated metabolic pathways were predicted by Kyoto Encyclopedia of Genes and Genomes pathway analysis. A Cytoscape network was constructed to explore the interrelationships of miRNAs, miRNA-target genes and target genes. A large number of miRNAs with diverse target genes will play important roles for further understanding some essential biological processes in E. denticulatum. The uncovered information can serve as an important reference for the protection and utilization of this unique red alga in the future.
Project description:Ultraviolet B (UV-B) light, as a physical elicitor, can promote the secondary metabolites biosynthesis in plants. We investigated effects of different energy levels of UV-B radiation on growth and bioactive compounds of Crepidiastrum denticulatum. Three-week-old seedlings were grown in a plant factory for 5 weeks. Plants were subjected to different levels of UV-B (0, 0.1, 0.25, 0.5, 1.0, and 1.25 W m-2), 6 h a day for 6 days. All UV-B treatments had no negative effect on the shoot dry weight; however, relatively high energy treatments (1.0 and 1.25 W m-2) inhibited the shoot fresh weight. UV-B light of 0.1, 0.25, and 0.5 W m-2 did not affect total chlorophyll and H2O2 contents; however, they increased total carotenoid content. On 4 days, 0.25 W m-2 treatment increased antioxidant capacity, total hydroxycinnamic acids (HCAs) content, and several sesquiterpenes. Treatments with 1.0 and 1.25 W m-2 increased total carotenoid, total HCAs, and H2O2 contents, and destroyed chlorophyll pigments, reducing maximum quantum yield of photosystem II and causing visible damage to leaves. Partial least squares discrimination analysis (PLS-DA) showed that secondary metabolites were distinguishably changed according to energy levels of UV-B. The potential of 0.25 W m-2 UV-B for the efficient production of bioactive compounds without growth inhibition in C. denticulatum was identified.