Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis

Abstract

Chondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117 C. crispus miRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes in C. crispus by constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.

Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169

“…The largest miRNA family was miR166, which had 11 members, while a majority (79.45%) of detected families had only one member (Figure 2). Similarity and conservation were observed among the miRNAs identified here in C-169 and the reported miRNAs families in microalgae Chondrus crispus [30], Porphyridium purpureum [32] and Eucheuma denticulatum [31]. At least nine miRNA families, including 157, 164, 166, 167, 168, 397, 408, 482, 535, existed in all four algae mentioned here (Figure 2) and in Botryococcus braunii [28].…”

“…According to the published data in other microalgae, miRNA target genes in Eucheuma denticulatum were highlighted to enrich in the porphyrin and chlorophyll metabolic pathway [31]. Peroxisome proliferator-activated receptor (PPAR) signaling pathways enriched in miRNA target genes were reported in Chondrus crispus [30], while phagocytosis and proteasome were emphasized as the most significant enriched pathway for conserved and novel miRNAs respectively in Porphyridium purpureum [32]. Lipid metabolism has not been mentioned in miRNA targets enriched pathways in microalgae other than C-169.…”

“…Compared with the large amount of miRNAs reported in various plants and animals [10,11,21,22], only limited reports of miRNAs were available in algae. To date, comprehensive miRNA profiles mainly revealed by high throughput sequencing were reported in diatom Phaeodactylum tricornutum [23], four green algae Chlamydomonas reinhardtii [24,25], Volvox carteri [26,27], Botryococcus braunii [28], Dunaliella salina [29] and four red algae Chondrus crispus [30], Eucheuma denticulatum [31], Porphyridium purpureum [32], Porphyridium cruentum [33], as well as two brown algae Ectocarpus siliculosus [34] and Saccharina japonica [35]. Recent studies in Chlamydomonas reinhardti indicated that induced expression of endogenous microRNA (miRNA1166.1) could enhance H 2 production [36], while artificial miRNAs were manipulated successfully to improve the production of H 2 and fatty acids [28,37,38].…”

realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)

“…However, little is known about its function and evolutionary trajectory in red algae. We incorporated four miRNA datasets that have been experimentally validated from Porphyridium purpureum ( 30 ) (Porphyridiophyaceae), C. crispus ( 31 ) (Florideophyaceae), Eucheuma denticulatum ( 32 ) (Florideophyaceae), P. yezoensis ( 33 ) (Bangiophyaceae) into realDB. Users can easily discover a miRNA and related information through our search system.…”

Identification of novel biomarkers correlated with prostate cancer progression by an integrated bioinformatic analysis

“…Recently, high throughput sequencing technology and multi-dimensional bioinformatics analysis have made tremendous progress, which may put a deep insight for disease occurrence in the molecular level. [ 30 , 31 ] WGCNA, a systems genetics approach that mainly tries to investigate the correlation between gene clusters and phenotypes, which could identify the physiologically relevant gene clusters for many diseases. [ 13 ] It constructs a gene co-expression network and provides a global interpretation of gene expression pattern for diseases.…”