Abstract
Micro-ribonucleic acids (miRNAs) are a large group of endogenous, tiny, non-coding RNAs consisting of 19–25 nucleotides that regulate gene expression at either the transcriptional or post-transcriptional level by mediating gene silencing in eukaryotes. They are considered to be important regulators that affect growth, development, and response to various stresses in plants. Alexandrium catenella is an important marine toxic phytoplankton species that can cause harmful algal blooms (HABs). To date, identification and function analysis of miRNAs in A. catenella remain largely unexamined. In this study, high-throughput sequencing was performed on A. catenella to identify and quantitatively profile the repertoire of small RNAs from two different growth phases. A total of 38,092,056 and 32,969,156 raw reads were obtained from the two small RNA libraries, respectively. In total, 88 mature miRNAs belonging to 32 miRNA families were identified. Significant differences were found in the member number, expression level of various families, and expression abundance of each member within a family. A total of 15 potentially novel miRNAs were identified. Comparative profiling showed that 12 known miRNAs exhibited differential expression between the lag phase and the logarithmic phase. Real-time quantitative RT-PCR (qPCR) was performed to confirm the expression of two differentially expressed miRNAs that were one up-regulated novel miRNA (aca-miR-3p-456915), and one down-regulated conserved miRNA (tae-miR159a). The expression trend of the qPCR assay was generally consistent with the deep sequencing result. Target predictions of the 12 differentially expressed miRNAs resulted in 1813target genes. Gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) annotations revealed that some miRNAs were associated with growth and developmental processes of the alga. These results provide insights into the roles that miRNAs play in the growth of A. catenella, and they provide the basis for further studies of the molecular mechanisms that underlie bloom growth in red tides species.
Highlights
As a class of biflagellated unicellular microorganisms, the free-swimming dinoflagellates play an important role in the primary production of the marine ecosystem[1]
Previous studies of A. catenella focused on transcriptome sequencing and analysis[11], proteomic analysis[12], characterization of genes related to proliferating cells[13], and gene expression in the decline phase of harmful algal blooms (HABs)[14] and the effect of different environmental conditions[15], which aimed to elucidate the molecular mechanisms responsible for blooming
To identify micro-ribonucleic acids (miRNAs) involved in the growth of the A. catenella, Illumina deep sequencing technology was used on two small RNA libraries that were constructed from two different developmental life stages, namely the lag phase(cultured for 2d) and the logarithmic phase
Summary
As a class of biflagellated unicellular microorganisms, the free-swimming dinoflagellates play an important role in the primary production of the marine ecosystem[1]. Many dinoflagellate species can produce toxins[5], and they account for 75% of all harmful algal bloom species(HABs).Blooms of toxic dinoflagellates have detrimental effects on the fishing industry, marine environments, and public health[6,7,8]. Within the dinoflagellate genus Alexandrium, many species can produce neurotoxins called paralytic shellfish toxins (PSTs), which can bring about paralytic shellfish poisoning. Alexandrium catenella is widely distributed all over the world and has the ability to produce PSTs [10]. Previous studies of A. catenella focused on transcriptome sequencing and analysis[11], proteomic analysis[12], characterization of genes related to proliferating cells[13], and gene expression in the decline phase of HABs[14] and the effect of different environmental conditions[15], which aimed to elucidate the molecular mechanisms responsible for blooming. No investigation of micro-ribonucleic acids (miRNAs) and their expression profiles in A. catenella have been reported to date
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