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Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis.

Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, Kong F, Zhong J, Ma Q - PLoS ONE (2015)

Bottom Line: Target predictions of the 12 differentially expressed miRNAs resulted in 1813 target 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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China.

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 1813 target 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.

No MeSH data available.


Length distribution and abundance of sequenced small RNA sequences in A. catenella libraries.Among the small RNAs in the range of 18–25 nt, the most abundant size was 24 nt, followed by 22 nt and 25 nt.
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pone.0138709.g001: Length distribution and abundance of sequenced small RNA sequences in A. catenella libraries.Among the small RNAs in the range of 18–25 nt, the most abundant size was 24 nt, followed by 22 nt and 25 nt.

Mentions: To identify 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 (mix of cultures grown for 7 d and 12 d, respectively). A total of 38,092,056(representing 9,311,258 unique reads) and 32,969,156(representing 7,713,621 unique reads) raw reads (SRP055721) were obtained from the lag phase and the logarithmic phase libraries, respectively. Subsequently, the sequence data were further refined to16,527,710 (43.39% of the raw reads) and 13,324,372(40.41% of the raw reads)clean reads of 18–25ntfor the lag phase and logarithmic phase libraries (Table 1). Among the unique reads,3,230,369(34.69% of the unique reads in the lag phase library) and 2,411,293 (31.26% of the unique reads in the logarithmic phase)were found to be similar to miRNAs. The unique read ratios of the miRNA candidates in the respective libraries were 34.69% and 31.26%.Several other types of non-coding RNAs, including tRNA, rRNA, snRNAs, and snoRNAs, were identified by alignment with the Rfam database. The number and proportion of different categories of small RNAs are given in Table 2.When the length distribution of 18–25nt silencing small RNAs in A. catenella was investigated (Fig 1),the most abundant reads fell into the 24nt fraction, which accounted for 15.96% and16.65%of two libraries, respectively, followed by the 22nt (15.52%, 16.21%), 25 nt(15.58%, 16.15%), and 23nt(15.72% and 16.12%)fractions.


Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis.

Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, Kong F, Zhong J, Ma Q - PLoS ONE (2015)

Length distribution and abundance of sequenced small RNA sequences in A. catenella libraries.Among the small RNAs in the range of 18–25 nt, the most abundant size was 24 nt, followed by 22 nt and 25 nt.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4580472&req=5

pone.0138709.g001: Length distribution and abundance of sequenced small RNA sequences in A. catenella libraries.Among the small RNAs in the range of 18–25 nt, the most abundant size was 24 nt, followed by 22 nt and 25 nt.
Mentions: To identify 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 (mix of cultures grown for 7 d and 12 d, respectively). A total of 38,092,056(representing 9,311,258 unique reads) and 32,969,156(representing 7,713,621 unique reads) raw reads (SRP055721) were obtained from the lag phase and the logarithmic phase libraries, respectively. Subsequently, the sequence data were further refined to16,527,710 (43.39% of the raw reads) and 13,324,372(40.41% of the raw reads)clean reads of 18–25ntfor the lag phase and logarithmic phase libraries (Table 1). Among the unique reads,3,230,369(34.69% of the unique reads in the lag phase library) and 2,411,293 (31.26% of the unique reads in the logarithmic phase)were found to be similar to miRNAs. The unique read ratios of the miRNA candidates in the respective libraries were 34.69% and 31.26%.Several other types of non-coding RNAs, including tRNA, rRNA, snRNAs, and snoRNAs, were identified by alignment with the Rfam database. The number and proportion of different categories of small RNAs are given in Table 2.When the length distribution of 18–25nt silencing small RNAs in A. catenella was investigated (Fig 1),the most abundant reads fell into the 24nt fraction, which accounted for 15.96% and16.65%of two libraries, respectively, followed by the 22nt (15.52%, 16.21%), 25 nt(15.58%, 16.15%), and 23nt(15.72% and 16.12%)fractions.

Bottom Line: Target predictions of the 12 differentially expressed miRNAs resulted in 1813 target 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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China.

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 1813 target 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.

No MeSH data available.