Unknown,Transcriptomics,Genomics,Proteomics

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Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

ABSTRACT: Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatomsâ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were differentially expressed in PT1, PT2 and PT3, and their potential targets were involved in various processes. Our results indicated that P. tricornutum contained novel miRNAs that differed from miRNAs of other organisms and that they might play important regulator roles in P. tricornutum metabolism. Constructing and sequencing small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions

ORGANISM(S): Phaeodactylum tricornutum

SUBMITTER: Guangce Wang

PROVIDER: E-GEOD-29321 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis.

Huang Aiyou A He Linwen L Wang Guangce G

BMC genomics 20110630

<h4>Background</h4>Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify ...[more]

PMID: 21718527

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Project description:We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions. Continuous, axenic culturing of P. tricornutum was done as described in Nymark et al. (2009). The cultures were incubated at 15M-BM-0C under cool white fluorescent light (Philips TLD 36W/96) providing a scalar irradiance (EPAR) of 100 M-NM-<mol m-2 s-1 under continuous white light (CWL) conditions. Upon the onset of the experiment the cultures were synchronized by 48 h dark-treatment (D48). Thereafter the algae were exposed to blue light (BL), green light (GL) or red light (RL) provided by a waveband specific LED panel (SL3500, Photon Systems Instruments). The algae were exposed to 0.5 h, 6 h or 24 h of: 1) 230 M-NM-<mol m-2 s-1 of RL, 2) 100 M-NM-<mol m-2 s-1 of GL, 3) 50 M-NM-<mol m-2 s-1 of BL or 4) 100 M-NM-<mol m-2 s-1 of WL respectively. Three biological replicas for each of the treatments were harvested. Data for the white light exposure and 48h dark treatment is described in GSE42039, PMID: 23520530.

Dataset Information

Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

Publications

Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis.

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