Identification of miRNA from Porphyra yezoensis by High-Throughput Sequencing and Bioinformatics Analysis

Liang, Chengwei; Zhang, Xiaowen; Zou, Jian; Xu, Dong; Ye, Naihao

doi:10.1371/journal.pone.0010698

Cited by 82 publications

(65 citation statements)

References 43 publications

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“…As already mentioned, candidate miRNAs have been identified or predicted in four algal species, C. reinhardtii (41,61,102), P. yezoensis (52), P. tricornutum (22,55), and E. siliculosus (17). To address the biological role(s) of these miRNAs, computational approaches have been used to predict their putative targets in three algae (17,52,61,102). However, since the genomes of these species are not fully annotated or are not available (candidate miRNAs were matched only to expressed sequence tags for P. yezoensis) and/or many genes have no known function, it is difficult to draw a conclusion as to whether predicted miRNA targets have any functional bias.…”

Section: Biological Roles Of Rna-mediated Silencing In Algaementioning

confidence: 99%

“…Likewise, endogenous noncoding sRNAs have been identified, by sRNA library sequencing, in the red alga Porphyra yezoensis (52), the diatom P. tricornutum (22), and the brown alga Ectocarpus siliculosus (17). Based on the ability of genomic sRNA loci (or of the corresponding transcripts) to fold back into hairpin secondary structures resembling miRNA precursors, miRNA candidates have been predicted in these three algal species (17,52,55). Interestingly, with the possible exception of candidate miRNAs identified in P. yezoensis (52), there appears to be little conservation of particular miRNA genes among algae or with those encoded in the genomes of land plants or animals (17,18,61,102 (16,22,24,42,43,44,76,77,79,87).…”

Section: Rnai Machinery In Algaementioning

confidence: 99%

“…Based on the ability of genomic sRNA loci (or of the corresponding transcripts) to fold back into hairpin secondary structures resembling miRNA precursors, miRNA candidates have been predicted in these three algal species (17,52,55). Interestingly, with the possible exception of candidate miRNAs identified in P. yezoensis (52), there appears to be little conservation of particular miRNA genes among algae or with those encoded in the genomes of land plants or animals (17,18,61,102 (16,22,24,42,43,44,76,77,79,87). In most cases, reduction of the steady-state levels of targeted mRNAs was observed, implying RNAi-mediated transcriptional repression and/or RNA degradation (16,22,42,43,44,76,77,79,87).…”

Section: Rnai Machinery In Algaementioning

confidence: 99%

“…Another major role of RNAi in higher eukaryotes is the regulation of endogenous gene expression by miRNAs and other sRNAs (5, 10, 18, 30, 36, 45, 49, 92). As already mentioned, candidate miRNAs have been identified or predicted in four algal species, C. reinhardtii (41,61,102), P. yezoensis (52), P. tricornutum (22,55), and E. siliculosus (17). To address the biological role(s) of these miRNAs, computational approaches have been used to predict their putative targets in three algae (17,52,61,102).…”

Section: Biological Roles Of Rna-mediated Silencing In Algaementioning

confidence: 99%

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RNA-Mediated Silencing in Algae: Biological Roles and Tools for Analysis of Gene Function

et al. 2011

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Algae are a large group of aquatic, typically photosynthetic, eukaryotes that include species from very diverse phylogenetic lineages, from those similar to land plants to those related to protist parasites. The recent sequencing of several algal genomes has provided insights into the great complexity of these organisms. Genomic information has also emphasized our lack of knowledge of the functions of many predicted genes, as well as the gene regulatory mechanisms in algae. Core components of the machinery for RNA-mediated silencing show widespread distribution among algal lineages, but they also seem to have been lost entirely from several species with relatively small nuclear genomes. Complex sets of endogenous small RNAs, including candidate microRNAs and small interfering RNAs, have now been identified by high-throughput sequencing in green, red, and brown algae. However, the natural roles of RNA-mediated silencing in algal biology remain poorly understood. Limited evidence suggests that small RNAs may function, in different algae, in defense mechanisms against transposon mobilization, in responses to nutrient deprivation and, possibly, in the regulation of recently evolved developmental processes. From a practical perspective, RNA interference (RNAi) is becoming a promising tool for assessing gene function by sequence-specific knockdown. Transient gene silencing, triggered with exogenously synthesized nucleic acids, and/or stable gene repression, involving genome-integrated transgenes, have been achieved in green algae, diatoms, yellow-green algae, and euglenoids. The development of RNAi technology in conjunction with system level "omics" approaches may provide the tools needed to advance our understanding of algal physiological and metabolic processes.Algae are a large group of aquatic, characteristically photoautotrophic, eukaryotic organisms. However, despite some shared features, like an aquatic lifestyle, the capacity to carry out photosynthesis in membrane-bound chloroplasts, and the lack of specialized organs characteristic of land plants, algae are very diverse phylogenetically (4,9,69,70,96). They include organisms derived from a primary endosymbiotic event (a heterotrophic eukaryote engulfing a photosynthetic cyanobacterium), as well as those derived from subsequent secondary or even tertiary endosymbiotic events (nonphotosynthetic or photosynthetic eukaryotes engulfing photosynthetic eukaryotes) (70). As a consequence of this complex evolutionary history, algae are distributed within four of the six major eukaryotic supergroups, namely, the Archaeplastida, Chromalveolata, Rhizaria, and Excavata (Table 1) (4,9,69,70,96). Regardless of whether these supergroups are monophyletic (4, 9, 69), it is clear that some algae are more closely related to apicomplexan parasites (Chromalveolata), for instance, than to land plants (Archaeplastida) (70).Algal species play important roles in marine, freshwater, and even terrestrial ecosystems. Notably, 30 to 50% of the planetary net photosynthetic productivity (t...

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Section: Biological Roles Of Rna-mediated Silencing In Algaementioning

confidence: 99%

Section: Rnai Machinery In Algaementioning

confidence: 99%

Section: Rnai Machinery In Algaementioning

confidence: 99%

Section: Biological Roles Of Rna-mediated Silencing In Algaementioning

confidence: 99%

See 2 more Smart Citations

RNA-Mediated Silencing in Algae: Biological Roles and Tools for Analysis of Gene Function

et al. 2011

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“…Because of its high specificity and efficiency, RNA interference has been proven to be an invaluable tool for analyzing the biological function of the target gene and adjusting the metabolism process considerably by sequence-specific knockdown (Cerutti et al, 2011;Schramke andAllshire, 2005, Waterhouse et al, 1998). A wide range of core RNAi machinery components, which promotes the transient gene silencing and stable gene repression experiments, was identified in the marine algae, red alga P. yezoensis (Liang et al, 2010), green alga D. salina (Jia et al, 2009), diatom P. tricornutum (De Riso et al, 2009, T. pseudonana (Armbrust et al, 2004), and brown alga Ectocarpus siliculosus (Cock et al, 2010). To investigate the potential of double-stranded RNA interference with gene expression in D. salina, a plasmid was constructed to express hairpin RNA containing sequences homologous to phytoene desaturase genes that were transformed into D. salina by electroporation for the transient suppression of gene expression (Sun et al, 2008).…”

Section: Rna Interference Technologymentioning

confidence: 99%