Identification of novel and candidate miRNAs in rice by high throughput sequencing

Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity

MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs that play important roles in many developmental processes and stress responses in plants and animals. Cotton (Gossypium hirsutum L.) is considered a relatively salt-tolerant non-halophytic plant species. To study the role of miRNAs in salt adaptation, a salt-tolerant cotton cultivar SN-011 and a salt-sensitive cultivar LM-6 were used to detect differentially expressed miRNAs. Using miRNA microarray analysis and a computational approach, 17 cotton miRNAs belonging to eight families were identified. Although they are conserved, 12 of them showed a genotype-specific expression model in both the cultivars. Under salt stress treatment, miR156a/d/e, miR169, miR535a/b and miR827b were dramatically down-regulated in SN-011, while miR167a, miR397a/b and miR399a were up-regulated. Only miR159 was found to be down-regulated in LM-6 under salt stress. To gain insight into their functional significance, 26 target genes were predicted and their functional similarity was further analyzed. Quantitative real-time PCR showed that the expression of seven target genes showed a significant inverse correlation with corresponding miRNAs. These differentially expressed miRNAs can help in further study into the role of transcriptome homeostasis in the adaptation responses of cotton to salt.

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

In plants, microRNAs (miRNAs) regulate their mRNA targets by precisely guiding cleavages between the 10th and 11th nucleotides in the complementary regions. High-throughput sequencing-based methods, such as PARE or degradome profiling coupled with a computational analysis of the sequencing data, have recently been developed for identifying miRNA targets on a genome-wide scale. The existing algorithms limit the number of mismatches between a miRNA and its targets and strictly do not allow a mismatch or G:U Wobble pair at the position 10 or 11. However, evidences from recent studies suggest that cleavable targets with more mismatches exist indicating that a relaxed criterion can find additional miRNA targets. In order to identify targets including the ones with weak complementarities from degradome data, we developed a computational method called SeqTar that allows more mismatches and critically mismatch or G:U pair at the position 10 or 11. Precisely, two statistics were introduced in SeqTar, one to measure the alignment between miRNA and its target and the other to quantify the abundance of reads at the center of the miRNA complementary site. By applying SeqTar to publicly available degradome data sets from Arabidopsis and rice, we identified a substantial number of novel targets for conserved and non-conserved miRNAs in addition to the reported ones. Furthermore, using RLM 5′-RACE assay, we experimentally verified 12 of the novel miRNA targets (6 each in Arabidopsis and rice), of which some have more than 4 mismatches and have mismatches or G:U pairs at the position 10 or 11 in the miRNA complementary sites. Thus, SeqTar is an effective method for identifying miRNA targets in plants using degradome data sets.

Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage

Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ~400 annotated miRNAs with current criteria and the finding that among these, ~150 had small interfering RNA-like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.

Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing

Background

MicroRNAs (miRNAs) are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L.), one of the most important oilseed crops cultivated worldwide.

Results

A library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search.

Conclusions

We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut.

Identification of novel maize miRNAs by measuring the precision of precursor processing

BACKGROUND

miRNAs are known to play important regulatory roles throughout plant development. Until recently, nearly all the miRNAs in maize were identified by comparative analysis to miRNAs sequences of other plant species, such as rice and Arabidopsis.

RESULTS

To find new miRNA in this important crop, small RNAs from mixed tissues were sequenced, resulting in over 15 million unique sequences. Our sequencing effort validated 23 of the 28 known maize miRNA families, including 49 unique miRNAs. Using a newly established criterion, based on the precision of miRNA processing from precursors, we identified 66 novel miRNAs in maize. These miRNAs can be grouped into 58 families, 54 of which have not been identified in any other species. Five new miRNAs were validated by northern blot. Moreover, we found targets for 23 of the 66 new miRNAs. The targets of two of these newly identified miRNAs were confirmed by 5'RACE.

CONCLUSION

We have implemented a novel method of identifying miRNA by measuring the precision of miRNA processing from precursors. Using this method, 66 novel miRNAs and 50 potential miRNAs have been identified in maize.

Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes

BACKGROUND

Cowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes.

RESULTS

We generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other.

CONCLUSIONS

These results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.

Deep sequencing of grapevine flower and berry short RNA library for discovery of novel microRNAs and validation of precise sequences of grapevine microRNAs deposited in miRBase

MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high-throughput sequencing technologies has enabled the discovery of novel miRNAs. Although there are two recent reports on high-throughput sequencing analysis of small RNA libraries from different organs of two wine grapevine varieties, there was a significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. In this study, a total of 130 conserved grapevine Vitis vinifera miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, other 80 unconserved Vv-miRNAs including 72 novel potential and 8 known but unconserved ones were found. Fifty-two (52.5%) of these 80 unconserved Vv-miRNAs exhibited differential poly(A)-tailed reverse transcriptase-polymerase chain reaction expression profiles in various grapevine tissues that could further confirm their existence in grapevine, among which 20 were expressed only in grapevine berries, indicating a degree of fruit-specificity. One hundred thirty target genes for 56 unconserved miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed. These results point to a regulatory role of miRNAs in grapevine berry development and response to various environments.

Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum

Sweet Sorghum is largely grown for grain production but also recently emerged as one of the model feedstock plants for biofuel production. In plants, microRNA (miRNA)-guided gene regulation plays a key role in diverse biological processes, thus, their identification in different plant species is essential to understand post-transcriptional gene regulation. To identify miRNAs in Sorghum, we sequenced a small RNA library. Sequence analysis revealed the identity of 29 conserved miRNA families. Importantly, 13 novel miRNAs are identified, seven of which are conserved in closely related monocots. Temporal expression analysis of conserved and novel miRNAs indicated differential expression of several miRNAs. Approximately 125 genes that play diverse roles have been predicted as targets and a few targets were experimentally validated. These results provided insights into miRNA-controlled processes in Sorghum and also laid the foundation for manipulating miRNAs or their targets for improving biomass production and stress tolerance in Sorghum.

Isolation and identification of novel microRNAs from Marsupenaeus japonicus

MicroRNAs (miRNAs) are a class of small noncoding RNAs that function as regulators of gene expression. They play essential roles in various biological processes, such as development, differentiation and immune response. In this study, we identified 35 miRNAs from Marsupenaeus japonicus. Among them, fifteen miRNAs exhibited high homology to the known miRNAs from other arthropods, while the rest might represent novel miRNAs. We further showed a correlation of WSSV infection and the expression levels of 22 miRNAs. This is the first report to identify miRNAs from the shrimp. Our results extend the knowledge of the gene regulation of crustacean, providing clues for future researches of shrimp immunity against virus infection.

Characterization of microRNAs identified in a table grapevine cultivar with validation of computationally predicted grapevine miRNAs by miR-RACE

Background

Alignment analysis of the Vv-miRNAs identified from various grapevine cultivars indicates that over 30% orthologous Vv-miRNAs exhibit a 1–3 nucleotide discrepancy only at their ends, suggesting that this sequence discrepancy is not a random event, but might mainly derive from divergence of cultivars. With advantages of miR-RACE technology in determining precise sequences of potential miRNAs from bioinformatics prediction, the precise sequences of vv-miRNAs predicted computationally can be verified with miR-RACE in a different grapevine cultivar. This presents itself as a new approach for large scale discovery of precise miRNAs in different grapevine varieties.

Methodology/Principal Findings

Among 88 unique sequences of Vv-miRNAs from bioinformatics prediction, 83 (96.3%) were successfully validated with MiR-RACE in grapevine cv. ‘Summer Black’. All the validated sequences were identical to their corresponding ones obtained from deep sequencing of the small RNA library of ‘Summer Black’. Quantitative RT-PCR analysis of the expressions levels of 10 Vv-miRNA/target gene pairs in grapevine tissues showed some negative correlation trends. Finally, comparison of Vv-miRNA sequences with their orthologs in Arabidopsis and study on the influence of divergent bases of the orthologous miRNAs on their targeting patterns in grapevine were also done.

Conclusion

The validation of precise sequences of potential Vv-miRNAs from computational prediction in a different grapevine cultivar can be a new way to identify the orthologous Vv-miRNAs. Nucleotide discrepancy of orthologous Vv-miRNAs from different grapevine cultivars normally does not change their target genes. However, sequence variations of some orthologous miRNAs in grapevine and Arabidopsis can change their targeting patterns. These precise Vv-miRNAs sequences validated in our study could benefit some further study on grapevine functional genomics.

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

BACKGROUND

MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of miRNAs at the global genome-level by high-throughout sequencing is essential to functionally characterize miRNAs in plants. Drought is one of the common environmental stresses limiting plant growth and development. To understand the role of miRNAs in response of plants to drought stress, drought-responsive miRNAs were identified by high-throughput sequencing in a legume model plant, Medicago truncatula.

RESULTS

Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 238 potential candidate miRNAs were identified, and among them 14 new miRNAs and 15 new members of known miRNA families whose complementary miRNA*s were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 29 new miRNAs/new members of known miRNA families, 8 miRNAs were responsive to drought stress with both 4 miRNAs being up- and down-regulated, respectively. The known and predicted targets of the drought-responsive miRNAs were found to be involved in diverse cellular processes in plants, including development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.

CONCLUSIONS

We identified 32 known members of 10 miRNA families and 8 new miRNAs/new members of known miRNA families that were responsive to drought stress by high-throughput sequencing of small RNAs from M. truncatula. These findings are of importance for our understanding of the roles played by miRNAs in response of plants to abiotic stress in general and drought stress in particular.

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

BACKGROUND

MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of miRNAs at the global genome-level by high-throughout sequencing is essential to functionally characterize miRNAs in plants. Drought is one of the common environmental stresses limiting plant growth and development. To understand the role of miRNAs in response of plants to drought stress, drought-responsive miRNAs were identified by high-throughput sequencing in a legume model plant, Medicago truncatula.

RESULTS

Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 238 potential candidate miRNAs were identified, and among them 14 new miRNAs and 15 new members of known miRNA families whose complementary miRNA*s were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 29 new miRNAs/new members of known miRNA families, 8 miRNAs were responsive to drought stress with both 4 miRNAs being up- and down-regulated, respectively. The known and predicted targets of the drought-responsive miRNAs were found to be involved in diverse cellular processes in plants, including development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.

CONCLUSIONS

We identified 32 known members of 10 miRNA families and 8 new miRNAs/new members of known miRNA families that were responsive to drought stress by high-throughput sequencing of small RNAs from M. truncatula. These findings are of importance for our understanding of the roles played by miRNAs in response of plants to abiotic stress in general and drought stress in particular.

Small RNA diversity in plants and its impact in development

MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development.

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Background

Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar.

Results

Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome.

Conclusions

Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.

Identification of potential microRNAs and their targets in Brassica rapa L

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20(th) position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

Background

Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development remains limited, and the dynamic profile of miRNAs in developing pollen is unknown.

Results

Using next-generation sequencing technology, we pyrosequenced small RNA populations from rice uninucleate microspores to tricellular pollen and control sporophytic tissues at the genome-wide level. We identified 292 known miRNAs, including members of all 20 families conserved in plants, and 75 novel miRNAs. Of the 292 known miRNAs, 202 were expressed, with 103 enriched, in developing pollen. More than half of these novel miRNAs displayed pollen-or stage-specific expression. Furthermore, analyzing the 367 miRNAs and their predicted targets indicated that correlation in expression profiles of pollen-enriched known miRNAs and their targets significantly differs from that of sporophyte-enriched known miRNAs and their targets in some functional terms, while novel miRNAs appeared to negatively regulate their targets. Importantly, gene ontology abundance analysis demonstrated chromatin assembly and disassembly was important in the targets of bicellular pollen-expressed novel miRNAs. Principal component analysis revealed pollen of all three stages was discriminated from sporophytes, largely because of the novel and non-conserved known miRNAs.

Conclusions

Our study, for the first time, revealed the differences in composition and expression profiles of miRNAs between developing pollen and sporophytes, with novel and non-conserved known miRNAs the main contributors. Our results suggest the important roles of the miRNA pathway in pollen development.

miRTour: Plant miRNA and target prediction tool

MicroRNAs (miRNAs) are important negative regulators of gene expression in plant and animals, which are endogenously produced from their own genes. Computational comparative approach based on evolutionary conservation of mature miRNAs has revealed a number of orthologs of known miRNAs in different plant species. The homology-based plant miRNA discovery, followed by target prediction, comprises several steps, which have been done so far manually. Here, we present the bioinformatics pipeline miRTour which automates all the steps of miRNA similarity search, miRNA precursor selection, target prediction and annotation, each of them performed with the same set of input sequences.

AVAILABILITY

The database is available for free at http://bio2server.bioinfo.uni-plovdiv.bg/miRTour/

Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate specific target mRNAs at the post-transcriptional level. Plant miRNAs have been implicated in developmental processes and adaptations to environmental stresses. Cadmium (Cd) is a non-essential heavy metal that is highly toxic to plants. To investigate the responsive functions of miRNAs under Cd stress, miRNA expression in Cd-stressed rice (Oryza sativa) was profiled using a microarray assay. A total of 19 Cd-responsive miRNAs were identified, of which six were further validated experimentally. Target genes were also predicted for these Cd-responsive miRNAs, which encoded transcription factors, and proteins associated with metabolic processes or stress responses. In addition, the mRNA levels of several targets were negatively correlated with the corresponding miRNAs under Cd stress. Promoter analysis showed that metal stress-responsive cis-elements tended to occur more frequently in the promoter regions of Cd-responsive miRNAs. These findings suggested that miRNAs played an important role in Cd tolerance in rice, and highlighted a novel molecular mechanism of heavy metal tolerance in plants.

High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs

Micro RNAS (miRNAs) are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance.

Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus) plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand) not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome.

In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes.

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice

Small silencing RNAs (sRNAs) are non-coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem-loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted-repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer-like (DCL)3- and RNA-dependent RNA polymerase (RDR)2-dependent MITE-derived ra-siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single-stranded stem-loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self-pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression.

Discovery of barley miRNAs through deep sequencing of short reads

Background

MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced genomes such as Arabidopsis, rice, poplar and Brachypodium have provided insights into the evolutionary relationships of this class of small RNAs among plants. However, miRNAs from barley, one of the most important cereal crops, remain unknown.

Results

We performed a large scale study of barley miRNAs through deep sequencing of small RNAs extracted from leaves of two barley cultivars. By using the presence of miRNA precursor sequences in related genomes as one of a number of supporting criteria, we identified up to 100 miRNAs in barley. Of these only 56 have orthologs in wheat, rice or Brachypodium that are known to be expressed, while up to 44 appear to be specifically expressed in barley.

Conclusions

Our study, the first large scale investigation of small RNAs in barley, has identified up to 100 miRNAs. We demonstrate that reliable identification of miRNAs via deep sequencing in a species whose genome has not been sequenced requires a more careful analysis of sequencing errors than is commonly performed. We devised a read filtering procedure for dealing with errors. In addition, we found that the use of a large dataset of almost 35 million reads permits the use of read abundance distributions along putative precursor sequences as a practical tool for isolating miRNAs in a large background of reads originating from other non-coding and coding RNAs. This study therefore provides a generic approach for discovering novel miRNAs where no genome sequence is available.

Characterization of statistical features for plant microRNA prediction

Background

Several tools are available to identify miRNAs from deep-sequencing data, however, only a few of them, like miRDeep, can identify novel miRNAs and are also available as a standalone application. Given the difference between plant and animal miRNAs, particularly in terms of distribution of hairpin length and the nature of complementarity with its duplex partner (or miRNA star), the underlying (statistical) features of miRDeep and other tools, using similar features, are likely to get affected.

Results

The potential effects on features, such as minimum free energy, stability of secondary structures, excision length, etc., were examined, and the parameters of those displaying sizable changes were estimated for plant specific miRNAs. We found most of these features acquired a new set of values or distributions for plant specific miRNAs. While the length of conserved positions (nucleus) in mature miRNAs were relatively longer in plants, the difference in distribution of minimum free energy, between real and background hairpins, was marginal. However, the choice of source (species) of background sequences was found to affect both the minimum free energy and miRNA hairpin stability. The new parameters were tested on an Illumina dataset from maize seedlings, and the results were compared with those obtained using default parameters. The newly parameterized model was found to have much improved specificity and sensitivity over its default counterpart.

Conclusions

In summary, the present study reports behavior of few general and tool-specific statistical features for improving the prediction accuracy of plant miRNAs from deep-sequencing data.

Evolution and functional diversification of MIRNA genes

MicroRNAs (miRNAs) are small regulatory RNAs found in diverse eukaryotic lineages. In plants, a minority of annotated MIRNA gene families are conserved between plant families, while the majority are family- or species-specific, suggesting that most known MIRNA genes arose relatively recently in evolutionary time. Given the high proportion of young MIRNA genes in plant species, new MIRNA families are likely spawned and then lost frequently. Unlike highly conserved, ancient miRNAs, young miRNAs are often weakly expressed, processed imprecisely, lack targets, and display patterns of neutral variation, suggesting that young MIRNA loci tend to evolve neutrally. Genome-wide analyses from several plant species have revealed that variation in miRNA foldback expression, structure, processing efficiency, and miRNA size have resulted in the unique functionality of MIRNA loci and resulting miRNAs. Additionally, some miRNAs have evolved specific properties and functions that regulate other transcriptional or posttranscriptional silencing pathways. The evolution of miRNA processing and functional diversity underscores the dynamic nature of miRNA-based regulation in complex regulatory networks.

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

BACKGROUND

MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research.

RESULTS

In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis suppressor of gene silencing 3 (AtSGS3) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.

CONCLUSIONS

We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.

Regulation of flowering time and floral patterning by miR172

Since the discovery of miRNAs in plants it has become clear that they are central to the regulation of many aspects of plant development and responses to the environment. miR172 regulates expression of a small group of AP2-like transcription factors in an evolutionarily ancient interaction. miR172 functions in regulating the transitions between developmental stages and in specifying floral organ identity. These two roles are conserved across monocotyledons and dicotyledons. Investigations into the roles of miR172 and its targets in phase changes in the model plant Arabidopsis have illustrated that this process is governed by complex regulatory systems. In addition to its conserved roles, miR172 has also acquired specialized species-specific functions in other aspects of plant development such as cleistogamy and tuberization.

Next-generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera

MicroRNAs (miRNAs) are key regulators in various physiological and pathological processes via post-transcriptional regulation of gene expression. The honey bee (Apis mellifera) is a key model for highly social species, and its complex social behaviour can be interpreted theoretically as changes in gene regulation, in which miRNAs are thought to be involved. We used the SOLiD sequencing system to identify the repertoire of miRNAs in the honey bee by sequencing a mixed small RNA library from different developmental stages. We obtained a total of 36,796,459 raw sequences; of which 5,491,100 short sequences were fragments of mRNA and other noncoding RNAs (ncRNA), and 1,759,346 reads mapped to the known miRNAs. We predicted 267 novel honey bee miRNAs representing 380,182 short reads, including eight miRNAs of other insects in 14,107,583 genome-mapped sequences. We verified 50 of them using stem-loop reverse-transcription PCR (RT-PCR), in which 35 yielded PCR products. Cross-species analyses showed 81 novel miRNAs with homologues in other insects, suggesting that they were authentic miRNAs and have similar functions. The results of this study provide a basis for studies of the miRNA-modulating networks in development and some intriguing phenomena such as caste differentiation in A. mellifera.

Identification and analysis of seven H₂O₂-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)

Plant microRNAs (miRNAs) have been shown to play critical roles in regulating gene expression at the post-transcriptional level. In this study, we employed high throughput sequencing combined with computational analysis to survey miRNAomes from the seedlings of rice under normal conditions and treatments of H₂O₂ that result in oxidative stress. Comparison of the miRNAomes and subsequent northern blot analysis identified seven miRNA families differentially expressed under H₂O₂ stress. Predicted and experimentally validated targets of these H₂O₂-responsive miRNAs are involved in different cellular responses and metabolic processes including transcriptional regulation, nutrient transport, auxin homeostasis, cell proliferation and programmed cell death. This indicates that diverse miRNAs form a complex regulatory network to coordinate plants’ responses under oxidative stress. In addition, we also discovered 32 new miRNAs in the seedlings of rice. Interestingly, of these new miRNAs, miR3981 was originally found to be a putative exonic miRNA located in the exon of AK106348, suggesting that plants may also use some exons as an miRNA source. This study is the first genome-wide investigation of H₂O₂-regulated miRNAs in plants and broadens our perspectives on the important regulatory roles of miRNAs in plant oxidative stress and physiological adaption.

Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags

MicroRNAs (miRNAs) are a new family of small RNA molecules found in plants and animals. We developed a comprehensive strategy for identifying new miRNA homologues by mining the repository of available citrus expressed sequence tags (ESTs). By adopting a range of filtering criteria, we identified a total of 38 potential miRNAs--nine, five, nine and 15 miRNAs in Citrus trifoliata (ctr-miRNAs), C. clementina (ccl-miRNAs), C. reticulata (crt-miRNAs) and C. sinensis (csi-miRNAs), respectively--from more than 430,000 EST sequences in citrus. Using the potential miRNA sequences, we conducted a further BLAST search of the mRNA database and found six potential target genes in these citrus species. Eight miRNAs were selected in order to verify their existence in citrus using Northern blotting, and the functions of several miRNAs in miRNA-mediated gene regulation are experimentally suggested. It appears that all these miRNAs regulate expression of their target genes by cleavage, which is the most common situation in gene regulation mediated by plant miRNAs. Our achievement in identifying new miRNAs in citrus provides a powerful incentive for further studies on the important roles of these miRNAs.

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for plant transcriptomics, including gene discovery, transcript quantification and marker discovery for non-model plants, as well as transcript annotation and quantification, small RNA discovery and antisense transcription analysis for model plants. We discuss the experimental design for analysis of plants with and without a sequenced genome, including considerations on sampling, RNA preparation, sequencing platforms and bioinformatics tools for data analysis. NGS technologies offer exciting new opportunities for the plant sciences, especially for work on plants without a sequenced genome, since large sequence resources can be generated at moderate cost.

siRNAs from miRNA sites mediate DNA methylation of target genes

Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give rise to two small RNA species, a 20- to 22-nt species and a 23- to 27-nt species, at the same site. Genetic analysis using small RNA pathway mutants reveals that the 20- to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 (AGO1). In contrast, the accumulation of the 23- to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3, RDR2 and Pol IV, components of the typical heterochromatic small interfering RNA (hc-siRNA) pathway. We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans. In addition, we find that at the miRNA-generating sites, some conserved canonical MIR genes also produce siRNAs, which also induce DNA methylation at some of their target sites. Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual functional MIRs exist broadly in plants.

Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses

MicroRNAs are a class of endogenous small RNA molecules (20-24 nucleotides) that have pivotal roles in regulating gene expression mostly at posttranscriptional levels in plants. Plant microRNAs have been implicated in the regulation of diverse biological processes including growth and stress responses. However, the information about microRNAs in regulating abiotic stress responses in rice is limited. We optimized a one-tube stem-loop reverse transcription quantitative PCR (ST-RT qPCR) for high-throughput expression profiling analysis of microRNAs in rice under normal and stress conditions. The optimized ST-RT qPCR method was as accurate as small RNA gel blotting and was more convenient and time-saving than other methods in quantifying microRNAs. With this method, 41 rice microRNAs were quantified for their relative expression levels after drought, salt, cold, and abscisic acid (ABA) treatments. Thirty-two microRNAs showed induced or suppressed expression after stress or ABA treatment. Further analysis suggested that stress-responsive cis-elements were enriched in the promoters of stress-responsive microRNA genes. The expressions of five and seven microRNAs were significantly affected in the rice plant with defects in stress tolerance regulatory genes OsSKIPa and OsbZIP23, respectively. Some of the predicted target genes of these microRNAs were also related to abiotic stresses. We conclude that ST-RT qPCR is an efficient and reliable method for expression profiling of microRNAs and a significant portion of rice microRNAs participate in abiotic stress response and regulation.

Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts

We applied deep sequencing technology to small RNA fractions from cells lytically infected with murine gammaherpesvirus 68 (gammaHV68) in order to define in detail small RNAs generated from a cluster of tRNA-related polycistronic structures located at the left end of the viral genome. We detected 10 new candidate microRNAs (miRNAs), six of which were confirmed by Northern blot analysis, leaving four as provisional. In addition, we determined that previously identified and annotated viral miRNA molecules were not necessarily represented as the most abundant sequence originating from a transcript. Based on these new small RNAs and previously reported gammaHV68 miRNAs, we were able to further describe and annotate the distinctive gammaHV68 tRNA-miRNA structures. We used this deep sequencing data and computational analysis to identify similar structures in the mouse genome and validated that these host structures also give rise to small RNAs. This reveals a possible convergent usage of tRNA/polymerase III (pol III) transcripts to generate small RNAs from both mammalian and viral genomes.

Prediction of miRNA targets, affected proteins and their homologs in Glycine max

microRNAs are small noncoding RNA gene products about 20-24nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. As miRNAs affect the morphology of plants and animals by the posttranscriptional regulation of genes involved in critical developmental events, it has been proposed that precise regulation of miRNAs activity during various stages of growth and in specific cell types is of central importance for normal plant development. In our work we focus on the plant miRNAs and predict the miRNA targets, affected proteins by miRNA and miRNA homologs of Glycine max. Our analyses were based on sequence complementarities between miRNAs and mRNAs. As a result, we predicted 573 targets for 44 mature miRNAs sequences among 69 mature miRNAs sequences were published in database. Study of affected proteins revealed that for very less number of miRNAs, protein products are known and they mostly involved in diverse physiological process like as element of photosynthesis system. Homology analyses for miRNAs suggested that 22 miRNAs of Glycine max show 418 miRNA homologs for different plant species.

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

BACKGROUND

Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of saline-alkaline stress transcriptome is mostly focused on saline (NaCl) stress and only limited information on alkaline (NaHCO3) stress is available.

RESULTS

Using Affymetrix Soybean GeneChip, we conducted transcriptional profiling on Glycine soja roots subjected to 50 mmol/L NaHCO3 treatment. In a total of 7088 probe sets, 3307 were up-regulated and 5720 were down-regulated at various time points. The number of significantly stress regulated genes increased dramatically after 3 h stress treatment and peaked at 6 h. GO enrichment test revealed that most of the differentially expressed genes were involved in signal transduction, energy, transcription, secondary metabolism, transporter, disease and defence response. We also detected 11 microRNAs regulated by NaHCO3 stress.

CONCLUSIONS

This is the first comprehensive wild soybean root transcriptome analysis under alkaline stress. These analyses have identified an inventory of genes with altered expression regulated by alkaline stress. The data extend the current understanding of wild soybean alkali stress response by providing a set of robustly selected, differentially expressed genes for further investigation.

Identification of microRNAs and their targets in switchgrass, a model biofuel plant species

In recent years, several plant species such as switchgrass, Miscanthus and Brachypodium have been recognized as potential model plant species for cellulosic bioenergy production. Of these, switchgrass has attracted much attention in the United States and worldwide because it can grow well on marginal lands and tolerate frequent drought spells. However, little is known about the basic biology of the traits that control these important characteristics in switchgrass. Genome-encoded approximately 21-24nt microRNAs (miRNAs) have emerged as critical regulators of gene expression important for normal growth and development and adaptation to abiotic stress, including nutrient-deprived conditions. To understand miRNA-guided post-transcriptional gene regulatory networks in this plant species, we sought to identify miRNAs in switchgrass. Using computational and experimental approaches, we identified approximately 20 conserved miRNA families. Temporal expression analysis indicated that some miRNAs have distinct tissue-specific expression, although most are ubiquitously expressed. Unlike in Arabidopsis and other plants, miR395 and miR399 were detected in plants grown on optimal levels of sulfate or phosphate in switchgrass, and were only slightly altered when exposed to sulfate or phosphate deficit conditions. Thirty-seven genes were predicted as targets for miRNAs, and 4 target mRNAs (Squamosa promoter binding-like factor, apetala 2-like, NAC domain containing transcription factor and HD-Zip homologs) were validated by 5'-RACE assays. These findings provide a snapshot of the miRNA component and possible targets in switchgrass.

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

BACKGROUND

MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants.

RESULTS

In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) which is an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues. Based on sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 63 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates whose precursors were all potentially generated from citrus ESTs. In addition, five miRNA* sequences were also sequenced. These sequences had not been earlier described in other plant species and accumulation of the 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes including one encoding IRX12 copper ion binding/oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.

CONCLUSION

Deep sequencing of short RNAs from C. trifoliata flowers and fruits identified 10 new potential miRNAs and 42 highly conserved miRNA families, indicating that specific miRNAs exist in C. trifoliata. These results show that regulatory miRNAs exist in agronomically important trifoliate orange and may play an important role in citrus growth, development, and response to disease.

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

BACKGROUND

MicroRNAs (miRNAs) are a class of small non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. MiRNAs can have large-scale regulatory effects on development and stress response in plants.

RESULTS

To test whether miRNAs play roles in regulating response to powdery mildew infection and heat stress in wheat, by using Solexa high-throughput sequencing we cloned the small RNA from wheat leaves infected by preponderant physiological strain Erysiphe graminis f. sp. tritici (Egt) or by heat stress treatment. A total of 153 miRNAs were identified, which belong to 51 known and 81 novel miRNA families. We found that 24 and 12 miRNAs were responsive to powdery mildew infection and heat stress, respectively. We further predicted that 149 target genes were potentially regulated by the novel wheat miRNA.

CONCLUSIONS

Our results indicated that diverse set of wheat miRNAs were responsive to powdery mildew infection and heat stress and could function in wheat responses to both biotic and abiotic stresses.

MiR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs

BACKGROUND

Among the hundreds of genes encoding miRNAs in plants reported, much more were predicted by numerous computational methods. However, unlike protein-coding genes defined by start and stop codons, the ends of miRNA molecules do not have characteristics that can be used to define the mature miRNAs exactly, which made computational miRNA prediction methods often cannot predict the accurate location of the mature miRNA in a precursor with nucleotide-level precision. To our knowledge, there haven't been reports about comprehensive strategies determining the precise sequences, especially two termini, of these miRNAs.

METHODS

In this study, we report an efficient method to determine the precise sequences of computationally predicted microRNAs (miRNAs) that combines miRNA-enriched library preparation, two specific 5' and 3' miRNA RACE (miR-RACE) PCR reactions, and sequence-directed cloning, in which the most challenging step is the two specific gene specific primers designed for the two RACE reactions. miRNA-mediated mRNA cleavage by RLM-5' RACE and sequencing were carried out to validate the miRNAs detected. Real-time PCR was used to analyze the expression of each miRNA.

RESULTS

The efficiency of this newly developed method was validated using nine trifoliate orange (Poncirus trifoliata) miRNAs predicted computationally. The miRNAs computationally identified were validated by miR-RACE and sequencing. Quantitative analysis showed that they have variable expression. Eight target genes have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in Poncirus trifoliate.

CONCLUSION

The efficient and powerful approach developed herein can be successfully used to validate the sequences of miRNAs, especially the termini, which depict the complete miRNA sequence in the computationally predicted precursor.

Transcriptome-wide identification of microRNA targets in rice

MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice (Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5' ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.

Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis

Background

miRNAs are a class of non-coding, small RNAs that are approximately 22 nucleotides long and play important roles in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. The red alga, Porphyra yezoensis is one of the most important marine economic crops worldwide. To date, only a few miRNAs have been identified in green unicellar alga and there is no report about Porphyra miRNAs.

Methodology/Principal Findings

To identify miRNAs in Porphyra yezoensis, a small RNA library was constructed. Solexa technology was used to perform high throughput sequencing of the library and subsequent bioinformatics analysis to identify novel miRNAs. Specifically, 180,557,942 reads produced 13,324 unique miRNAs representing 224 conserved miRNA families that have been identified in other plants species. In addition, seven novel putative miRNAs were predicted from a limited number of ESTs. The potential targets of these putative miRNAs were also predicted based on sequence homology search.

Conclusions/Significance

This study provides a first large scale cloning and characterization of Porphyra miRNAs and their potential targets. These miRNAs belong to 224 conserved miRNA families and 7 miRNAs are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development.