The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
Arabidopsis/metabolism* ; Oryza/metabolism* ; RNA, Circular/metabolism* ; RNA, Plant/metabolism* ; Sequence Analysis, RNA/methods*

Miscanthus sinensis Anderss is a perennial C4-grass. It is a promising bioenergy plant, which has been proposed as general feedstock for biomass and lignocellulosic biofuel production. In this study, the flower and leaf buds transcriptomes of Miscanthus sinensis Anderss were sequenced by the platform of Illumina HiSeq 2000. In total 98 326 Unigenes were generated by de novo assembly with an average length of 822 bp and N50 of 1 023 bp. Based on the NR, NT, Swiss-Prot, KEGG, GO and COG databases (Evalue < le-5), 74 134 (75.40%) Unigenes were annotated. A total of 45 507 Unigenes were mapped into different GO terms. In KEGG pathways identification, 36 710 sequences were assigned to 128 KEGG pathways. Sorghum bicolor (37 731, 60.86%), Zea mays (16 258, 26.22%), and Oryza sativa (3 065, 4.94%) showed high similarity to Miscanthus sinensis Anderss. And 24 photosynthesis-related enzyme genes were identified. The result provides a foundation for further characterizing the functional genes in Miscanthus sinensis Anderss.
Biofuels ; Gene Expression Profiling ; Genes, Plant ; Poaceae ; genetics ; metabolism ; RNA, Plant ; genetics ; Sequence Analysis, RNA ; Transcriptome

OBJECTIVETo study the total RNA and mRNA differential expression in leaves of Pinellia ternata under high temperature, provide more information of the molecular mechanism of the sprout tumble.

METHODThe total RNA and mRNA differential expression in leaves of P. ternata at different stress time was analyzed.

RESULTThe results showed that the trend of total RNA content was divided into three descending stages and two ascending stages, the total RNA content was the highest at 0, 6 h, but it was the lowest at and 42 h, as well as when the sprout tumbled. The differential display showed that the polymorphism and type of bands of the sample at 6 h were similar to those at 0 h. But the bands numbers at other time were far less than those at 0, 6 h. And there were some different mRNA differential expression bands between the different samples.

CONCLUSIONIn the process of the sprout tumble caused by high temperature stress, the RNA and mRNA differential expression in leaves of P. ternata changed.

Gene Expression Regulation, Plant ; Hot Temperature ; Pinellia ; genetics ; metabolism ; Plant Leaves ; genetics ; metabolism ; RNA, Messenger ; genetics ; metabolism ; RNA, Plant ; genetics ; metabolism

Arnebia euchroma is the main source for medicinal herb Zicao. and its most important component shikonin compounds have high medicinal and industrial value. This research is aimed to build overexpression vectors and RNAi vectors for key secondary metabolism genes of A. euchroma, and bulid platform for constructions of related transgenic lines using GATEWAY technology. To build genetic material based genetic research platform is to provide a great convenience for digging and functional verification of the genes on secondary metabolic pathway, and also to fill the gaps in transgenic research of A. euchroma. This study is also important for the cultivation of shikonin high-yielding strains of A. euchroma.
Boraginaceae ; genetics ; metabolism ; Genetic Vectors ; genetics ; metabolism ; Plant Proteins ; genetics ; metabolism ; RNA Interference ; Secondary Metabolism

This study aimed to explore the potentiating effect and mechanism of the extract of Jingfang Granules(JFG) on the activation of macrophages. The RAW264.7 cells were treated with JFG extract and then stimulated by multiple agents. Subsequently, mRNA was extracted, and reverse transcription-polymerase chain reaction(RT-PCR) was used to measure the mRNA transcription of multiple cytokines in RAW264.7 cells. The levels of cytokines in the cell supernatant were detected by enzyme-linked immunosorbent assay(ELISA). In addition, the intracellular proteins were extracted and the activation of signaling pathways was determined by Western blot. The results showed that JFG extract alone could not promote or slightly promote the mRNA transcription of TNF-α, IL-6, IL-1β, MIP-1α, MCP-1, CCL5, IP-10, and IFN-β, and significantly enhance the mRNA transcription of these cytokines in RAW264.7 cells induced by R848 and CpG in a dose-dependent manner. Furthermore, JFG extract also potentiated the secretion of TNF-α, IL-6, MCP-1, and IFN-β by RAW264.7 cells stimulated with R848 and CpG. As revealed by mechanism analysis, JFG extract enhanced the phosphorylation of p38, ERK1/2, IRF3, STAT1, and STAT3 in RAW264.7 cells induced by CpG. The findings of this study indicate that JFG extract can selectively potentiate the activation of macrophages induced by R848 and CpG, which may be attributed to the promotion of the activation of MAPKs, IRF3, and STAT1/3 signaling pathways.
Tumor Necrosis Factor-alpha/metabolism* ; Interleukin-6/metabolism* ; Plant Extracts/metabolism* ; Lipopolysaccharides/pharmacology* ; Macrophages ; Cytokines/metabolism* ; RNA, Messenger/metabolism*

Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates. In comparison with genome sequences of dicot-infecting Turnip mosaic virus (TuMV) and monocot-infecting Cocksfoot streak virus (CSV), viral-derived small interfering RNAs (vsiRNAs) displayed positive correlations between AV-PTGS efficiency and G+C content (GC%). Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases. This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations, and AGO associated Arabidopsis endogenous siRNA populations, indicating that plant AGOs operated with G-preference. We further propose a hypothesis that AV-PTGS imposes selection pressure(s) on the evolution of plant viruses. This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination, suggesting that plant virus evolution to have low GC% genomes would have a unique function, which is to reduce the host AV-PTGS attack during infections.
Arabidopsis ; enzymology ; genetics ; virology ; Base Composition ; Dactylis ; enzymology ; genetics ; virology ; Genes, Plant ; Genes, Viral ; Models, Genetic ; Mustard Plant ; enzymology ; genetics ; virology ; Plant Diseases ; genetics ; virology ; Plant Proteins ; metabolism ; Plant Viruses ; genetics ; pathogenicity ; Plants ; enzymology ; genetics ; virology ; Potyvirus ; genetics ; pathogenicity ; RNA Interference ; RNA, Plant ; genetics ; RNA, Small Interfering ; chemistry ; genetics ; metabolism ; RNA, Viral ; chemistry ; genetics ; metabolism ; RNA-Induced Silencing Complex ; metabolism ; Ribonuclease III ; metabolism ; Selection, Genetic ; Substrate Specificity

With the development of high-throughput sequencing technology, circular RNAs (circRNAs) have gradually become a hotspot in the research on non-coding RNA. CircRNAs are produced by the covalent circularization of a downstream 3' splice donor and an upstream 5' splice acceptor through backsplicing, and they are pervasive in eukaryotic cells. CircRNAs used to be considered byproducts of false splicing, whereas an explosion of related studies in recent years has disproved this misconception. Compared with the rich studies of circRNAs in animals, the study of circRNAs in plants is still in its infancy. In this review, we introduced the discovery of plant circRNAs, the discovery of plant circRNAs, the circularization feature, expression specificity, conservation, and stability of plant circRNAs and expounded the identification tools, main types, and biogenesis mechanisms of circRNAs. Furthermore, we summarized the potential roles of plant circRNAs as microRNA (miRNA) sponges and translation templates and in response to biotic/abiotic stress, and briefed the degradation and localization of plant circRNAs. Finally, we discussed the challenges and proposed the future directions in the research on plant circRNAs.
Animals ; MicroRNAs/metabolism* ; Organelle Biogenesis ; Plants/metabolism* ; Protein Biosynthesis/physiology* ; RNA, Circular/metabolism* ; RNA, Plant/metabolism* ; Research/trends* ; Stress, Physiological/genetics*

The genes of short armed hammerhead ribozyme targeting against two sites on positive strand (194-196) and negative strand (89-91) of ASSVd were designed, synthesized and cloned according to the action manner of hammerhead ribozyme. The full lengths of the genes are 42 bp (RzASSVd(+)) and 40 bp (RzASSVd(-)). After transcription in vitro, the ASSVd positive and negative RNA labeled with 32P were mixed with the ribozyme transcript and incubated 3-4 h at 50 degrees C or 37 degrees C. The results were assayed on 8% PAGE (containing 8 mol/L urea) and autoradiogrammed. As predicted, the transcript of the active RzASSVd(-) could cleave the ASSVd negative strand RNA with a high activity but had no cleavage effect on the ASSVd positive strand. The transcript of the RzASSVd(+) gene could cleave the ASSVd positive strand but its cleavage activity was very low. As the same, it cannot cleave the negative strand either. On the base of the result, we construct dimmer ribozyme gene pGEMRzASSVd(+/-) containing both RzASSVd(+) and RzASSVd(-).
Cloning, Molecular ; Malus ; virology ; Plant Diseases ; virology ; RNA, Catalytic ; genetics ; metabolism ; therapeutic use ; RNA, Viral ; metabolism ; Substrate Specificity ; Transcription, Genetic ; Viroids ; metabolism

Pre-harvest sprouting of wheat is caused by a series of enzymes, in which alpha-amylase plays a key role. Thioredoxin (trx) is an important protein capable of reducing S-S to -SH. The authors transferred the anti-trxs gene into wheat ( Triticum aestivum L.) cultivar Wanmai 48 in 2000 in order to obtain a transgenic line with low activities of trx and alpha-amylase in wheat seeds to enhance their resistance to pre-harvest sprouting. In this work, a pair of specific anti-trxs primers were used in PCR test to validate the transgenic plants in T4 lines. A pair of primers of a wheat actin gene cDNA and a pair of trxs gene primers were used in the reverse transcription PCR test to measure the relative content of trx mRNA in the transgenic positive lines. The experiments of pre-harvest sprouting were carried out to test the resistance to pre-harvest sprouting. The results showed that there were 13 positive lines with the anti-trxs gene among 18 transgenic lines. In the maturity stage, the 8 relative contents of the trx mRNA in the 13 positive lines were reduced evidently (P < 0.01). The trx mRNA was correlated with the sprouting parameters significantly (r = 0.7181) . 6 lines with low trx mRNA showed stronger resistance to pre-harvest sprouting during the period from 30 days after anthesis to 10 days after maturity. Compared with non-transgenic plant (Wanmai 48, CK), the average sprouting time of these lines was postponed by 2.7 days (P < 0.01), the sprouting ratio of seeds on spikes and the spike sprouting degree were reduced by 35.5% (P < 0.01) and 47.5% (P < 0.01), respectively. However, 25 days after maturity, the sprouting capacity of the positive lines recovered gradually, and no significant differences were found between them (P > 0.05) . Thus, it can be concluded that the wheat pre-sprouting was controlled effectively in some 00T89 transgenic lines as a result of the expression of anti-trxs gene.
Genes, Plant ; Germination ; genetics ; Plant Proteins ; genetics ; metabolism ; Plants, Genetically Modified ; genetics ; growth & development ; metabolism ; RNA, Messenger ; metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds ; genetics ; growth & development ; Thioredoxins ; genetics ; metabolism ; Transformation, Genetic ; Triticum ; genetics ; growth & development ; metabolism ; alpha-Amylases ; metabolism

The preliminary role of calcineurin B-like protein-interacting protein kinases (CIPKs) in stress response is defined but the exact function of OsCIPK10 gene in rice stress response and its expression pattern yet unclear. In this study we explored the possible functions of OsCIPK10 gene by reverse genetics approaches and also revealed its expression pattern by GUS staining. From the preliminary study of this gene we presumed its function to assist plant to resist stress but over-expressed OsCIPK10 rice transgenic lines showed no significant phenotypic differences from the wild type either under high salt or low potassium conditions, however the gene knockdown plants using inverted repeat strategy presented meaningful healthy plants compared to wild type under the stress of salt. Further we checked the expression profile under high salt and low potassium conditions in wild type and found that OsCIPK10 decreases under high salt and increases on low potassium conditions. So we speculate that OsCIPK10 is actually going to function in response to high salt and low potassium stress. We also explored the expression pattern of this gene using Gus staining and found that gene expresses in all plant tissues, the only exception observed was its higher expression in the vascular tissues.
Cloning, Molecular ; Genes, Plant ; Oryza ; enzymology ; genetics ; Plant Proteins ; genetics ; metabolism ; Plants, Genetically Modified ; genetics ; metabolism ; Potassium ; pharmacology ; Protein-Serine-Threonine Kinases ; genetics ; metabolism ; RNA Interference ; RNA, Small Interfering ; genetics ; Salt-Tolerant Plants ; genetics ; Sodium Chloride ; pharmacology ; Stress, Physiological