Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting digestion, and as a cholagogic in China. However, there is confusion about the drug's botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs. Comparative sequencing of the 18S rRNA gene in nuclear ribosomal DNA (rDNA) and trnK gene in chloroplast DNA (cpDNA) was carried out in order to examine interspecies phylogeny and to identify ultimately Curcuma species. A total of a hundred of accessions of eighteen species were analyzed. This resulted in an aligned matrix of 1810 bp for 18S rDNA and 2 800 bp for trnK. 18S rDNA sequence divergence within the ingroup ranged from 0-0.05%, trnK ranged from 0-0.19%. One base transversion-substituted site (from cytosine to thymine) was observed from the upstream of 18S rDNA at nucleotide position 234 in C. kwangsiensis and Japanese population of C. zedoaria which have separated genetic distance to other Curcuma taxa. Two noncoding regions embedded in trnK intron showed higher variability, including nucleotide substitutions, repeat insertion and deletions. Based on consensus of relationship, eighteen major lineages within Curcuma are recognized at the species level. The results suggest that Curcuma is monophyletic with 100% bootstrap support and sister to the genera Hedychium and Zingiber. The trnK sequences showed considerable variations between Curcuma species and thus were revealed as a promising candidate for barcoding of Curcuma species, which provide valuable characters for inferring relationship within species but are insufficient to resolve relationships among closely related taxa.
China ; Curcuma ; classification ; genetics ; DNA Mutational Analysis ; DNA, Chloroplast ; genetics ; DNA, Plant ; genetics ; Introns ; Japan ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Plants, Medicinal ; classification ; genetics ; Plastids ; genetics ; RNA, Ribosomal, 18S ; genetics ; Sequence Analysis, DNA

The purpose of this study was to explore the expression pattern of miRNA in the process of embryo dormancy and provide a reference for the mechanism of regulating seed dormancy and germination by miRNA. We used high-throughput sequencing technology, bioinformatics analysis and real-time fluorescent quantitative PCR(qPCR) technology to sequence, screen and identify miRNAs of dormant and dormant embryos. The results showed that there were 23 811 977, 24 276 695, 20 611 876 and 20 601 811 unique sequences in the four sample libraries during the period of dormancy and dormancy release. MiRNAs are mainly distributed between 21 and 24 nt, among which the length of 24 nt occurred most frequently. A total of 31 known miRNAs were identified, belonging to 13 different families. 93 new miRNAs were predicted by bioinformatics software. Ten miRNAs(mir156 a-5 p, mir160 a-5 p, mir160 h-1, mir169 a-5 p, mir157 d, mir159 a-1, mir395-3, mir156 f-5 p, mir156-2 and mir171 a-3 p) were screened out. In this study, 10 miRNAs related to seed dormancy release were identified. The target genes mainly involved carbohydrate metabolism, plant hormone signal transduction, cell division and growth. The results of qRT-PCR showed that the sequencing results were consistent with the actual results.
Gene Expression Regulation, Plant ; Humans ; Liliaceae ; MicroRNAs ; Plant Dormancy ; RNA, Plant ; Seeds

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 extract RNA from Pinellia ternata and lay a foundation for studying the formation mechanism of P. ternata.

METHODBy modifying the method recommended by Guanidinium for extracting total RNA from plant tissues rich in phenolic and polysaccharidic compounds, a simple and convenient method for extraction of total RNA from the tubers, stems and leaves of P. ternate containing abundant polyphenols and polysaccharides was established. High concentrated p-mercaptoethanol was added in the RNA extracted buffer to remove polyphenols, phenol and chloroform were used to eliminate proteins, and isopropanol and sodium acetate were used to precipitate polysaccharides.

RESULTThe A260/A230 value of RNA extracted with improved method were all over 2.0 and the values of A260/A280 were between 1.7 and 2.0. The electrophoresis bands were cleared on agarosegel and integrity of RNA was good.

CONCLUSIONThe results showed that RNA obtained from the tubers, stems and leaves of P. ternate with this method had high purity and quality and could be used in molecular biological research, as DDRT-PCR and reverse Northern blotting analysis directly. This method is simple, economic, stable performance, and has a good repeatability as well as is suitable for extracting total RNA of medicinal plants with high concentrations of phenolics and polysaccharides.

Blotting, Northern ; Pinellia ; genetics ; Plant Leaves ; genetics ; Plant Stems ; genetics ; Plant Tubers ; genetics ; Polymerase Chain Reaction ; RNA, Plant ; isolation & purification

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*

The 21-24 nucleotides small RNA that generated from double strands RNA can trigger two types of epigenetic gene silencing in plants. One is Post-Transcriptional Gene Silencing (PTGS), characterized by cleavage of homologous mRNA in cytoplasm. Transcriptional Gene Silencing (TGS) is another one, in which transcription inhibition is obtained through small RNA-directed DNA methylation of homologous promoter region. Here we summarized the relationship and differences between PTGS and TGS, the current achievement in the study of RNA silencing spreading, as well as the discrepancy of exogenous and endogenous gene silencing, and discussed the underlying reasons in the end.
DNA Methylation ; genetics ; Epigenesis, Genetic ; physiology ; Genome, Plant ; genetics ; Plant Immunity ; genetics ; RNA Interference ; RNA, Plant ; genetics ; RNA, Small Interfering ; genetics ; Transcription, Genetic ; genetics

OBJECTIVETo establish a method for isolation of the total RNA from Fagopyrum cymosum callus.

METHODThe improved method combining that of CTAB extraction with the LiCl precipitation was used to isolate the total RNA from the four F. cymosum callus. The quality of the RNA was detected by UV spectrophotometric analysis, 0.8% non-denaturing agarose gel electrophoresis and RNA reverse transcription.

RESULTThe bands of 28S and 18S could be seen clearly by agarose gel electrophoresis, and the value of A260/A280 was between 1.9 and 2.0. The cDNA which was reverse-transcribed by the total RNA showed a wide length rage of 500 bp-5 kb.

CONCLUSIONThe RNA extracted by this method meets the requirement of reverse transcription-polymerase chain reaction (RT-PCR), construction of cDNA libraries, et al. This improved method can be used to isolate the total RNA from F. cymosum callus with the advantage of simpleness, efficiency and low cost.

Fagopyrum ; genetics ; growth & development ; RNA, Plant ; analysis ; isolation & purification

Schisandra sphenanthera is dioecious and only the fruits of female plants can be used as medicine and food. It is of great significance for the cultivation and production of S. sphenanthera to explore the differences between male and female plants at the non-flowering stage and develop the identification markers at non-flowering or seedling stage. In this study, the transcriptome of male and female leaves of S. sphenanthera at the non-flowering stage was sequenced by Illumina high-throughput sequencing technology and analyzed based on bioinformatics. A total of 236 682 transcripts were assembled by Trinity software and 171 588 were chosen as unigenes. Finally, 1 525 differentially expressed genes(DEGs) were identified, with 458 up-regulated and 1 067 down-regulated in female lea-ves. The down-regulated genes mainly involve photosynthesis, photosynthesis-antenna protein, carbon fixation in photosynthetic or-ganisms, and other pathways. Real-time quantitative PCR(qPCR) identified two genes between male and female leaves and one of them was a HVA22-like gene related to floral organ development and abscisic acid(ABA). Enzyme linked immunosorbent assay(ELISA) was applied to determine the content of ABA, auxin, gibberellin, and zeatin riboside(ZR) in leaves of S. sphenanthera. The results showed that the content of ABA and ZR in male leaves was significantly higher than that in female leaves. The involvement of down-regulated genes in female leaves in the photosynthesis pathway and the significant differences in the content of endogenous hormones between male and female leaves lay a scientific basis for analyzing the factors affecting sex differentiation of S. sphenanthera.
Abscisic Acid ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Plant Leaves/genetics* ; RNA-Seq ; Schisandra ; 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

The NAC family is an important transcription factor which regulate plant growth and development， signal transduction， and stress response.In this study， the protein identification， subfamily classification， the determination of physical and chemical properties， protein structure， and expression pattern of NAC family were performed using bioinformatic methods based on the RNA-seq data of ginger. The results showed that a total of 72 NAC transcription factors were identified in 271.1 Mb total nucleotides， and they could be clustered into 13 subfamilies according to the phylogenetic tree.The physical and chemical properties， structure analysis revealed that the amino acid number and isoelectric point were different among 13 NAC subfamilies; the secondary structure of NACs transcription factors mainly consist of random coil， and the tertiary structure is similar.In addition，the expression patterns of genes under different soil moisture and Ralstonia solanacearum infection showed that 23 NACs were differentially expressed， which were mainly distributed in Ⅷ，Ⅶ， and ⅩⅤ subfamilies related to plant senescence， hormone metabolism and cell wall metabolism.The results provide some valuable information for the research and development of NAC transcription factors in ginger.
Gene Expression Regulation, Plant ; Ginger ; genetics ; Multigene Family ; Phylogeny ; Plant Proteins ; genetics ; Protein Structure, Tertiary ; RNA, Plant ; genetics ; Sequence Analysis, RNA ; Transcription Factors ; genetics