The high quality of gene set is necessary to study the functional research of genes. Although perilla is cultivated as an oil crop and as a vegetable crop in Asian countries such as Korea, Japan, northeast China and Nepal, the reference genome is absent. To assembly perilla gene set, we sequenced the various tissues of perilla (Perilla citriodora) RNA-seq with Illumina HiSeq platform, generating 548,549,314 short reads. When de novo transcriptome assembly was performed with five samples, 86,396 and 38,413 transcripts were assembled as total and representative transcripts, respectively. Using 1,917,424 proteins at Phytozome ver. 9.1, we annotated the perilla assembled transcripts, and 66,139(76.55%) and 24,030(62.55%) transcripts showed the similarity with known plant proteins (E-value < 1e-10) as total and representative transcripts, respectively. Among the diverse molecular functions, we were interested in the regulatory components, such as transcription factor and transcription regulator. Using this data, we identified 499 transcripts annotated the putative transcription factor differentially expressed transcripts. 165 putative transcription factors were significantly expressed in perilla flower and 121 putative transcription factors in both leaf and flower. This study provides the perilla reference gene set and the understanding of the molecular regulation of transcription factor dependent on the tissue.

Rice bran has been reckoned as a potential source of edible oil contained 15-20 % of oil, in its natural state, also contains several constituents of potential significance in diet and health. Interest has focused primarily upon gamma-oryzanol, tocotrienols, and tocopherols, all of which demonstrate antioxidant properties. We analyzed the transcriptome profiles for rice grain from high and low oil content lines at the early milky stage using the Illumina sequencing method. This analysis indicated that many transcripts showed different expressions level between high and low oil content rice. The functional classification of those genes indicated their connection with various metabolic pathways, oil transport, signal transduction, transcriptional regulation, and other processes. The results obtained here will enable to understand how changes in oil concentration or availability are interpreted into adaptive responses in early milky stage of rice. Based on the functional annotation of the differentially expressed genes, the possible processes that regulate these expressed transcripts in rice grain was further analyzed. The candidate transcripts may provide genetic resources that may be useful in the improvement of oil contents of rice.

Zinc (Zn) deficiency is one of the important abiotic factors limiting rice productivity world-wide and also a widespread nutritional disorder affecting human health. Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. We analyzed the transcriptome profiles for rice grain from high zinc content and low zinc content lines at the early milky stage using the Illumina Sequencing method. The analysis results for the sequencing data indicated that many transcripts showed different expressions between high zinc content and low zinc content in early milky stage of rice and RT-qPCR analyses confirmed the expression patterns of selected transcripts. Functional analysis of the differentially expressed transcripts indicated that genes have functional annotation and their functions are mainly involved in oxidation-reduction, metabolic, transport , transcript regulation, defense response and photosynthetic processes. Based on the functional annotation of the differentially expressed genes, the possible process that regulates these differentially expressed transcripts in rice grain responding to Zinc at the early milky stage was further analyzed. The functional classification of those genes indicated their connection with various metabolic pathways, Zinc transport, signal transduction, transcriptional regulation, and other processes related to growth and development in early milky stage of rice. Using Illumina sequencing technology, the differences between the transcriptomes of high zinc content and low zinc content lines the early milky stage was described here for the first time. The candidate transcripts may provide genetic resources that may be useful in the improvement of Zinc concentration of rice. The model proposed here is based on differences in expression and transcription between two rice lines. In addition, the model may support future studies on the molecular mechanisms underlying plant responses to Zinc.

Water-deficiency is one of the most serious challenges which restrict crop production. Root is the primary tissues exposed to water limitation in soil. Although a number of transcriptome data under water limitation have been produced in rice, but most of them have analyzed the effect of leaf or shoot. Thus, understanding of relating molecular mechanism is still limited. To get global view of the effect on water deficiency in rice root, we carried out RNA-Seq experiment. To do this, we compared the RNA-Seq transcriptome data of 3 day samples under water deficiency with those of unstressed rice roots with unstressed control. As a result, we identified 1,098 genes upregulated in water stress condition for 3 days. Gene ontology (GO) enrichment analysis revealed that 18 GO terms are overrepresented. Of them, valyl-tRNA aminoacylation, transcription from RNA polymerase II promoter, glycine catabolic process, and L-phenylalanine catabolic process are more significant, indicating that transcription of new transcripts, control of translation fidelity, and reuse of primary and secondary metabolites can be activated during water stress.

Bulb onion (Allium cepa) is one of the second most widely cultivated and consumed vegetable crops in the world. During winter where the temperature can be as low, plant could get cold injury and limit the production of bulb onion. However, the genomic resources available for bulb onion are still very limited. To date, no studies about heritably durable cold and freezing tolerance were carried out in bulb onion genotypes using high-throughput sequencing technology was applied. We sequenced cold (2°C) freezing (-5 and -15°C) treated and control (25°C) samples of contrasting genotypes of A. cepa lines and obtained 4,52,194,370 total high quality reads. After de novo assembly reads were assembled into 54,047 genes finally generated with an average length of 1,331 bp. Based on the similarity search aligning all genes with known public non-redundant (NR) database, including Swiss-prot, KEGG and COG. Differentially expressed genes (DEGs) were investigated using FPKM method. Overall, 92,862 genes were differentially regulated in all libraries were identified. Additionally, increase our understanding of the DEGs, we performed GO and KEGG pathway enrichment analyses. Based on FDR<=0.01 value in cold freezing tolerant line candidate genes were selected and discussed. Finally 25 candidate genes were examined using qRT-PCR were differentially regulated and known to be associated with cold and freezing stresses. Moreover, in silico prediction of putative molecular marker 4,437 SSRs and 6,076 SNPs. Our study is the first to provide the transcriptome sequence resource of Allium spp., for cold and freezing stress. We identified large set of genes to determine its DEGs profile under cold and freezing condition using two different genotypes. These data provides a valuable resource of genetic and genomic studies of Allium spp.

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong (Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95 Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST search against the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotated and classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as well as in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembrane transporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgor pressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantly detected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefolius accession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuable resource for understanding the structure and function of the ginseng transcriptomes.

Melatonin has several known physiological functions, the main one being synchronization of daily and seasonal rhythms. In addition, melatonin has been reported to influence reproduction and behavioral rhythms with varying results depending on the species. To date, it remains unknown how this rhythm in locomotor activity is controlled endogenously, although there must be coordination of chemical and molecular drivers. However, the species is poorly characterized at molecular level with little sequence information available in public databases. The aim of study was to clarify involvement of endogenous melatonin rhythms and locomotor activity in day-night activity of the eel, Anguilla japonica which is an economically important but endangered species. The levels during daytime (zeitgeber time; ZT 6) were significantly (P<0.05) lower than those during nighttime (ZT 18). A similar pattern was persisted under DD conditions, whereas it disappeared under LL conditions and ocular melatonin levels remained low. Therefore, it is likely that ocular melatonin levels of the nocturnal eel reared under LD and DD conditions fluctuate in a daily/circadian manner and night-related physiological processes are dependent on eel locomotor activities which is a nocturnal species. We found that similar number of genes were differentially expressed between day (ZT6) and nighttime (ZT18), suggesting that during the nighttime also important in differential gene expression with daytime. This work also provides essential information for further studies investigating the molecular basis of daily/circadian system in this species.

Legume and rhizobia symbiosis plays an important role in conversion of atmospheric dinitrogen to ammonia. On a global scale, this interaction represents a key entry point for reduced nitrogen into the biosphere, and as a consequence this symbiosis is important in both natural and agricultural systems. Symbiotic development of nodule organ is triggered by chito-oligosaccharide signals (Nod factors) from the bacterium which are perceived by the legume root. Understanding the molecular and cellular processes that underlie Nod factor perception is one focus of legume biology. Although forward genetics has proved to be an important tool to identify key players in Nod factor perception, we still know relatively little regarding the functional networks of genes and proteins that connect the earliest steps of Nod factor perception to immediate downstream outcomes. To elucidate genes and proteins that link Nod factor perception to cellular and physiological responses we are taking a discovery-based strategy based on whole transcriptome profiling using RNA-seq analysis in the roots of Medicago truncatula in response to Sinorhizobium meliloti. Functional characterization of a number of candidate genes is currently in progress to further examine their role in nodulation such as generating transgenic plants

Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in Brassica rapa. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiffu. Additionally, homo- and hetero-dimerization test between selected bZIP proteins indicated the Bra020735 is a key regulator in cold response. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. These results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response.

Platycodon grandiflorum, which is the only species in the genus Platycodon of the family Campanulaceae, is an herbaceous flowering perennial. P. grandiflorum is generally known as bellflower or balloon flower indicating its ornamental uses. It has also been traditionally used as a medicinal crop in East Asia, which is widely employed as an antiphlogistic, antitussive, and expectorant. However, marker-assisted selection and molecular breeding in P. grandiflorum has lagged behind other plants such as pepper and tomato because of the lack of genetic information and effective molecular markers. Transcriptome sequencing provides an effective way to obtain large amount of sequence data when there is no available genome sequence. In this study, we performed a transcriptome analysis in platycodons, which has not been attempted previously. We analyzed simple sequence repeats (SSRs) using RNA-seq data. Di-nucleotide motifs were the most abundant repeats (39% ~ 40%) followed by mono- (26% ~ 32%), tri- (25% ~ 31%), tetra- (1.5% ~ 1.9 %), penta- (0.3% ~ 1%) in three platycodon accessions. Based on the SNP information obtained from RNA-seq analysis, we developed 12 PCR-based markers in Platycodon. The number of alleles ranged from two to seven with the average PIC value of 0.373. These 12 markers were applied to 21 platycodon accessions and a phylogenetic tree was constructed. The markers developed in this study could be introduced in molecular breeding program of platycodons. The SSR information obtained from RNA-seq analysis could be further utilized for developing genic-SSR markers in platycodons. Since platycodon is considered as an orphan crop, which has not been actively deployed for genetic study, the sequence information obtained from this study will contribute to further genetic improvements, genomic information and gene discovery in platycodon

Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae), is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54 Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 ‘isogroups’ and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variants analysis identified a total of 9,701 and 12,741 potential SNPs for both cultivars, which eventually resulted in 1,025 and 1,059 genotype specific SNPs, for both the varieties, respectively. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Cabbage (Brassica oleracea) is one of the most important vegetable crops in the world. Yet, its sensitivity to cold stress, especially at the seedling stage, could limit the production. Until now, only, few studies about heritably durable cold tolerance were carried out in cabbage. Hence this study was done to characterize the transcriptome profiles of two cabbage genotypes with contrasting responses to cold stress using Illumina Hiseq short read (paired-end) sequencing technology. MicroRNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. Thisstudy,wesoughttoprovideamorecomprehensivepredictionofB. oleracea cold responsive miRNAs based on high through put sequencing using two contrasting genotypes. The raw sequences were processed for removal of poor-quality and adaptor sequences. Then, the high quality unigenes (58,094) reads were applied for length filtering. Then, unigenes reads were used in a BLASTN search against of Rfam database and known miRNA database (miRBase 18.0) to removal of non-coding RNA’s and identifies conserved miRNA’s in B. oleracea. Further, novel reads were searched against B. oleracea genome. Their flanking sequences in the genome were used to predict their secondary structures, target prediction, and functional analysis. This is first report to identify novel miRNAs for cold stress through high throughput techniques. Our findings will provide an overview of potential miRNAs involved in cold stress, which may provide important clues on the function of miRNAs in from B. oleracea and other closely related Brassica species.

A sugary mutant with low total starch and high sugar content was compared with its wild type Sindongjin for grain-filling caryopses. In the present study, developing seeds of Sindongjin and sugary mutant from the 11th day after flowering (DAF) were subjected to RNA sequencing (RNA-Seq). A total of 30,385 and 32,243 genes were identified in Sindongjin and sugary mutant. Transcriptomic changes analysis showed that 7,713 differentially expressed genes (DEGs) (log2 Fold change ≥1, false discovery rate (FDR) ≤ 0.001) were identified based on our RNA-Seq data, with 7,239 genes up-regulated and 474 down-regulated in the sugary mutant. A large number of DEGs were found related to metabolic, biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction and starch/sugar metabolism. Detailed pathway dissection and quantitative real time PCR (qRT-PCR) demonstrated that most genes involved in sucrose to starch synthesis are up-regulated, whereas the expression of the ADP-glucose pyrophosphorylase small subunit (OsAGPS2b) catalyzing the first committed step of starch biosynthesis was specifically inhibited during the grain-filling stage in sugary mutant. Further analysis suggested that the OsAGPS2b is a considerable candidate gene responsible for phenotype of sugary mutant.

Legume and rhizobia symbiosis plays an important role in conversion of atmospheric dinitrogen to ammonia. On a global scale, thin interaction represent a key entry point for reduced nitrogen into the biosphere, and as a consequence this symbiosis in important in both natural and agricultural systems. Symbiotic development of nodule organ in triggered by chito-oligosaccharide signals(Nod factors) from the bacterium which are perceived by the legume root. Understanding the molecular and cellular processes that underlie Nod factor perception is one focus of legume biology. Although forward genetics has proved to be an important tool to elucidate key players in Nod factor perception, we still know relatively little regarding the functional networks of genes and proteins that connect the earliest steps of Nod factor perception to immediate downstream outcomes. To identify genes and proteins that link Nod factor perception to cellular and physiological responses we are taking a discovery-based strategy on large-scale transcriptome profiling using RNA sequencing in the roots of Medicago truncatula in response to Sinorhizobium meliloti. Functional characterization of a number of candidate genes is currently in progress to further examine their role in nodulation.

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying developmental seeds. In the study, the seeds of 10th day after flowering (DAF) were conducted RNA-Seq of the variety Shindongjin and Sugary mutant using RNA-seq technique. Approximately 202 and 214 million high-quality paired-end reads (101-bp in size) were generated in Shindongjin and Sugary mutant, respectively. Comprehensive analysis on the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism of starch biosynthesis in seeds. Quantitative real-time PCR was also used to validate the expression profiles of 28 rice genes encoding six classes of enzymes, viz., ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme at different developmental grain- filling stages (DAF 1-14) between Shindongjin and Sugary mutant. The results showed that the expression of most of starch synthesis genes were up-regulated except the cytosolic AGPase small subunit2b (AGPS2b), which sharply decreased at grain-filling stages in Sugary mutant. These results will expand our understanding of the complex molecular and cellular events in rice grain-filling stages and provide a fundamental understanding of future studies on developmental endosperm in rice and other cereal crops.