Because of the physiological and immunological similarities between pigs and humans, porcine embryonic stem cells (ESCs) have been identified as important candidates in preliminary studies on human disease. A comparative understanding of pig ESCs with the human is required to achieve these goals. To gain insights into pig stem cells, the transcriptome of pig ES-like cells were compared with pig preimplantation embryos and human/mouse pluripotent stem cells by RNA-seq analysis. As a result, pig stem cells were more similar to late epiblasts of pig preimplantation embryos than early ICM as revealed by transcriptome analysis, suggesting that pig stem cells are in a developmentally primed state. Moreover, the physiological and biological functions of pig ESCs were more similar to those of human PSCs than to those of mouse PSCs, as determined by direct differentiation and GO/KEGG term analysis. Overall, our data indicate that pig ESCs are in a primed pluripotent state resembling human PSCs. Our findings will facilitate both the development of large animal models for human stem cell therapy and the generation of pluripotent stem cells from other domestic animals for agricultural use. This work was supported by the Korea Institute of Planning and Evaluation for Technology in food, agriculture, forestry, and fisheries (IPET) through the Development of High Value-Added Food Technology Program funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA; 118042-03-1-HD020), and partially supported by the grants from the Agenda Program of Rural Development Administration, Republic of Korea (No. PJ01362402)

Rapid identification of pest species found under quarantine is an important factor in preventing an economic loss of agricultural commodities. In this study, we analyzed RNA-Seq of the larvae of C. sasakii, G. molesta and G. dimorpha, which are serious pests in several fruits in Korea and are difficult to discriminate by species in their larval stage because of lack of a morphological character. To select immunological diagnostic markers, discriminating the larvae of C. sasakii from the G. molesta and G. dimorpha, RNA-Seq was performed for the larvae of the three insects. The 454 pyrosequencing generated 3,058-4,686 contigs for each three pest species, which assembled into 2,584-3,970 isotigs with average lengths of 829-1,244 bp. Functional annotation of the sequencing results generated 774 orthologs for the three pest species, and 12 isotigs were finally registered as candidate markers for species discrimination through bioinformatical screening, literature search, and gene expression study. The selected candidates include serine proteases, serpins, 27 kDa glycoprotein and storage protein with a constitutive gene expression in their larvae, pupae and adult stage.

Background : Narcissus tazetta (N. tazetta), belonging to the Amaryllidaceae family, is a bulbous plant distributed in Korea, China, and Japan. Amaryllidaceae family plants contained galantamine exhibiting dominant and selective acetylcholinesterase inhibition. In this study, transcriptome analysis of N. tazetta was carried out. Methods and Results : The results of studies conducted in duplicate revealed the presence of a total of 305,228 and 370,567 unigenes, acquired from 69,605,788 and 59,770,506 raw reads, respectively, after trimming the raw reads using CutAdapt, assembly using Trinity package, and clustering using CD-Hit-EST. The resulting unigenes were annotated based on the NCBI Non-redundant protein database, as N. tazetta is genetically closer to Phoenix dactylifera and Elaeis guineensis. The unigenes of N. tazetta were clustered into three major categories: biological processes, cellular components, and molecular functions, with 51 functional sections. A large number of unigenes (11,371 and 15,535 from replicates 1 and 2, respectively) were categorized in the biological process cluster, followed by the cellular component cluster, and the molecular function cluster. With respect to the biological process category, the unigenes were assigned to 23 functional sections. The majority of unigenes were involved in cellular processes. Among the unigenes clustered as the cellular component with 14 sections, most genes were associated with the cell and cell parts. Furthermore, 156,584 and 201,353 unigenes, respectively, matched the molecular function cluster with 14 sections, of which most unigenes were related to metabolic process and cellular process. Conclusion : This study provides functional information of N. tazetta and highlights the use of the Illumina platform for transcriptome research.

Background : Lycoris radiata (L. radiata), which belongs to Amaryllidaceae family, is native to Northeast Asia including Korea, Japan, and China. It is known for its high ornamental and medicinal values. Extensive research has been conducted in a several fields, including molecular biology, morphology, pharmacology, physiology, palynology, and chromosomal biology. The plant is notable for its various biological activities, including anti-cancer, anti-malarial, anti-microbial, reduction in blood pressure, anti-inflammatory, cytotoxicity, and neuroprotective effects. Methods and Results : The results of studies conducted in duplicate revealed the presence of a total of 325,609 and 404,019 unigenes, acquired from 9,913,869,968 and 10,162,653,038 raw reads, respectively, after trimming the raw reads using CutAdapt, assembly using Trinity package, and clustering using CD-Hit-EST. The resulting unigenes were annotated based on the NCBI Non-redundant protein database, as L. radiata is genetically closer to Elaeis guineensis and Phoenix dactylifera. The unigenes of L. radiata were clustered into three major categories: biological processes, cellular components, and molecular functions, with 51 functional sections. A large number of unigenes (203,157 and 224,813 from replicates 1 and 2, respectively) were categorized in the biological process cluster, followed by the cellular component cluster, and the molecular function cluster. With respect to the biological process category, the unigenes were assigned to 23 functional sections. The majority of unigenes were involved in cellular processes. Among the unigenes clustered as the cellular component with 14 sections, most genes were associated with the cell and cell parts. Furthermore, 78,017 and 88,817 unigenes, respectively, matched the molecular function cluster with 14 sections, of which most unigenes were related to binding and catalytic activity. Conclusion : This study provides functional information of L. radiata and highlights the use of the Illumina platform for transcriptome research.

Background : Several members of the genus Clausena have a great potential as a candidate for the identification of new drug lead molecules, but lack of their genomic information can be a hindrance for the verification of the genetic background for future use. To broaden and delve into the genomic features of this genus, Clausena excavata, an important medicinal plant in many Asian countries, was used for RNA-seq analysis. Methods and Results : A ten ㎍ of the total RNA was used for mRNA isolation using oligo-dT beads and random sheared mRNAs were used to prepare a cDNA library for a illumina hiseq 2500 analysis. In total, 17,580,456 trimmed clear reads from the illumina hiseq 2500 were used for de novo assembly using three assemblers, CLC genomics workbench, velvet-oases, and Trinity. A total of 16,638 non-redundant unigenes with an average length of 755 bp were generated by the assembly. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2,305 genes in the cellular component, 5,577 in the biological processes, and 8,056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4,374 genes. Among annotated genes, 3,006 were mapped to 123 metabolic pathways by KEGG metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism. Conclusion : In the present study, genomic resources of the genus Clausena were enriched through RNA-seq and SSR markers, which will serve as valuable resources for genomic/genetic studies of the genus Clausena and close relatives.

Background : Although Oplopana elatus is a valuable medicinal plant that, like ginseng, recommends itself as source of herbal preparations, little molecular information on this plant is available. Therefore, to analyze the terpenoid biosynthetic pathway in O. elatus, we employed an RNA-seq approach. Methods and Results : To generate a transcriptome library of O. elatus, total RNA was extracted from different tissues, including leaves, stem, and root. A pooled RNA sample was prepared by combining equivalent RNA from different tissues. Using pair-end read with the Illumina platform, a total of 78,646,554 raw sequencing reads were generated. After data cleaning, approximately 77 million high-quality reads were obtained with 98% G20 (base quality of greater than 20). The high-quality reads were assembled into 208,959 unigenes with an average length of 1,073 bp and an N50 of 1,768 bp. Consistent with our prediction, which was based on the KEGG pathway assignment, we found 122 unigenes encoding 47 putative enzymes involved in the biosynthesis of terpenoid and triterpenoid saponins in the O. elatus transcriptome library. Conclusion : The transcriptome dataset generated in this study will serve as a valuable resource for accelerating genomic and functional genomic research in O. elatus and in the family Araliaceae.

Platycodon grandiflorum A. is a perennial plant belongs to Campanulaceae family. This plant has been used herbal medicine ingredient in East Asia. Because of the high saponin content, it is an economically important medicinal plant in Korea. It has been reported that saponins of P. grandiflorum were mainly synthesized in root tissues. The studies about root growth of the plant were few. Expansin is an important protein playing a role in root growth of plants, and is known as a nonenzymatic protein. Expansins are novel plant cell wall loosening proteins leading to turgor-driven cell extension. Expansin encoding genes exist in multigene family, and there are more than 30 genes in Arabidopsis thaliana. and more than 50 genes in Oryaza sativa. Therefore, identification of the genes was difficult in P. grandiflorum because of the lack of genome sequence. Recently, the development of next generation sequencing (NGS) technologies make it possible to obtain the target genes sequences rapidly and precisely. In this study, to identify the expansin encoding genes in P. grandiflorum, we used RNA-seq analysis with Illumina HiSeq platform. We analyzed whole transcriptome of P. grandiflorum through the RNA-seq analysis based on next generation seuqencing. CLC Genomics Workbench software (Clc Bio inc.) was used for assembly. We assembled 122,663 contigs and search 123 contigs were identified from the search using 61 expansin gene

Pre-harvest sprouting (PHS) is the precocious germination condition of grains while the spike is still in the mother plant. Because PHS in wheat drastically reduced the quality and economic value of wheat grain, the improving PHS wheat is one of the most important breeding goal in Korean wheat breeding program In this study, we evaluated PHS and germination index (GI) in 33 Korean wheat cultivars, and performed transcriptome analysis between Keumkang (susceptible) and Woori (tolerance). A total of 33 Korean wheat cultivars were used for PHS (28 cultivars) and GI assessment in greenhouse. The DAF (Day After Fertilization) 35 of keumkang and Woori spikes were harvested to perform transcriptome analysis using RNA-sequencing. Each transcriptome was compared with PHS or ABA treated DAF 35 Keumkang and Woori spikes. The PHS in 28 Korean cultivars and GI in 33 cultivars were ranged from 1.33% to 87.44% and from 0.01% to 2.41%, respectively. Woori was demonstrated the second lowest PHS and the lowest GI, however, Keumkang was 23th of 28 cultivars in PHS and 13th of 33 cultivars in GI analysis. Six cDNA library from the DAF 35 of Keumkang and Woori wheat grain, PHS treated DAF 35 of Keumkang and Woori, and ABA treated DAF 35 of Keumkang and Woori were constructed and sequenced. A total of 53.37 Gb of high-quality reads were obtained using HiSeq 2500. The average mapping rate of assembled transcripts were 88.98%. The differentially expressed genes (DEG) revealed total 332 DEG (105 annotated) were upregulated in DAF 35 Woori library, total 5694 DEG (4623 annotated) were upregulated in PHS treated DAF 35 Keumkang library in comparison with DAF 35 Keumkang library. A total of 86 DEG (51 annotated) were upregulated in PHS treated DAF 35 Woori library in comparison with PHS treated DAF 35 Keumkang library. The Gene ontology and further analysis will be discussed.

Platycodon grandiflorum is a herbal flowering perennial plant belongs to Campanulaceae family. The saponins derived from P. grandiflorum were termed platycosides and platycodin D, which is the most abundant saponin in the plant and pharmacologically active component, was intensively studied. Platycodin D is synthesized from triterpenoids by several enzymes including cytochrome P450. Cytochrome P450 is known to exist in superfamily in plant kingdom and essential roles in saponin biosynthetic pathway by hydroxylation or oxidation of triterpene skeletons. However, the key genes of P450 involved in biosynthesis of saponin was not identified because of its low conservation rate in amino acid sequence level among plant species and gene superfamilies. Recently, next generation sequencing (NGS) technology is rapidly developed as a method to discover target genes. In this study, we tried to identify P450 genes involved in saponin biosynthetic pathway from the various tissues of P. grandiflorum using RNA-seq analysis. The sequencing was performed using Illumina Hi-Seq platform after cDNA library preparation. The produced reads were assembled using CLC Genomics Workbench software (CLC Bio, Inc.). We obteined 122,663 contigs and found out 191 putative P450 genes. The phylogenetic relationship was analyzed and putative genes related to platicoside biosysthesis were selected and cloned for further analysis.

Platycodon grandiflorum is a species of herbaceous flowering perennial plant of the family Campanulaceae. The major ingredients are platycosides, terpenoid saponins. It contains 1-4 % of the dry weight and there are about 20 types of platycosides. Among them, platycodin D have various pharmacological effects on cough and cold. Platycosides are synthesized from oleanane by mevalonic acid pathway and cytochrome P450s and UGTs are important enzymes in the saponin biosynthesis. UGT is glucose transfer enzyme and act on the final step of the secondary metabolite biosynthesis. In this study, we tried to identify UGT genes involved in saponin biosynthetic pathway from the various tissues of P. grandiflorum and non germinated seeds using RNA-seq analysis. The sequencing was performed using Illumina Hi-Seq platform after cDNA library preparation. The produced reads were assembled using CLC Genomics Workbench software (CLC Bio, Inc.). We obtained 122,663 contigs and found 137 putative UGT genes. The phylogenetic relationship was analyzed and putative genes related to platicoside biosysthesis were selected and cloned for further analysis.

In Brassica as matter of seedling manner, they have the bilocular ovary and 20~28 seeds per silique after fertilization. Rarely some of B. juncea and yellow sarson (Brassica rapa ssp, tricolaris) have multilocular ovary. In this stdudy, the LP8 (YS-033, CGN06835) is shown tetralocular ovary as well as high seed yields. As microscope study for the different size of immature bud sections and we have known the floral meristem with already four locules in immature buds less size than 1mm of LP8. To identify of determining of tetralocular ovary formation, RNA-seq was carried out on the isolated RNA from less than 1mm and from 1mm of bud size respectively. By contrast tetralocular ovay and bilocular ovary, Chiifu is used. A total of 994 differentially expressed genes(DEGs) are detected in only LP8. Among the DEGs, we identify 18 DEGs in only immature buds of less size than 1mm. The expression patterns of 18 DEGs are validated by real time quantitative PCR and these genes are cloned and the sequence analyzed. At present, 12 candidated gene are analyzed by sequencing and there are detected by large fragment insertion as well as SNPs in sequence comparison to Chiifu. We will perform the genetic transformation of these DEG genes in Arabidopsis for relation between genes and tetralocular ovary. Our results will be helpful in understanding for mechanisms of tetraovular ovary in Brassica rapa.

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.

The advent of Next Generation Sequencing (NGS) technology has changed the research paradigm and become an essential tool for recent biological and medical study. In today’s market, there are several sequencing platforms which have specific sequencing principle, and the result of each sequencing platform has different characteristics among them. Hence, each sequencing method became more specialized for specific research purpose, and researchers who consider NGS analysis have to understand the very basic characteristics of each NGS platform. NGS is used in various studies and they are usually classified into 5 categories (Re-sequencing, RNA-seq, de novo assembly, Metagenomics and Epigenomics) of analysis. In this session, we will introduce the characteristics of sequencing platforms and examples of recent research on each of the 5 analysis categories. In addition, we will talk about the benefit of NGS study compared to the traditional study and how these NGS technologies can be applied in developmental biology research.

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

The newly developed varieties, Jayoung (violet flesh color) and Hongyoung (red flesh color) that harboring various anthocyanins and flavonoids in flesh colored potato are highly increase their interesting not only for food but also functional characteristics such as anti-inflammatory effects. Up to date, most of the molecular markers developed in potato are linked to disease resistance including late blight and PVY, nematode. A few markers linked to economically important functional materials such as anthocyanin biosynthesis are published. With the low cost and high throughput of NGS (Next Generation Sequencing) technology, numerous molecular markers are highly increased in may crops. Among the molecular markers, SNPs (Single nucleotide Polymorphisms) are most useful markers owing to their large numbers in inter and intra varieties in potato. Here we reported SNPs discovery from transcriptome sequencing data acquired from colored flesh potato cultivars, Jayoung and Hongyoung with white flesh color Atlantic. Total RNA was isolated from shoot in tuber after breaking dormancy about 2cm length. Short read sequence data were obtained form Illumina Hiseq2000 and the raw dat set were trimmed with Q socore over 20. Sequencing data were align to reference genome (Solanum tuberosum v4.03, http://potatogeomics.plantbiolgy.msu.edu). About 70% of sequence read were mapped int to reference genome. 139,050, 140,976 and 146,429 total SNPs were discovered in Hongyoung, Jayoung and Atlantic, respectively. All SNPs are mapped into the psedomolecules in reference genome by chromosome. SNPs are also analyzed with homozygous and heterozygous SNPs and genic and intergenic region. SNPs are compared with Potato Infinium 8K Chip data. SNPs found in candidate genes of anthocyanin biosynthesis were discovered. These SNPs information of flesh colored potato will be further analyzed for the allele mining for anthocyanin syhthesis and control region