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Kim S.,Seoul National University | Park M.,Seoul National University | Yeom S.-I.,Seoul National University | Kim Y.-M.,Seoul National University | And 68 more authors.
Nature Genetics | Year: 2014

Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species. © 2014 Nature America, Inc. © 2014 Nature America, Inc.


Shin G.-H.,Insilicogen Inc. | Shin G.-H.,TU Berlin | Veen M.,Focus Ingredients GmbH | Stahl U.,TU Berlin | And 2 more authors.
Yeast | Year: 2012

Saccharomyces cerevisiae strains with deregulated sterol and fatty acid biosynthesis pathways were analysed for sterol and fatty acid content and mRNA profiles, with the aim of identifying interactions between lipid biosynthesis pathways. Acetyl CoA carboxylase ACC1 and fatty acid synthases FAS1/FAS2 were overexpressed in wild-type and squalene-overproducing strains. ACC1 overexpression led to decreased fatty acid content in the squalene-overproducing strain (factor of 0.7), while sterols and squalene were increased (factor of 1.5). In the wild-type strain, ACC1 overexpression led to increased levels of both fatty acids and squalene/sterols (factors of 4.0 and 1.7, respectively). This parallel activation of the two pathways seems to be due to transcriptional co-regulation of ACC1 and HMG1. While FAS1 and FAS2 overexpression had no effect in the wild-type strain, FAS2 overexpression induced significant increase of sterols and squalene (factors of 7.2 and 1.3, respectively) and a concomitant decrease of both saturated and unsaturated fatty acids in the squalene-overproducing strain (factor of 0.6). The microarray expression profiles showed that genes upregulated in ACC1-overexpressing strains are FAS1, ERG11, ERG28, ERG5, ERG2 and ERG20, supporting the observed increase of zymosterol and saturated fatty acids. The high ACC1 expression level due to overexpression correlated with increased transcript levels of sphingolipid and sterol biosynthesis genes. The relationship between was shown using the Pathway Studio™ program. © 2012 John Wiley & Sons, Ltd.


PubMed | National Institute of Development Administration, Insilicogen Inc. and Chonnam National University
Type: Journal Article | Journal: PloS one | Year: 2016

Cockroaches are surrogate hosts for microbes that cause many human diseases. In spite of their generally destructive nature, cockroaches have recently been found to harbor potentially beneficial and medically useful substances such as drugs and allergens. However, genomic information for the American cockroach (Periplaneta americana) is currently unavailable; therefore, transcriptome and gene expression profiling is needed as an important resource to better understand the fundamental biological mechanisms of this species, which would be particularly useful for the selection of novel antimicrobial peptides. Thus, we performed de novo transcriptome analysis of P. americana that were or were not immunized with Escherichia coli. Using an Illumina HiSeq sequencer, we generated a total of 9.5 Gb of sequences, which were assembled into 85,984 contigs and functionally annotated using Basic Local Alignment Search Tool (BLAST), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) database terms. Finally, using an in silico antimicrobial peptide prediction method, 86 antimicrobial peptide candidates were predicted from the transcriptome, and 21 of these peptides were experimentally validated for their antimicrobial activity against yeast and gram positive and -negative bacteria by a radial diffusion assay. Notably, 11 peptides showed strong antimicrobial activities against these organisms and displayed little or no cytotoxic effects in the hemolysis and cell viability assay. This work provides prerequisite baseline data for the identification and development of novel antimicrobial peptides, which is expected to provide a better understanding of the phenomenon of innate immunity in similar species.


PubMed | National Academy of Agricultural Science NAAS, Insilicogen Inc., Wonkwang University, Anyang Institute of Technology and NAAS
Type: Journal Article | Journal: PloS one | Year: 2015

Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40 reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.


Kim K.M.,Sungkyunkwan University | Park J.-H.,Insilicogen Inc. | Bhattacharya D.,Rutgers University | Yoon H.S.,Sungkyunkwan University
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

First-generation Sanger DNA sequencing revolutionized science over the past three decades and the current next-generation sequencing (NGS) technology has opened the doors to the next phase in the sequencing revolution. Using NGS, scientists are able to sequence entire genomes and to generate extensive transcriptome data from diverse photosynthetic eukaryotes in a timely and cost-effective manner. Genome data in particular shed light on the complicated evolutionary history of algae that form the basis of the food chain in many environments. In the Eukaryotic Tree of Life, the fact that photosynthetic lineages are positioned in four supergroups has important evolutionary consequences. We now know that the story of eukaryotic photosynthesis unfolds with a primary endosymbiosis between an ancestral heterotrophic protist and a captured cyanobacterium that gave rise to the glaucophytes, red algae and Viridiplantae (green algae and land plants). These primary plastids were then transferred to other eukaryotic groups through secondary endosymbiosis. A red alga was captured by the ancestor(s) of the stramenopiles, alveolates (dinoflagellates, apicomplexa, chromeridae), cryptophytes and haptophytes, whereas green algae were captured independently by the common ancestors of the euglenophytes and chlorarachniophytes. A separate case of primary endosymbiosis is found in the filose amoeba Paulinella chromatophora, which has at least nine heterotrophic sister species. Paulinella genome data provide detailed insights into the early stages of plastid establishment. Therefore, genome data produced by NGS have provided many novel insights into the taxonomy, phylogeny and evolutionary history of photosynthetic eukaryotes. © 2014 IUMS.


PubMed | National Institute of Development Administration, Insilicogen Inc., Hallym University, King Saud University and 4 more.
Type: | Journal: BMC genomics | Year: 2016

Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei.A total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei.We have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid.


PubMed | Insilicogen Inc., Seoul National University, Wonkwang University, National Academy of Agricultural Science and National Institute of Agricultural science
Type: | Journal: Evolutionary bioinformatics online | Year: 2016

We developed a multilayered screening method that integrates both genome and transcriptome data to effectively identify regulatory genes in rice (


PubMed | University of Jaffna, Insilicogen Inc., Marine Life Research, Nihon University and National Institute of Fisheries Science
Type: | Journal: Developmental and comparative immunology | Year: 2017

A -galactoside binding lectin, designated as galectin-2, was identified and characterized from rock bream Oplegnathus fasciatus (OfGal-2). The cDNA of OfGal-2 comprised of 692 bp with a coding sequence of 396 bp, encoding a putative polypeptide of 131 amino acids. Gene structure analysis of OfGal-2 revealed a four exon-three intron organization. A single carbohydrate-binding domain containing all seven important residues for carbohydrate binding was located in the third exon, which formed a carbohydrate-binding pocket. Homology screening and sequence analysis demonstrated that OfGal-2 is an evolutionarily conserved proto-type galectin. OfGal-2 transcripts were detected in several healthy fish tissues, with the highest level observed in the intestine, followed by the liver. The expression of OfGal-2 was elevated upon the injection of various mitogenic stimulants and pathogens in a time-dependent manner. Upregulated expression in the liver after tissue injury suggested its role as a damage-associated molecular pattern. Recombinant OfGal-2 protein had hemagglutinating potential and possessed affinity towards lactose and galactose. Moreover, the recombinant protein agglutinated and bound potential pathogenic bacteria and a ciliate. The results of this study indicate that the galectin-2 from rock bream has a potential role in immunity, particularly in the recognition of invading pathogens.

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