Publications by authors named "Yeonhwa Jo"

48 Publications

Transcriptome Assembly of Two Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids.

Int J Mol Sci 2021 Feb 19;22(4). Epub 2021 Feb 19.

Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea.

species produce a high amount of phytoecdysteroids (PEs), which are widely used in traditional medicine in the Pacific islands. The PEs in two different species, (MP) and (MS), were examined using high-performance liquid chromatography (HPLC). In particular, MS produces a high amount of 20-hydroxyecdysone, which is the main active compound in PEs. To identify genes for PE biosynthesis, we generated reference transcriptomes from sterile frond tissues using the NovaSeq 6000 system. De novo transcriptome assembly after deleting contaminants resulted in 57,252 and 54,618 clean transcripts for MP and MS, respectively. The clean transcripts for each species were annotated according to gene ontology terms, UniProt pathways, and the clusters of the orthologous group protein database using the MEGAN6 and Sma3s programs. In total, 1852 and 1980 transcription factors were identified for MP and MS, respectively. We obtained transcripts encoding for 38 and 32 enzymes for MP and MS, respectively, potentially involved in mevalonate and sterol biosynthetic pathways, which produce precursors for PE biosynthesis. Phylogenetic analyses revealed many redundant and unique enzymes between the two species. Overall, this study provides two reference transcriptomes that might be useful for further studies regarding PE biosynthesis in species.
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http://dx.doi.org/10.3390/ijms22042085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923240PMC
February 2021

Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize.

Mol Plant Pathol 2021 Apr 28;22(4):465-479. Epub 2021 Feb 28.

Department of Entomology and Plant Pathology, NC State University, Raleigh, North Carolina, USA.

Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1-D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1-D-mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2-infected leaves from the near-isogenic lines H95 and H95:Rp1-D, which differed for the presence of Rp1-D. We observed up-regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up-regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1-D and H95 with an additional H95:Rp1-D-specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1-D-mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance-specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance-specific responses to P. sorghi.
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http://dx.doi.org/10.1111/mpp.13040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938627PMC
April 2021

Transcriptome Profiling of Human Follicle Dermal Papilla Cells in response to Porphyra-334 Treatment by RNA-Seq.

Evid Based Complement Alternat Med 2021 13;2021:6637513. Epub 2021 Jan 13.

Anti-aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea.

Porphyra-334 is a kind of mycosporine-like amino acid absorbing ultraviolet-A. Here, we characterized porphyra-334 as a potential antiaging agent. An assay revealed that porphyra-334 dramatically promoted collagen synthesis in fibroblast cells. The effect of porphyra-334 on cell proliferation was dependent on the cell type, and the increase of cell viability by porphyra-334 was the highest in keratinocyte cells among the three tested cell types. An clinical test with 22 participants demonstrated the possible role of porphyra-334 in the improvement of periorbital wrinkles. RNA-sequencing using human follicle dermal papilla (HFDP) cells upon porphyra-334 treatment identified the upregulation of metallothionein- (MT-) associated genes, confirming the antioxidant role of porphyra-334 with MT. Moreover, the expression of genes involved in nuclear chromosome segregation and the encoding of components of kinetochores was upregulated by porphyra-334 treatment. Furthermore, we found that several genes associated with the hair follicle cycle, the hair follicle structure, the epidermal structure, and stem cells were upregulated by porphyra-334 treatment, suggesting the potential role of porphyra-334 in hair follicle growth and maintenance. In summary, we provided several new pieces of evidence of porphyra-334 as a potential antiaging cosmetic agent and elucidated the expression network in HFDP cells upon porphyra-334.
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http://dx.doi.org/10.1155/2021/6637513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817261PMC
January 2021

Gene expression profile of human follicle dermal papilla cells in response to Camellia japonica phytoplacenta extract.

FEBS Open Bio 2021 Mar 14;11(3):633-651. Epub 2021 Feb 14.

Anti-aging Research Institute of BIO-FD&C Co., Ltd., Incheon, Korea.

Camellia japonica L. is a flowering tree with several medicinal and cosmetic applications. Here, we investigated the efficacy of C. japonica placenta extract (CJPE) as a potential therapeutic agent for promotion of hair growth and scalp health by using various in vitro and in vivo assays. Moreover, we performed transcriptome analysis to examine the relative expression of human follicle dermal papilla cells (HFDPC) in response to CJPE by RNA-sequencing (RNA-seq). In vitro assays revealed upregulation of the expression of hair growth marker genes in HFDPC after CJPE treatment. Moreover, in vivo clinical tests with 42 adult female participants showed that a solution containing 0.5% CJPE increased the moisture content of the scalp and decreased the scalp's sebum content, dead scalp keratin, and erythema. Furthermore, RNA-seq analysis revealed key genes in HFDPC which are associated with CJPE. Interestingly, genes associated with lipid metabolism and cholesterol efflux were upregulated. Genes upregulated by CJPE are associated with several hormones, including parathyroid, adrenocorticotropic hormone, α-melanocyte-stimulating hormone (alpha-MSH), and norepinephrine, which are involved in hair follicle biology. Furthermore, some upregulated genes are associated with the regulation of axon guidance. In contrast, many genes downregulated by CJPE are associated with structural components of the cytoskeleton. In addition, CJPE suppressed genes associated with muscle structure and development. Taken together, this study provides extensive evidence that CJPE may have potential as a therapeutic agent for scalp treatment and hair growth promotion.
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http://dx.doi.org/10.1002/2211-5463.13076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931240PMC
March 2021

Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing.

Microorganisms 2020 Nov 12;8(11). Epub 2020 Nov 12.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Soybean ( L.) is one of the most important crop plants in the Republic of Korea. Here, we conducted a soybean virome study. We harvested a total of 172 soybean leaf samples showing disease symptoms from major soybean-growing regions in the Republic of Korea. Individual samples were examined for virus infection by RT-PCR. Moreover, we generated eight libraries representing eight provinces by pooling samples and four libraries from single samples. RNA-seq followed by bioinformatics analyses revealed 10 different RNA viruses infecting soybean. The proportion of viral reads in each transcriptome ranged from 0.2 to 31.7%. Coinfection of different viruses in soybean plants was very common. There was a single dominant virus in each province, and this geographical difference might be related to the soybean seeds that transmit viruses. In this study, 32 viral genome sequences were assembled and successfully used to analyze the phylogenetic relationships and quasispecies nature of the identified RNA viruses. Moreover, RT-PCR with newly developed primers confirmed infection of the identified viruses in each library. Taken together, our soybean virome study provides a comprehensive overview of viruses infecting soybean in eight geographical regions in the Republic of Korea and four single soybean plants in detail.
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http://dx.doi.org/10.3390/microorganisms8111777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7698195PMC
November 2020

First report of Cherry virus F infecting Japanese plum in Korea.

Plant Dis 2020 Nov 3. Epub 2020 Nov 3.

Seoul National University, Department of Agricultural Biotechnology, 5103-ho, 200-dong, Daehak-dong, Kwanak-gu, Seoul, Korea (the Republic of), 08826;

Cherry virus F (CVF) is a tentative member of the genus Fabavirus in the family Secoviridae, consisting of two RNA segments (Koloniuk et al. 2018). To date, CVF has been documented in only sweet cherry (Prunus avium) in the Czech Republic (Koloniuk et al. 2018), Canada, and Greece. In May 2014, we collected leaf samples from four symptomatic (leaf spots and dapple fruits) and two asymptomatic Japanese plum cultivars (Sun and Gadam) grown in an orchard in Hoengseong, South Korea, to identify viruses and viroids infecting plum trees. Total RNA from individual plum trees was extracted using two commercial kits: Fruit-mate for RNA Purification Kit (Takara, Shiga, Japan) and RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). We generated six mRNA libraries from the six different plum cultivars for RNA-sequencing using the TruSeq RNA Library Preparation Kit v2 (Illumina, CA, U.S.A.) as described previously (Jo et al. 2017). The mRNA libraries were paired-end (2 X 100 bp) sequenced with a HiSeq 2000 system (Macrogen, Seoul, Korea). The raw sequence reads were de novo assembled by Trinity program v. 2.8.6, with default parameters (Haas et al. 2013). The assembled contigs were subjected to BLASTX search against the non-redundant protein database in NCBI. Of the two asymptomatic cultivars, the transcriptome of asymptomatic plum cv. Gadam contained five contigs specific to CVF. Two and three contigs were specific to CVF RNA1 (2,571 reads, coverage 42.15%) and RNA2 (2,025 reads, coverage 53.04%), respectively. The size of these five contigs ranged from 241 to 5,986 bp. Contigs of 5,986 and 3,867 bp in length, referred to as CVF isolate Gadam RNA1 (GenBank MN896996) and RNA2 (GenBank MN896995), respectively, were subjected to BLASTP search against NCBI's non-redundant protein database. The results showed that the polyprotein sequences of RNA1 and RNA2 shared 95.3% and 93.11% amino acid identities with isolates SwC-H_1a from the Czech Republic (GenBank acc. no. AWB36326) and Stac-3B_c8 from Canada (AZZ10055), respectively. To confirm the infection of CVF in cv. Gadam, RT-PCR was conducted using CVF RNA1-specific primers designed based on the CVF reference genome sequences (MH998210 and MH998216), including 5'-CCACCAAATAGGCAAGAGGTCAC-3' (position 3190-3212) and 5'-CACAATCACCATCAATGGTCTCTGC-3' (position 3742-3766), and CVF RNA2-specific primers, including 5'-CTGCTTTATGATGCTAGACATCAAGATG-3' (position 1015-1042) and 5'-ACAATAGGCATGCTCATCTCAACCTC-3' (position 1594-1619). We amplified 577-bp RNA1-specific and 605-bp RNA2-specific amplicons that were cloned and then performed Sanger sequencing. Sequencing of the cloned amplicons for isolate Gadam RNA1 (GenBank MN896993) and RNA2 (GenBank MN896994) revealed values of 99.48% and 99.17% nucleotide identity to that of RNA1 and RNA2 determined by high-throughput sequencing, respectively. Additionally, we tested five plants for each of the six plum cultivars grown in the same orchard. The detection of CVF was carried out through PCR using the primers and protocol described above. Of the 30 trees, CVF was detected in three trees of cv. Gadam by both primer pairs. To our knowledge, this is the first report of CVF infecting Japanese plum and the first report of the virus in Korea. However, its prevalence in other Prunus species, including apricot, European plum, and peach, should be further elucidated.
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http://dx.doi.org/10.1094/PDIS-08-20-1725-PDNDOI Listing
November 2020

Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics.

Int J Mol Sci 2020 Oct 13;21(20). Epub 2020 Oct 13.

Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Tomato ( L.) and pepper ( L.) plants belonging to the family are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family grown in Vietnam.
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http://dx.doi.org/10.3390/ijms21207565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593927PMC
October 2020

Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics.

Plants (Basel) 2020 Aug 18;9(8). Epub 2020 Aug 18.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar "Hahong" by DNA- and RNA-sequencing. We found the dominance of followed by , , and in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including , , , and . Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to as umbra-like virus 1 (MULV1) from . Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing.
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http://dx.doi.org/10.3390/plants9081052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464454PMC
August 2020

Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing.

PeerJ 2020 29;8:e9588. Epub 2020 Jul 29.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

Background: Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees.

Methods: To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database.

Results: We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses-ACLSV, PBNSPaV, and PNRSV-in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea.
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http://dx.doi.org/10.7717/peerj.9588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395596PMC
July 2020

Anti-Aging Effects of (Edelweiss) Callus Culture Extract Through Transcriptome Profiling.

Genes (Basel) 2020 02 21;11(2). Epub 2020 Feb 21.

Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea.

Edelweiss () in the family is a wildflower that grows in rocky limestone places. Here, we investigated the efficacy of edelweiss callus culture extract ( callus culture extract; LACCE) using multiple assays from to as well as transcriptome profiling. Several assay results showed the strong antioxidant activity of LACCE in response to UVB treatment. Moreover, LACCE suppressed inflammation and wrinkling; however, moisturizing activity was increased by LACCE. The clinical test demonstrated that constant application of LACCE on the face and skin tissues improved anti-periorbital wrinkles, skin elasticity, dermal density, and skin thickness compared with the placebo. The RNA-Sequencing results showed at least 16.56% of human genes were expressed in keratinocyte cells. LACCE up-regulated genes encoding several KRT proteins; DDIT4, BNIP3, and IGFBP3 were involved in the positive regulation of the developmental process, programmed cell death, keratinization, and cornification forming skin barriers, which provide many advantages in the human skin. By contrast, down-regulated genes were stress-responsive genes, including metal, oxidation, wounding, hypoxia, and virus infection, suggesting LACCE did not cause any harmful stress on the skin. Our comprehensive study demonstrated LACCE is a promising agent for anti-aging cosmetics.
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http://dx.doi.org/10.3390/genes11020230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074254PMC
February 2020

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars.

Sci Rep 2020 02 13;10(1):2588. Epub 2020 Feb 13.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

The sweet potato in the family Convolvulaceae is a dicotyledonous perennial plant. Here, we conducted a comprehensive sweet potato virome study using 10 different libraries from eight regions in Korea and two different sweet potato cultivars by RNA-Sequencing. Comprehensive bioinformatics analyses revealed 10 different virus species infecting sweet potato. Moreover, we identified two novel viruses infecting sweet potato referred to as Sweet potato virus E (SPVE) in the genus Potyvirus and Sweet potato virus F (SPVF) in the genus Carlavirus. Of the identified viruses, Sweet potato feathery mottle virus (SPFMV) was the dominant virus followed by Sweet potato virus C (SPVC) and SPVE in Korea. We obtained a total of 30 viral genomes for eight viruses. Our phylogenetic analyses showed many potyvirus isolates are highly correlated with geographical regions. However, two isolates of SPFMV and a single isolate of Sweet potato virus G (SPVG) were genetically distant from other known isolates. The mutation rate was the highest in SPFMV followed by SPVC and SPVG. Two different sweet potato cultivars, Beni Haruka and Hogammi, were infected by seven and five viruses, respectively. Taken together, we provide a complete list of viruses infecting sweet potato in Korea and diagnostic methods.
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http://dx.doi.org/10.1038/s41598-020-59518-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018812PMC
February 2020

RNA viromes of the oriental hybrid lily cultivar "Sorbonne".

BMC Genomics 2018 Oct 13;19(1):748. Epub 2018 Oct 13.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Background: The lily is a perennial flowering plant belonging to the genus Lilium in the family Liliaceae. Most cultivated lily plants are propagated by bulbs. Therefore, numerous lily bulbs are frequently infected by diverse viruses causing viral diseases. To date, no study has examined the viromes of plants of one type with identical genetic backgrounds collected from different geographical regions.

Results: Here, we examined different viromes of the lily cultivar "Sorbonne" using 172 gigabytes of transcriptome data composed of 23 libraries from four different projects for the cultivar "Sorbonne." We identified 396 virus-associated contigs from all but one library. We identified six different viruses, including Plantago asiatica mosaic virus (PlAMV), Cucumber mosaic virus (CMV), Lily symptomless virus (LSV), Tulip virus X (TVX), Lily mottle virus (LMoV), and Tobacco rattle virus (TRV). Of them, PlAMV was the most common virus infecting the lily. Scale and flower samples possessed a high number of virus-associated reads. We assembled 32 nearly complete genomes for the six identified viruses possessing the polyadenylate tails. Genomes of all six viruses were highly conserved in the lily cultivar "Sorbonne" based on mutation analysis. We identified defective RNAs from LSV, TVX, and PlAMV localized in the triple gene block region. Phylogenetic analyses showed that virus genomes are highly correlated with geographical regions and host plants.

Conclusions: We conducted comprehensive virome analyses of a single lily cultivar, "Sorbonne," using transcriptome data. Our results shed light on an array of lily virome-associated topics, including virus identification, the dominant virus, virus accumulation in different plant tissues, virus genome assembly, virus mutation, identification of defective RNAs, and phylogenetic relationships of identified viruses. Taken together, we provide very useful methods and valuable results that can be applied in other virome-associated studies.
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http://dx.doi.org/10.1186/s12864-018-5138-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186116PMC
October 2018

Barley RNA viromes in six different geographical regions in Korea.

Sci Rep 2018 09 5;8(1):13237. Epub 2018 Sep 5.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Barley is a kind of cereal grass belonging to the family Poaceae. To examine viruses infecting winter barley in Korea, we carried out a comprehensive study of barley RNA viromes using next-generation sequencing (NGS). A total of 110 barley leaf samples from 17 geographical locations were collected. NGS followed by extensive bioinformatics analyses revealed six different barley viromes: Barley yellow mosaic virus (BaYMV), Barley mild mosaic virus (BaMMV), Barley yellow dwarf virus (BYDV), Hordeum vulgare endornavirus (HvEV), and Barley virus G (BVG). BaYMV and HvEV were identified in all libraries, while other viruses were identified in some specific library. Based on the number of virus-associated reads, BaYMV was a dominant virus infecting winter barley in Korea causing yellow disease symptoms. We obtained nearly complete genomes of six BaYMV isolates and two BaMMV isolates. Phylogenetic analyses indicate that BaYMV and BaMMV were largely grouped based on geographical regions such as Asia and Europe. Single nucleotide polymorphisms analyses suggested that most BaYMV and BaMMV showed strong genetic variations; however, BaYMV isolate Jeonju and BaMMV isolate Gunsan exhibited a few and no SNPs, respectively, suggesting low level of genetic variation. Taken together, this is the first study of barley RNA viromes in Korea.
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http://dx.doi.org/10.1038/s41598-018-31671-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125401PMC
September 2018

Identification of viral domains integrated into Arabidopsis proteome.

Mol Phylogenet Evol 2018 11 17;128:246-257. Epub 2018 Aug 17.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea. Electronic address:

Horizontal gene transfer (HGT) contributes to the genome evolution of living organisms. In particular, several recent studies provide convincing data on the integration of viral sequences into diverse organisms. Here, we identified 101 viral domains integrated into the model plant Arabidopsis proteome. Functional analysis based on gene ontology (GO) terms indicates that viral domains in the Arabidopsis proteome were involved in various stress responses with binding functions. Protein interaction networks support the strong protein interactions of viral domains with other Arabidopsis proteins. A proteome-wide analysis gave a comprehensive evolutionary view of viral domains integrated into 41 plant proteomes, revealing the specific and conserved integration of viral domains into plant proteomes. Phylogenetic analyses revealed the possible HGT between viral domains and plant proteomes. Our results provide an overview of the integration of viral domains into plant proteomes and their possible functional roles associated with plant defense mechanisms.
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http://dx.doi.org/10.1016/j.ympev.2018.08.009DOI Listing
November 2018

Peach RNA viromes in six different peach cultivars.

Sci Rep 2018 01 30;8(1):1844. Epub 2018 Jan 30.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.
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http://dx.doi.org/10.1038/s41598-018-20256-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789896PMC
January 2018

Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data.

Plant Pathol J 2017 Oct 1;33(5):478-487. Epub 2017 Oct 1.

Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
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http://dx.doi.org/10.5423/PPJ.OA.03.2017.0060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624490PMC
October 2017

Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine.

Genome Announc 2017 Sep 14;5(37). Epub 2017 Sep 14.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea

Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus in the family .
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http://dx.doi.org/10.1128/genomeA.00995-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597771PMC
September 2017

Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine.

Genome Announc 2017 Sep 14;5(37). Epub 2017 Sep 14.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea

Here, we report the genome sequence of grapevine virus K (GVK), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVK is 7,476 nucleotides in length and encodes 5 open reading frames. GVK is a putative member of the genus in the family .
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http://dx.doi.org/10.1128/genomeA.00994-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597770PMC
September 2017

The pepper virome: natural co-infection of diverse viruses and their quasispecies.

BMC Genomics 2017 06 8;18(1):453. Epub 2017 Jun 8.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

Background: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host.

Results: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host.

Conclusions: Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.
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http://dx.doi.org/10.1186/s12864-017-3838-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465472PMC
June 2017

Sequence variability of in different chrysanthemum cultivars.

PeerJ 2017 26;5:e2933. Epub 2017 Jan 26.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein. (CSVd), a member of the family , causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.
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http://dx.doi.org/10.7717/peerj.2933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274516PMC
January 2017

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.

BMC Genomics 2016 08 9;17:579. Epub 2016 Aug 9.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

Background: Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study.

Results: We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes.

Conclusions: Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination.
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http://dx.doi.org/10.1186/s12864-016-2994-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977635PMC
August 2016

Genome Sequence of Dengue virus 3 from the Pythium insidiosum Transcriptomes.

Front Microbiol 2016 15;7:926. Epub 2016 Jun 15.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, Republic of Korea; The Taejin Genome InstituteHoengseong, Republic of Korea.

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http://dx.doi.org/10.3389/fmicb.2016.00926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908670PMC
July 2016

De novo transcriptome assembly of Setatria italica variety Taejin.

Genom Data 2016 Jun 5;8:121-2. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea.

Foxtail millet (Setaria italica) belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.
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http://dx.doi.org/10.1016/j.gdata.2016.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878839PMC
June 2016

De novo transcriptome assembly of two Vigna angularis varieties collected from Korea.

Genom Data 2016 Jun 5;8:119-20. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoengseong 25239, Republic of Korea.

The adzuki bean (Vigna angularis), a member of the family Fabaceae, is widely grown in Asia, from East Asia to the Himalayas. The adzuki bean is known as an ingredient that adds sweetness to diverse desserts made in Eastern Asian countries. Libraries prepared from two V. angularis varieties referred to as Taejin Black and Taejin Red were paired-end sequenced using the Illumina HiSeq 2000 system. The raw data in this study can be available in NCBI SRA database with accession numbers of SRR3406660 and SRR3406553. After de novo transcriptome assembly using Trinity, we obtained 324,219 and 280,056 transcripts from Taejin Black and Taejin Red, respectively. We predicted a total of 238,321 proteins and 179,519 proteins for Taejin Black and Taejin Red, respectively, by the TransDecoder program. We carried out BLASTP on the predicted proteins against the Swiss-Prot protein sequence database to predict the putative functions of identified proteins. Taken together, we provide transcriptomes of two adzuki bean varieties by RNA-Seq, which might be usefully applied to generate molecular markers.
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http://dx.doi.org/10.1016/j.gdata.2016.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878840PMC
June 2016

De novo transcriptome assembly of Sorghum bicolor variety Taejin.

Genom Data 2016 Jun 5;8:117-8. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoengseong, 25239, Republic of Korea.

Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.
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http://dx.doi.org/10.1016/j.gdata.2016.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878842PMC
June 2016

De novo transcriptome assembly of two different apricot cultivars.

Genom Data 2015 Dec 19;6:275-6. Epub 2015 Oct 19.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.

Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.
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http://dx.doi.org/10.1016/j.gdata.2015.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664767PMC
December 2015

De novo transcriptome assembly of two different Prunus mume cultivars.

Genom Data 2015 Dec 19;6:273-4. Epub 2015 Oct 19.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.

Prunus mume, belonging to the Prunus genus, is an Asian tree, and its common names are Chinese plum and Japanese plum. P. mume are cultivated for fruit production as well as ornamental purposes. In this study, we conducted de novo transcriptome assembly for two selected P. mume cultivars referred to as Takada and Wallyoung (commercially important cultivars for fruit production and ornamental trees, respectively) by RNA-sequencing. We obtained 9.14 GB and 9.48 GB sequence data from Takada and Wallyoung (NCBI accession numbers: SRX1187101 and SRX1187169), respectively. De novo transcriptome assembly identified 130,989 and 116,941 transcripts for Takada and Wallyoung, respectively. In addition, we identified 96,681 and 91,429 proteins from Takada and Wallyoung, respectively, by TransDecoder program. We performed BLASTP against the NCBI non-redundant (nr) datasets to annotate identified proteins. This study provides transcriptomes and proteomes for two different P. mume cultivars, which might be useful for comparative transcriptome analyses and assist development of genetic markers.
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http://dx.doi.org/10.1016/j.gdata.2015.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664763PMC
December 2015

De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle.

Genom Data 2015 Dec 19;6:271-2. Epub 2015 Oct 19.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.

Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170). De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.
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http://dx.doi.org/10.1016/j.gdata.2015.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664768PMC
December 2015

De novo transcriptome assembly of two different Prunus salicina cultivars.

Genom Data 2015 Dec 19;6:262-3. Epub 2015 Oct 19.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.

Plum is a globally grown stone fruit and can be divided into several species. In particular, the Prunus salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. The transcriptome data for Prunus salicina has not been reported to our knowledge. In this study, we performed de novo transcriptome assembly for two selected P. salicina cultivars referred to as Akihime and Formosa (commercially important plum cultivars in Korea) using next generation sequencing. We obtained a total of 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly using Trinity revealed 155,169 and 160,186 transcripts for Akihime and Formosa. Next, we identified 121,278 and 116,544 proteins from Akihime and Formosa using TransDecoder. We performed BLASTP against the NCBI non-redundant (nr) dataset to annotate proteins. Taken together, this is the first transcriptome data for P. salicina to our knowledge.
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http://dx.doi.org/10.1016/j.gdata.2015.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664772PMC
December 2015

De novo transcriptome assembly of two different peach cultivars grown in Korea.

Genom Data 2015 Dec 19;6:260-1. Epub 2015 Oct 19.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.

Peach (Prunus persica) is one of the most popular stone fruits worldwide. Next generation sequencing (NGS) has facilitated genome and transcriptome analyses of several stone fruit trees. In this study, we conducted de novo transcriptome analyses of two peach cultivars grown in Korea. Leaves of two cultivars, referred to as Jangtaek and Mibaek, were harvested and used for library preparation. The two prepared libraries were paired-end sequenced by the HiSeq2000 system. We obtained 8.14 GB and 9.62 GB sequence data from Jangtaek and Mibaek (NCBI accession numbers: SRS1056585 and SRS1056587), respectively. The Trinity program was used to assemble two transcriptomes de novo, resulting in 110,477 (Jangtaek) and 136,196 (Mibaek) transcripts. TransDecoder identified possible coding regions in assembled transcripts. The identified proteins were subjected to BLASTP search against NCBI's non-redundant database for functional annotation. This study provides transcriptome data for two peach cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.
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http://dx.doi.org/10.1016/j.gdata.2015.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664764PMC
December 2015