The Taejin Genome Institute

gil, South Korea

The Taejin Genome Institute

gil, South Korea
SEARCH FILTERS
Time filter
Source Type

Jo Y.,Seoul National University | Cho J.K.,The Taejin Genome Institute | Choi H.,Seoul National University | Lian S.,Qingdao Agricultural University | And 2 more authors.
Plant Disease | Year: 2017

The peach (Prunus persica) is not only a popular stone fruit tree worldwide, but also a host to diverse plant viruses and viroids. Nectarine stem pitting-associated virus (NSPaV), a putative member of the genus Luteovirus (family Luteoviridae), is a novel virus that has been recently identified in the United States (Bag et al. 2015; Villamor et al. 2016), Japan, and China. In a 2016 survey of viruses infecting diverse peach cultivars in Korea, we examined different peach cultivars grown in five orchards. Of the peach cultivars showing viral disease symptoms, Daeok (DO), a kind of common peach from an orchard in Wonju, Korea, showed discoloration, yellowishness, and spotting in the leaves, along with stem-pitting symptoms. Five DO plants were symptomatic. Leaf samples from a single DO plant were subjected to RNA sequencing as described previously (Jo et al. 2016). We conducted MEGABLAST using assembled contigs against the viral reference database from NCBI. We identified 32 contigs associated with the following five viral genomes: Apple chlorotic leaf spot virus (ACLSV) (four contigs), Hop stunt viroid (HSVd) (six contigs), Peach latent mosaic viroid (PLMVd) (12 contigs), NSPaV (nine contigs), and Plum bark necrosis and stem pitting-associated virus (PBNSPaV) (one contig). The infections of ACLSV, HSVd, and PLMVd in peach have been previously identified in Korea; however, the infections of NSPaV and PBNSPaV in peach have not been reported in Korea. To confirm the coinfection of NSPaV and PBNSPaV in the symptomatic five peach trees, RT-PCR was performed using NSPaV-specific primers, forward 5′-ATGATTTTCGATCTCCTTATTTCTGCC-3′ (position 132-158) and reverse 5′-GGCACGGATGAAGTGTCGTGC-3′ (position 869-849), based on the NSPaV reference genome (accession no. NC_027211.1) and PBNSPaV-specific primers, forward 5′-GGGAGTCATCCCGTTGGTTCT-3′ (position 494-514) and reverse 5′-GACTCCCTGAGATTTAACTTTCTCAGC-3′ (position 1096-1070), based on the PBNSPaV reference genome (NC_009992.1). The amplified products of 738 bp (NSPaV) and 603 bp (PBNSPaV) were cloned in the pGEM-T-Easy Vector (Promega, Wisconsin, U.S.), followed by Sanger sequencing. NSPaV isolate DO (KY174965) shared 92% of its nucleotide identity (681/739 nt) with the known isolate NSPaV/SF04522E in peach from the United States, while PBNSPaV isolate DO (KY174967) shared 99% of its nucleotide identity (589/597 nt) with PR258-2 isolate in peach from France. Furthermore, the coinfection of ACLSV, HSVd, and PLMVd in five peach trees for the DO cultivar was confirmed by RT-PCR. Our results showed that all the examined peach trees were coinfected by at least three viruses and two viroids. Although the peach cultivar DO displayed viral disease symptoms, it was hard to determine the viral pathogen responsible due to the coinfection of viruses and viroids. However, our results provide a list of peach viruses that might be required for the development of virus-free peach plants. To the best of our knowledge, this is the first report of NSPaV and PBNSPaV infecting a peach cultivar in Korea. © 2017, American Phytopathological Society. All rights reserved.


Jo Y.,Seoul National University | Lian S.,Qingdao Agricultural University | Cho J.K.,The Taejin Genome Institute | Choi H.,Seoul National University | And 2 more authors.
Plant Disease | Year: 2017

The peach (Prunus persica) is one of the most popular stone fruit trees in the world. Recent studies have shown that peach trees are infected by several viruses and viroids (Yu et al. 2013). Apricot pseudo-chlorotic leaf spot virus (APCLSV), belonging to the genus Trichovirus in the family Betaflexiviridae, is closely related to Apple chlorotic leaf spot virus (ACLSV) (Liberti et al. 2005). Thus far, APCLSV has been identified in apricot, Japanese plum, plum, and peach trees in Australia, China, the Czech Republic, France, Hungary, Jordan, Italy, Spain, and Turkey (Niu et al. 2012; Šafářová et al. 2012). However, APCLSV has not yet been detected in Korea. To identify viruses infecting different peach cultivars, leaf samples showing chlorotic leaf spots and mild mosaic symptoms were collected from six different peach cultivars grown in various orchards located in Incheon, Hoengseong, Yeoju, and Wonju in Korea during May 2013. Total RNA was extracted from the leaf samples and subjected to next-generation sequencing (NGS) using Illumina’s HiSeq 2000 system followed by bioinformatics analyses (Jo et al. 2016). A transcriptome from the peach cultivar Baekcheon (BC) contained six contigs (3,728 reads) associated with APCLSV, resulting in a nearly complete genome sequence of APCLSV isolate BC with 7,485 nt. The BLAST result showed that APCLSV isolate BC shared 83% of the identity of isolate Sus2 from Italy (accession no. AY713379.1) To confirm the infection of APCLSV in the peach cultivar BC, RT-PCR was conducted using APCLSV-specific primers, forward 5′-ATGCAAGTGAGGGGTCACAAG-3′ (position 5704-5724), and reverse 5′-GTCAAACCAGGATCATCCAGAG-3′ (position 6161-6140) based on the APCLSV reference genome (NC_006946.1) (Liberti et al. 2005). The 458-bp amplified product was cloned in the pGEM-T-Easy Vector (Promega, Wisconsin, U.S.) followed by Sanger sequencing. The sequence analysis showed that APCLSV isolate BC (KY038931) was clustered with ARPox1 isolate from apricot in Italy, sharing 94% of the nucleotide identity (431/458 nt). In addition, we investigated APCLSV infection in the other samples detected by RNA sequencing by RT-PCR; however, APCLSV infection was not found in the other peach cultivars. As previously reported, APCLSV has been frequently reported in mixed infections with ACLSV (Šafářová et al. 2012). RT-PCR using ACLSV-specific primers confirmed that the BC cultivar was also infected by ACLSV. Our NGS-based approach was efficient at identifying APCLSV infecting a peach cultivar with a nearly complete genome of APCLSV. The viral disease symptoms caused by APCLSV in the host have not been reported due to the coinfection of APCLSV with other viruses. APCLSV has been identified in one out of six cultivars in this study; a few other peach cultivars might be infected by APCLSV. A wide-ranging examination of APCLSV infection in diverse peach cultivars might be required in the near future. Taken together, this is the first report of APCLSV infecting a peach cultivar in Korea to our knowledge. © 2017, American Phytopathological Society. All rights reserved.


Jo Y.H.,Seoul National University | Lian S.,Qingdao Agricultural University | Cho J.K.,The Taejin Genome Institute | Choi H.S.,Seoul National University | And 2 more authors.
Plant Disease | Year: 2017

To date, several viruses and viroids infecting peach trees have been identified worldwide, but in Korea, only Apple chlorotic leaf spot virus (ACLSV), Prunus necrotic ringspot virus (PNRSV), and Peach latent mosaic viroid (PLMVd) have been reported (Cho et al. 2012; Jo et al. 2016). Recently, we conducted RNA sequencing to identify viruses and viroids infecting peach trees. We sampled leaves showing chlorotic leaf spots and mild mosaic symptoms from six peach cultivars grown in various orchards in Korea during May 2013. The collected leaves were subjected to total RNA extraction using Fruit-mate for RNA Purification (Takara, Shiga, Japan) and the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions. Six mRNA libraries were prepared for RNA sequencing using the TruSeq RNA Library Preparation Kit v2 (Illumina, CA, U.S.A.) based on the manufacturer’s manual and were sequenced using Illumina’s HiSEquation 2000 system (Macrogen, Seoul, Korea). Peach transcriptomes were de novo assembled by the Trinity program using default parameters (Haas et al. 2013) and subjected to a MEGABLAST search against the virus reference database from NCBI. All six peach transcriptomes contained several contigs associated with viruses and viroids. Of the six transcriptomes, a transcriptome from the peach cultivar Mibaek contained one contig (8,423 bp) associated with Cherry necrotic rusty mottle virus (CNRMV) showing 91% identity to FC4 isolate from Japan (accession no. EU188438.1) and four contigs associated with ACLSV. However, the number of CNRMV-associated reads (44,338) was much higher than that of ACLSV-associated reads (5,466). To confirm the infection of CNRMV in the peach cultivar Mibaek, we carried out RT-PCR using CNRMV-specific primers, forward 5ʹ-ATTTTAGTTATGGGTGATCCTGCT-3ʹ (position 4102-4125), and reverse 5ʹ-AAGAATTTGTGCACGACCCC-3ʹ (position 4640-4621) based on the CNRMV reference genome (NC_002468.1). The amplified product of 539 bp was cloned in the pGEM-T-Easy Vector (Promega, WI, U.S.A.) followed by Sanger sequencing. The sequence analysis suggested CNRMV isolate MB (KX280759) was clustered with FC4 isolate sharing 91% of nucleotide identity (488/539 nt). In addition, we investigated CNRMV infection in the other samples detected by RNA sequencing by RT-PCR; however, CNRMV infection was not found in these cultivars. Furthermore, we found that the Mibaek cultivar was infected by Hop stunt viroid (HSVd) and PLMVd by RT-PCR. CNRMV is one of the quarantine viruses in Korea. The infection of CNRMV in sweet cherry trees has been previously reported in Korea; however, the infection of CNRMV in peach trees has not been reported. Our report suggests that CNRMV might be a potential threat to peach cultivation in Korea. Taken together, this is the first report of CNRMV infecting a peach cultivar in Korea to our knowledge. © The American Phytopathological Society.


Jo Y.,Seoul National University | Lian S.,Qingdao Agricultural University | Cho J.K.,The Taejin Genome Institute | Choi H.,Seoul National University | And 2 more authors.
Plant Disease | Year: 2017

The peach (Prunus persica) is a popular stone fruit worldwide. Peach trees are prone to infections of many viruses and viroids. In a survey of peach trees for viruses and viroids during May 2013, leaf samples from five different peach cultivars were collected in South Korea and were subjected to total RNA extraction using the method combining Fruit-mate for RNA Purification (Takara, Shiga, Japan) and the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Five libraries for RNA-Seq were generated using the total RNAs as templates by the TruSeq RNA Library Preparation Kit v2 (Illumina, CA) according to the manufacturer’s instructions. The prepared libraries were 101-bp paired-end sequenced using Illumina’s HiSEquation 2000 system (Macrogen, Seoul, Korea). Raw data (39 GB) were subjected to de novo transcriptome assembly using the Trinity program (Haas et al. 2013), and the assembled contigs were blasted using MEGABLAST against a viral reference database in NCBI. Nonviral sequences and endogenous viral-like sequences were removed by blasting against the peach reference genome. Several contigs similar to Asian prunus virus (APV), Apple chlorotic leaf spot virus (ACLSV), and Peach latent mosaic viroid (PLMVd) were identified from two peach cultivars, Baekcheonhwangdo (BC) and Janghowonhwangdo (JH), with yellow-colored fruits. The 10 and 11 APV-contigs from the BC and JH cultivars, respectively, were further analyzed. A BLAST search and alignment of contigs on the APV reference genomes revealed that the BC cultivar was infected by only APV2 while the JH cultivar was infected by both APV1 and APV2. For instance, a contig of 9,413 bp from the BC cultivar was matched to known APV2 isolate Bonsai (KT893295.1) with 90% identity. From the JH cultivar, a contig of 8,709 bp was matched to APV1 isolate Bungo (KT893293.1) with 91% identity, and a second contig of 9,406 bp was matched to APV2 isolate Tatao25 (KT893297.1) with 89% identity. To confirm the presence of APV1 and APV2, virus-specific primer pairs [APV1_CP_F1 5′-ACCTCAAGTGTTGAGAATCCTTTCAAGC-3′ (position 7544-7571) and APV1_CP_R1 5′-TTCGTCACCAGCATGATGTTCCA-3′ (position 8304-8282) amplifying a product with 761 bp, APV2_CP_F1 5′-AAAATTGTTTGGAACATCATGCTG-3′ (position 8234-8257) and APV2_CP_R1 5′-TCAGTCCATCTCCTTTCCCTTCAA-3′ (position 85551-8528) amplifying a product with 318 bp] were designed based on the coat protein sequences from a previous study (Marais et al. 2016) and this study. The amplified PCR products were sequenced by Sanger sequencing. The sequences (KX280757 and KX280758) of the APV2 from BC and JH, respectively, were 94 and 93% identical to that of APV2 isolate Tatao25, confirming the infections of APV2 in the BC and JH cultivars. Using APV1-specific primers, the PCR product was amplified only from the JH cultivar. The sequence (KX962059) of APV1 was 96% identical to that of APV1 isolate APV_1_D2363 (KR998047.1). The infections of ACLSV and PLMVd in the two cultivars were also confirmed by RT-PCR, showing that the trees were infected by multiple pathogens. The two cultivars showed very mild disease symptoms, including leaf spots and chlorosis, in some young leaves during 2014–15 and produced high-quality peach fruits. To our knowledge, this is the first report of APV1 and APV2 infecting peach trees in Korea. © 2017, American Phytopathological Society. All rights reserved.


Jo Y.,Seoul National University | Choi H.,Seoul National University | Kim S.-M.,South Korean National Institute of Crop Science | Kim S.-L.,South Korean National Institute of Crop Science | And 3 more authors.
BMC Genomics | Year: 2017

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. © 2017 The Author(s).


Jo Y.,Seoul National University | Lian S.,Qingdao Agricultural University | Cho J.K.,The Taejin Genome Institute | Chu H.,Seoul National University | And 3 more authors.
Plant Disease | Year: 2017

Japanese apricot (Prunus mume Siebold and Zuccarini), in the family Rosaceae, is a popular stone fruit crop in China, Japan, and Korea. To date, several viruses infecting Japanese apricot, such as Prunus necrotic ringspot virus (PNRSV), Nectarine stem pitting-associated virus (NSPaV) (Candresse et al. 2017), Cherry virus A (CVA) (Marais et al. 2008), Plum pox virus (PPV), Asian prunus virus 1 (APV1), and APV2 (Marais et al. 2016), have been reported. Since APV2 and CVA have also been found in symptomless trees, the exact symptoms caused by each virus have not been determined. It has been reported that GF305 peach seedlings infected by APV2 displayed enlarged veins on old leaves (Marais et al. 2016). In general, both APV2 and CVA are transmitted by grafting; however, the vectors transmitting the two viruses are unknown. To detect and identify viruses and viroids infecting Japanese apricot in Korea, leaf samples from two cultivars, Takada and Wallyoung (WY), grown in an orchard in September 2015, were harvested. Both plants did not display any observable disease symptoms. Five leaves from a single plant for each cultivar were used for total RNA extraction using Fruit-mate for RNA Purification (Takara, Shiga, Japan) and the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) following the manufacturers’ instructions. Two libraries were generated and paired-end sequenced by Illumina’s HiSeq 2000 system (Macrogen, Seoul, Korea) as described previously (Jo et al. 2016). Raw sequenced reads were assembled by the Trinity program (Haas et al. 2013), and the assembled contigs were subjected to a MEGABLAST search against a viral reference database. MEGABLAST identified APV2 (two contigs) and CVA (two contigs) only from the cultivar WY. Using the obtained contigs, we assembled the draft genome for APV2 isolate WY of 9,389 nt (GenBank accession KY445748) and CVA isolate WY of 7,365 nt (KY445749). To confirm coinfection of APV2 and CVA, we conducted reverse transcription (RT)-PCR using APV2-specific primers (5′-GTACCCCCTGGGGAGGAGG-3′ [position 1,994–2,012] and 5′-CTTTTCGTTGTCAGAGTGAAAACCAAT-3′ [position 2,542–2,516]) based on the APV2 reference sequence (NC_028868.1) and CVA-specific primers (5′-CAATCTCCCTTTCTTCGAAGGATTTT-3′ [position 1,240–1,265] and 5′-GAATTTACAACAAACCTCCAATAACTTTGA-3′ [position 2,073–2,044]) primers based on the CVA reference genome sequence (NC_003689.1). The amplified 549- and 834-bp PCR products for APV2 and CVA, respectively, were cloned in pGEM-T-Easy Vector (Promega, Wisconsin, U.S.A.) and sequenced. The 549-bp PCR sequence of APV2 isolate WY (KY445743) was 86% identical to the isolate APV_2_Q86 from peach (P. persica L. Batch) from the U.S.A. (KR998049.1), while the 834-bp PCR sequence of CVA isolate WY (KY445745) was 85% identical to isolate ChYT52 from Cherry from China (KX370827.1). Due to the high sequence similarity of APV1, APV2, and APV3 (Marais et al. 2016), RT-PCR was conducted using APV1- and APV3-specific primers, and no PCR product was obtained for APV1 and APV3. As a result, the cultivar WY was coinfected by APV2 and CVA. To our knowledge, our study is the first report of APV2 and CVA infecting Japanese apricot in Korea as well as the first report of CVA in Korea. However, our study showed infection of the two viruses in one cultivar, and their prevalence in other Japanese apricots should be further examined. © 2017, American Phytopathological Society. All Rights Reserved.


PubMed | National Science Foundation, Korea University, The Taejin Genome Institute, Qingdao Agricultural University and Seoul National University
Type: | Journal: Genomics data | Year: 2016

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 8.748GB 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.


PubMed | National Science Foundation, The Taejin Genome Institute, Qingdao Agricultural University and Seoul National University
Type: | Journal: Genomics data | Year: 2016

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.


PubMed | National Science Foundation, Korea University, The Taejin Genome Institute, Qingdao Agricultural University and Seoul National University
Type: | Journal: Genomics data | Year: 2016

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 8.676GB 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.


Jo Y.,Seoul National University | Choi H.,Seoul National University | Kim S.-M.,South Korean National Institute of Crop Science | Kim S.-L.,South Korean National Institute of Crop Science | And 3 more authors.
BMC Genomics | Year: 2016

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. © 2016 The Author(s).

Loading The Taejin Genome Institute collaborators
Loading The Taejin Genome Institute collaborators