Deep Sequencing Analysis of Apple Infecting Viruses in Korea

조인숙,Davaajargal Igori,임승모,최국선,John Hammond,임현섭,문재선 한국식물병리학회 2016 Plant Pathology Journal Vol.32 No.5

Deep sequencing has generated 52 contigs derivedfrom five viruses; Apple chlorotic leaf spot virus(ACLSV), Apple stem grooving virus (ASGV), Applestem pitting virus (ASPV), Apple green crinkle associatedvirus (AGCaV), and Apricot latent virus (ApLV)were identified from eight apple samples showingsmall leaves and/or growth retardation. Nucleotide (nt)sequence identity of the assembled contigs was from68% to 99% compared to the reference sequences ofthe five respective viral genomes. Sequences of ASPVand ASGV were the most abundantly represented bythe 52 contigs assembled. The presence of the five virusesin the samples was confirmed by RT-PCR usingspecific primers based on the sequences of each assembledcontig. All five viruses were detected in threeof the samples, whereas all samples had mixed infectionswith at least two viruses. The most frequentlydetected virus was ASPV, followed by ASGV, ApLV,ACLSV, and AGCaV which were withal found inmixed infections in the tested samples. AGCaV wasidentified in assembled contigs ID 1012480 and 93549,which showed 82% and 78% nt sequence identity withORF1 of AGCaV isolate Aurora-1. ApLV was identifiedin three assembled contigs, ID 65587, 1802365,and 116777, which showed 77%, 78%, and 76% ntsequence identity respectively with ORF1 of ApLVisolate LA2. Deep sequencing assay was shown to bea valuable and powerful tool for detection and identificationof known and unknown virome in infectedapple trees, here identifying ApLV and AGCaV incommercial orchards in Korea for the first time.

Nucleotide sequence and genome organization of atractylodes mottle virus, a new member of the genus Carlavirus

Zhao, Fumei,Igori, Davaajargal,Lim, Seungmo,Yoo, Ran Hee,Lee, Su-Heon,Moon, Jae Sun Springer-Verlag 2015 Archives of virology Vol.160 No.11

Genomic detection and characterization of a Korean isolate of Little cherry virus 1 sampled from a peach tree.

Lim, Seungmo,Igori, Davaajargal,Yoo, Ran Hee,Zhao, Fumei,Cho, In-Sook,Choi, Gug-Seoun,Lim, Hyoun-Sub,Lee, Su-Heon,Moon, Jae Sun M. Nijhoff ; Kluwer Academic Publishers 2015 Virus genes Vol.51 No.2

<P>A peach tree (Prunus persica) showing yellowing and mild mottle symptoms was analyzed using high-throughput RNA sequencing to determine the causal agent. A total of nine contigs similar to Little cherry virus 1 (LChV-1) were produced, and all the contigs showed nucleotide sequence identity (lower than 83??%) and query coverage (higher than 73??%) with LChV-1. The symptomatic peach sample was confirmed to be infected with LChV-1-like virus as a result of reverse transcription-polymerase chain reaction using primers designed based on sequences of the contigs. Occurrence of diseases caused by LChV-1 in Prunus species has been reported. Complete 16,931-nt genome of the peach virus composed of eight open reading frames was determined, and conserved domains including viral methyltransferase, viral helicase 1, RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homologue (HSP70h), HSP90h and closterovirus coat protein (CP) were identified. Phylogenetic trees based on amino acid sequence alignments between the peach virus and members in the family Closteroviridae showed that the virus was most similar to LChV-1. Pairwise comparisons based on amino acid sequence alignments of three genes (RdRp, HSP70h and CP) between the peach virus and LChV-1 isolates showed the highest amino acid sequence identities, with 84.32??% for RdRp, 85.48??% for HSP70h and 80.45??% for CP. These results indicate that this is the first report for the presence of LChV-1 in South Korea and may be one of the first reports of natural infection of peach by LChV-1. Although it is not clear if LChV-1 YD isolate was responsible for specific symptoms observed, detection and characterization of the peach tree-infecting LChV-1 in South Korea would be useful in terms of the epidemiology of LChV-1.</P>

The Virome Analysis Responsible for Growth Retardation in Cnidium officinale

Se Eun Kim(김세은),Davaajargal Igori,Jeong A Kwon(권정아),Jae Sun Moon(문제선) 한국약용작물학회 2023 한국약용작물학회 학술대회논문집 Vol.2023 No.1

Deep Sequencing Analysis of Apple Infecting Viruses in Korea

Cho, In-Sook,Igori, Davaajargal,Lim, Seungmo,Choi, Gug-Seoun,Hammond, John,Lim, Hyoun-Sub,Moon, Jae Sun The Korean Society of Plant Pathology 2016 Plant Pathology Journal Vol.32 No.5

Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled. The presence of the five viruses in the samples was confirmed by RT-PCR using specific primers based on the sequences of each assembled contig. All five viruses were detected in three of the samples, whereas all samples had mixed infections with at least two viruses. The most frequently detected virus was ASPV, followed by ASGV, ApLV, ACLSV, and AGCaV which were withal found in mixed infections in the tested samples. AGCaV was identified in assembled contigs ID 1012480 and 93549, which showed 82% and 78% nt sequence identity with ORF1 of AGCaV isolate Aurora-1. ApLV was identified in three assembled contigs, ID 65587, 1802365, and 116777, which showed 77%, 78%, and 76% nt sequence identity respectively with ORF1 of ApLV isolate LA2. Deep sequencing assay was shown to be a valuable and powerful tool for detection and identification of known and unknown virome in infected apple trees, here identifying ApLV and AGCaV in commercial orchards in Korea for the first time.

Characteristics of a Lettuce mosaic virus Isolate Infecting Lettuce in Korea

Lim, Seungmo,Zhao, Fumei,Yoo, Ran Hee,Igori, Davaajargal,Lee, Su-Heon,Lim, Hyoun-Sub,Moon, Jae Sun The Korean Society of Plant Pathology 2014 Plant Pathology Journal Vol.30 No.2

Lettuce mosaic virus (LMV) causes disease of plants in the family Asteraceae, especially lettuce crops. LMV isolates have previously been clustered in three main groups, LMV-Yar, LMV-Greek and LMV-RoW. The first two groups, LMV-Yar and LMV-Greek, have similar characteristics such as no seed-borne transmission and non-resistance-breaking. The latter one, LMV-RoW, comprising a large percentage of the LMV isolates contains two large subgroups, LMV-Common and LMV-Most. To date, however, no Korean LMV isolate has been classified and characterized. In this study, LMV-Muju, the Korean LMV isolate, was isolated from lettuce showing pale green and mottle symptoms, and its complete genome sequence was determined. Classification method of LMV isolates based on nucleotide sequence divergence of the NIb-CP junction showed that LMV-Muju was categorized as LMV-Common. LMV-Muju was more similar to LMV-O (LMV-Common subgroup) than to LMV-E (LMV-RoW group but not LMV-Common subgroup) even in the amino acid domains of HC-Pro associated with pathogenicity, and in the CI and VPg regions related to ability to overcome resistance. Taken together, LMV-Muju belongs to the LMV-Common subgroup, and is expected to be a seed-borne, non-resistance-breaking isolate. According to our analysis, all other LMV isolates not previously assigned to a subgroup were also included in the LMV-RoW group.

Characteristics of a Lettuce mosaic virus Isolate Infecting Lettuce in Korea

임승모,임현섭,문제선,유란희,이수헌,Fumei Zhao,Davaajargal Igori 한국식물병리학회 2014 Plant Pathology Journal Vol.30 No.2

Lettuce mosaic virus (LMV) causes disease of plants in the family Asteraceae, especially lettuce crops. LMV isolates have previously been clustered in three main groups, LMV-Yar, LMV-Greek and LMV-RoW. The first two groups, LMV-Yar and LMV-Greek, have similar characteristics such as no seed-borne transmission and non-resistance-breaking. The latter one, LMV-RoW, comprising a large percentage of the LMV isolates contains two large subgroups, LMV-Common and LMV-Most. To date, however, no Korean LMV isolate has been classified and characterized. In this study, LMV-Muju, the Korean LMV isolate, was isolated from lettuce showing pale green and mottle symptoms, and its complete genome sequence was determined. Classification method of LMV isolates based on nucleotide sequence divergence of the NIb-CP junction showed that LMV-Muju was categorized as LMV-Common. LMV-Muju was more similar to LMV-O (LMV-Common subgroup) than to LMV-E (LMV-RoW group but not LMV-Common subgroup) even in the amino acid domains of HC-Pro associated with pathogenicity, and in the CI and VPg regions related to ability to overcome resistance. Taken together, LMV-Muju belongs to the LMV-Common subgroup, and is expected to be a seed-borne, non-resistance-breaking isolate. According to our analysis, all other LMV isolates not previously assigned to a subgroup were also included in the LMV-RoW group.

국내 배추와 중국 유래 청경채의 영양성분 비교

간치맥(Ganchimeg Gantumar),조만현(Man Hyun Jo),다바잘갈(Davaajargal Igori),함인기(In Ki Ham),이은모(Eun Mo Lee),이왕희(Wang-Hee Lee),임용표(Yongpyo Lim),안길환(Gilhwan An),박종태(Jong-Tae Park) 한국식품영양과학회 2013 한국식품영양과학회지 Vol.42 No.9

본 연구는 중국유래 14 품종 청경채의 영양적 특성을 평가하고자 수행되었다. 14종의 신규 청경채(Brassica rapa L.ssp. chinensis)를 대표적인 국산 배추(Brassica rapa L.ssp. pekinensis) 4 품종과 함께 2008년 충남 예산에서 재배하여 수확한 후 녹색 부위와 백색 부위로 나누어 부위 별 각종 영양 성분 분석을 수행하였다. 청경채의 수분 및 회분함량은 배추에 비교하여 유의적 차이가 없었으나 수분은 백색 부위에서, 회분은 녹색 부위에서 높게 나타났다. 전체적인 무기염류 함량은 배추에 비하여 청경채가 높은 것으로 측정되었는데 특히 녹색 부위의 함유량이 유의적으로 높은 것으로 드러났다. 특히 현대인의 건강에 매우 중요한 Ca과 Mg의 함유량은 청경채(Ca녹색: 2.57, Ca백색: 2.04; Mg녹색: 0.422, Mg백색: 0.301 mg/g 신선물 기준)가 배추(Ca녹색:0.805, Ca백색: 0.477; Mg녹색: 0.244, Mg백색: 0.101 mg/g신선물 기준)에 비하여 매우 높았다. 환원당의 함량은 청경채와 배추가 유사한 값을 나타내었고 색에 따른 유의적 차이도 없었다. 펙틴은 부위에 따른 차이는 있으나 청경채에서 그 함량이 높게 나타났고, 식물 조직의 경도에 영향이 큰 셀룰로오스의 함량은 청경채가 약 4배 이상 배추보다 높았다. 비타민 C와 E 함량은 청경채와 배추가 유사한 것으로 측정되었다. 위와 같이 청경채는 영양적으로 매우 우수하여 소비자들에게 권장할 만한 매일 섭취해야 할 주요 채소작물의 하나로 손색이 없음을 알 수 있었다. 또한 청경채는 국내배추의 품질 향상을 위한 육종 소재로서도 활용가치가 높을 것으로 사료된다. The nutritional components of 14 new cultivars of pak choi (Brassica rapa L. ssp. chinensis) from China were analyzed and compared with 4 cultivars of Chinese cabbage (Brassica rapa L. ssp. pekinensis) popular in Korea. Leaves were separated into green parts (GP) and white parts (WP) for the analyses. The moisture and ash content in the 14 new cultivars of pak choi were not significantly different from the currently popular cultivars of Chinese cabbage. In addition, the levels of vitamin C and E were very similar between the two kinds of Brassica rapa. In contrast, the overall mineral content was higher in the new pak choi cultivars. Specifically, minerals important for human health, calcium and magnesium, were significantly greater in pak choi cultivars (calcium GP 2.57, WP 2.04; magnesium GP 0.422, WP 0.301 mg/g fresh weight) compared to currently popular cultivars (calcium GP 0.805, WP 0.477; magnesium GP 0.244, WP 0.101 mg/g fresh weight). Although the content of reducing sugars was similar, cellulose content (which correlates with the hardness of plant tissue) was four times higher in the new pak choi cultivars compared to currently popular cultivars. These results demonstrate that the new pak choi cultivars have superb nutritional benefits for human health and could be a good food source as a daily staple vegetable.