• Journal of Ginseng Research
• /
• 제41권4호
• /
• pp.469-476
• /
• 2017

Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

• 한국균학회소식:학술대회논문집
• /
• 한국균학회 2015년도 추계학술대회 및 정기총회
• /
• pp.41-41
• /
• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• International Journal of Computer Science & Network Security
• /
• 제21권2호
• /
• pp.205-211
• /
• 2021

Plants are important for humanity. They intervene in several areas of human life: medicine, nutrition, cosmetics, decoration, etc. The large number of varieties of these plants requires an efficient solution to identify them for proper use. The ease of recognition of these plants undoubtedly depends on the classification of these species into family; however, finding the relevant characteristics to achieve better automatic classification is still a huge challenge for researchers in the field. In this paper, we have developed a new automatic plant classification technique based on artificial neural networks. Our model uses leaf texture characteristics as parameters for plant family identification. The results of our model gave a perfect classification of three plant families of the Ivorian flora, with a determination coefficient (R2) of 0.99; an error rate (RMSE) of 1.348e-14, a sensitivity of 84.85%, a specificity of 100%, a precision of 100% and an accuracy (Accuracy) of 100%. The same technique was applied on Flavia: the international basis of plants and showed a perfect identification regression (R2) of 0.98, an error rate (RMSE) of 1.136e-14, a sensitivity of 84.85%, a specificity of 100%, a precision of 100% and a trueness (Accuracy) of 100%. These results show that our technique is efficient and can guide the botanist to establish a model for many plants to avoid identification problems.

• 농업과학연구
• /
• 제49권1호
• /
• pp.121-128
• /
• 2022

Fusarium wilt disease caused by Fusarium species is a major problem affecting cultivated cucurbit plants worldwide. Fusarium species are well-known soil-borne pathogenic fungi that cause Fusarium wilt disease in several cucurbit plants. In this study, we aimed to identify and classify pathogenic Fusarium species from cultivated Korean cucurbit plants, specifically watermelon and cucumber. Thirty-six Fusarium isolates from different regions of Korea were obtained from the National Institute of Horticulture and Herbal Science Germplasm collection. Each isolate was morphologically and molecularly identified using an internal transcribed spacer of ribosomal DNA, elongation factor-1α, and the beta-tubulin gene marker sequence. Fusarium species that infect the cucurbit plant family could be divided into three groups: Fusarium oxysporum (F. oxysporum), Fusarium solani (F. solani), and Fusarium equiseti (F. equieti). Among the 36 isolates examined, six were non-pathogenic (F. equiseti: 15-127, F. oxysporum: 14-129, 17-557, 17-559, 18-369, F. solani: 12-155), whereas 30 isolates were pathogenic. Five of the F. solani isolates (11-117, 14-130, 17-554, 17-555, 17-556) were found to be highly pathogenic to both watermelon and cucumber plants, posing a great threat to cucurbit production in Korea. The identification of several isolates of F. equiseti and F. oxysporum, which are both highly pathogenic to bottle gourd, may indicate waning resistance to Fusarium species infection.

• 한국자원식물학회지
• /
• 제36권4호
• /
• pp.290-298
• /
• 2023

본 연구에서는 닥나무 속 식물에 대한 InDel 마커를 개발하였다. 전국의 닥나무 속 식물 22개체를 수집하였고, 수집한 닥나무 속 식물 중 6개체를 차세대염기서열 분석(NGS)을 실시하였다. NGS를 통하여 얻은 염기서열 정보를 기존에 발표되었던 닥나무 엽록체 서열과 비교하여 InDel 마커 후보를 선발하였다. 선발한 마커 후보를 수집된 닥나무 속 식물에 적용하여 마커의 특성 검정을 통해 총5개의 엽록체 기반 마커를 개발하였다. 개발된 InDel 마커를 22개의 유전자원에 적용한 후 군집 분석을 실시한 결과, 총5개의 그룹으로 나뉘었다. 본 연구에서 개발된 마커들은 닥나무 속의 육종이나 종 판별에 활용할 수 있을 것이라 판단된다.

• 한국자원식물학회:학술대회논문집
• /
• 한국자원식물학회 2018년도 추계학술대회
• /
• pp.64-64
• /
• 2018

The genus Cenchrus (Poaceae), containing ca. 97 species, is distributed throughout Australia, Africa and Indian sub-continent and which was introduced to the United States and Mexico for use in improved pasture. In Korea, especially Daecheong Island, it is one of the most hazardous invasive plant, which causes serious environmental threats, biodiversity damages and physically negative impact on humans and animals. It can cause serious damage to farms, fields and white sand beaches. However, the chloroplast (cp) genome sequences and information of Cenchrus longispinus have been not addressed, so we provide the complete cp genome of Cenchrus longispinus using next-generation sequencing technology. The size of cp genomes of this Daecheong Island species (Cenchrus longispinus) is 137,144 bp, and it shows a typical quadripartite structure. Consisting of the large single copy (LSC; 80,223 bp), small single copy (SSC; 12,449 bp), separated by a pair of inverted repeats (IRs; 22,236 bp). This cp genome contains 75 unique genes, 4 rRNA coding genes, 33 tRNA coding genes and 21 duplicated in the IR regions, with the gene content and organization are similar to other Poaceae cp genomes. Our comparative analysis identified four cpDNA regions (rpl16, rbcL, ndhH and ndhF) from three Cenchrus species, two Setaria species and one Pennisetum species which may be useful for molecular identification.

• 한국식물병리학회:학술대회논문집
• /
• 한국식물병리학회 1999년도 임시총회 및 추계 학술발표회
• /
• pp.32.2-32
• /
• 1999

• The Plant Pathology Journal
• /
• 제18권6호
• /
• pp.313-316
• /
• 2002

Systemic virus symptoms caused by a Potexvirus were observed on leaves of infected hosta (Hasta spp.) plants cultivated in Seoul, Korea. Symptoms on diseased hosta plants include mosaic, mottle, irregular blotchy patches, and chlorotic spots on or distortion of the leaves. No other viruses, such as Cucumber mosaic virus, Lily symptomless virus, or Potyvirus, were detected from the same plants by electron microscopy and by Western blot and RT-PCR analyses, indicating that they were singly infected by the potexvirus. The symptoms differed among cultivars and species of hosta, and affected the quality of plants for commercialization, as well as, plant growth and flowering of susceptible cultivars. Most of the cultivars and species investigated were susceptible to the virus, while some were not infected by the virus at all. Purified virus particles were of filamentous type with unaggregated forms 540 nm in length, which is a typical potexviral morphology. The virus consisted of a single-stranded RNA molecule of 6 kb long for genome and single component of coat protein (CP) about 27 kDa. The CP strongly reacted with the antiserum against Hosta vims X (HVX), suggesting that the virus is an isolate of HVX. This is the first report of the occurrence and identification of HVX from hosta plants in Korea.

• 한국작물학회지
• /
• 제42권2호
• /
• pp.236-246
• /
• 1997

우리나라의 자원식물 중 식용으로 이용할 수 있는 식물종에 대한 연구로서 식용자원의 발생 이황에 대한 연구와 유전자원 수집을 통해 얻어진 결과는 다음과 같다. 1. 우리나라에 발생하는 식용 자원식물 중 74 개과에 속하는 609종의 발생이 확인되었다. 2. 식용 자원식물의 수에 다른 과별 순위는 국화과＞백합과＞십자화과＞콩과＞장미과＞산형과＞화본과＞석죽과 순으로 나타났다. 3. 국화과, 십자화과, 백합과에 속하는 대부분의 식용식물은 경엽부를 채소로서 이용하고 있었으며, 장미과의 식물과 콩과 식물 중 일부는 과실이나 종자를 식용 자원으로 이용할 수 있었다. 4. 재배하는 작물종과 식물분류학적으로 근연관계에 있는 종의 수가 많은 화본과 식물은 직접 식용으로 이용할 수 있는 종의 수가 극히 적었다. 5. 수집된 종자들의 발아률은 종마다 다양하여 자원식물의 식용을 위해서는 발아율의 낮은 종의 발아율 개선에 대한 연구가 선행되어야 한다.

• The Plant Pathology Journal
• /
• 제25권1호
• /
• pp.13-20
• /
• 2009

Ninety isolates of Colletotrichum species from new persimmon tree twigs and 50 isolates from pepper plant fruits were isolated via single-spore isolation. Of the 140 isolates, 26 were examined for mycelial growth, carbendazim sensitivity, and ITS sequence. Four of the isolates from the persimmon trees, which were cultivated exclusively in an orchard, showed fast mycelial growth and sensitivity to carbendazim, while five of the pepper isolates showed slower mycelial growth and were resistant to the fungicide. However, 17 isolates from persimmon trees cultivated with pepper plants in the same orchard showed slow mycelial growth like the pepper isolates and they were sensitive to carbendazim like the persimmon isolates. ITS sequence analysis of these 27 isolates led to the identification of the 22 persimmon isolates as C. gloeosporioides and the five pepper isolates as C. acutatum. PCR with species-specific primers confirmed that the 90 isolates from persimmon were C. gloeosporioides whereas the 50 isolates from pepper were C. acutatum. The 90 persimmon isolates of C. gloeosporioides and 50 pepper isolates of C. acutatum were compared by a wound inoculation test to determine their capacity for host cross-infection. All of the C. acutatum isolates from pepper caused typical symptoms of anthracnose on the fruits of pepper plants and twigs of persimmon; they differed from the C. gloeosporioides isolates from persimmon, more than 90% of which were able to infect only persimmon. Amplified fragment length polymorphism analysis revealed the existence of two groups (C. gloeosporioides and C. acutatum isolates group). At 80% genetic similarity, the C. gloeosporioides group was defined within four clusters, while the C. acutatum group was within three clusters. However, these clusterings were unrelated with the virulence of Colletotrichum species against pepper fruits.