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Jong-Wook Chung
Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea

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Journal article
Published: 07 July 2021 in Mycobiology
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Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.

ACS Style

Hyejin An; Hwa-Yong Lee; Hyeran Shin; Jun Hyoung Bang; Seahee Han; Youn-Lee Oh; Kab-Yeul Jang; Hyunwoo Cho; Tae Kyung Hyun; Jwakyung Sung; Yoon-Sup So; Ick-Hyun Jo; Jong-Wook Chung. Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers. Mycobiology 2021, 1 -9.

AMA Style

Hyejin An, Hwa-Yong Lee, Hyeran Shin, Jun Hyoung Bang, Seahee Han, Youn-Lee Oh, Kab-Yeul Jang, Hyunwoo Cho, Tae Kyung Hyun, Jwakyung Sung, Yoon-Sup So, Ick-Hyun Jo, Jong-Wook Chung. Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers. Mycobiology. 2021; ():1-9.

Chicago/Turabian Style

Hyejin An; Hwa-Yong Lee; Hyeran Shin; Jun Hyoung Bang; Seahee Han; Youn-Lee Oh; Kab-Yeul Jang; Hyunwoo Cho; Tae Kyung Hyun; Jwakyung Sung; Yoon-Sup So; Ick-Hyun Jo; Jong-Wook Chung. 2021. "Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers." Mycobiology , no. : 1-9.

Journal article
Published: 21 May 2021 in Agronomy
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Amaranthus species are widely used as grain and leaf vegetables around the world and are potential dietary sources of antioxidants and phenolic compounds. In this study, we examined the variation in total flavonoid contents, total polyphenol contents, and antioxidant activities among 120 accessions of nine Amaranthus species. The antioxidant activity of DPPH (2,2-diphenyl-1-picrylhydrazyl) of the 120 amaranth accessions ranged from 1.1 (A. tricolor) to 75.2 (A. tricolor mg ascorbic acid equivalents (AAE)/g in 2018, and 8.5 (A. tricolor) to 68.8 (A. dubius) mg AAE/g in 2019. ABTS (2,2′-azinobis (3-ethylbenzothiazoline 6-sulfonate)) antioxidant activity ranged from 16.7 (A. tricolor) to 78.3 (A. hypochondriacus) mg AAE/g in 2018, and 36.6 (A. tricolor) to 79.2 (A. dubius) mg AAE/g in 2019. Total flavonoid content (TFC) of 2018 and 2019 ranged from 21.7 (A. caudatus) to 52.7 (A. hybridus) and from 22.3 (A. viridis) to 54.7 (A. tricolor), respectively Antioxidant activities were compared using two methods and all components were measured in plants grown both in 2018 and 2019. We identified wide variation among the accessions and between plants grown in the two years. Antioxidant activities and phytochemical contents were consistently negatively correlated. The nine species and 120 accessions clustered into three groups according to their antioxidant activities, total flavonoid contents, and total polyphenol contents in each year. These results provide information about the nutritional profiles of different Amaranthus species.

ACS Style

Jun-Hyoung Bang; Kyung Lee; Won Jeong; Seahee Han; Ick-Hyun Jo; Seong Choi; Hyunwoo Cho; Tae Hyun; Jeehye Sung; Junsoo Lee; Yoon-Sup So; Jong-Wook Chung. Antioxidant Activity and Phytochemical Content of Nine Amaranthus Species. Agronomy 2021, 11, 1032 .

AMA Style

Jun-Hyoung Bang, Kyung Lee, Won Jeong, Seahee Han, Ick-Hyun Jo, Seong Choi, Hyunwoo Cho, Tae Hyun, Jeehye Sung, Junsoo Lee, Yoon-Sup So, Jong-Wook Chung. Antioxidant Activity and Phytochemical Content of Nine Amaranthus Species. Agronomy. 2021; 11 (6):1032.

Chicago/Turabian Style

Jun-Hyoung Bang; Kyung Lee; Won Jeong; Seahee Han; Ick-Hyun Jo; Seong Choi; Hyunwoo Cho; Tae Hyun; Jeehye Sung; Junsoo Lee; Yoon-Sup So; Jong-Wook Chung. 2021. "Antioxidant Activity and Phytochemical Content of Nine Amaranthus Species." Agronomy 11, no. 6: 1032.

Journal article
Published: 11 May 2021 in Journal of Fungi
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Agaricus bisporus is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the A. bisporus genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 A. bisporus accessions for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0–0.499 (mean = 0.265) and 0.0–0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with F-statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299–0.499) and major allele frequency (MAF, range 0.524–0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.

ACS Style

Hyejin An; Hwa-Yong Lee; Donghwan Shim; Seong Choi; Hyunwoo Cho; Tae Hyun; Ick-Hyun Jo; Jong-Wook Chung. Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus). Journal of Fungi 2021, 7, 375 .

AMA Style

Hyejin An, Hwa-Yong Lee, Donghwan Shim, Seong Choi, Hyunwoo Cho, Tae Hyun, Ick-Hyun Jo, Jong-Wook Chung. Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus). Journal of Fungi. 2021; 7 (5):375.

Chicago/Turabian Style

Hyejin An; Hwa-Yong Lee; Donghwan Shim; Seong Choi; Hyunwoo Cho; Tae Hyun; Ick-Hyun Jo; Jong-Wook Chung. 2021. "Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus)." Journal of Fungi 7, no. 5: 375.

Research article
Published: 09 February 2021 in Frontiers in Plant Science
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Recently, within the Fabaceae family, the Vicia genus has been recognized for its vital role in sustainable agriculture. Vicia species are economically important grain and forage crops. However, the presence of complex morphological characteristics makes identification and recognition of native species difficult. In this study, the possibility of using DNA barcoding regions (ITS2, matK, and rbcL) to distinguish among 19 Vicia taxa (59 accessions) found in South Korea was evaluated. The sequence alignment analysis revealed considerable nucleotide diversity (π) between the loci, in which ITS2 showed the highest mean interspecific distance, whereas there was no intraspecific variability among the barcode regions in 12 of the 19 taxa. Phylogenetic analysis of combined barcoding regions revealed well-resolved phylogeny with the highest species level discrimination. Combinations of barcode loci were also used in classification at the subgenera and section levels. The results revealed that the combined barcoding regions can be used effectively to differentiate the following species: Vicia angustifolia var. segetilis, Vicia bungei, Vicia villosa, Vicia cracca, Vicia dasycarpa, Vicia hirsuta, Vicia tetrasperma, Vicia amurensis, Vicia hirticalycina, and Vicia chosenensis. However, it is difficult to differentiate the species of Vicia unijuga, Vicia unijuga var. kaussanensis, Vicia linearifolia, Vicia unijuga f. angustifolia, Vicia nipponica, Vicia amoena, Vicia venosa var. cuspidata, Vicia pseudo-orobus, and Vicia japonica with the tested barcode regions. These species come under sect. Vicilla and are found to be closely related or species that have recently undergone speciation; thus, it has limitation to distinguish with recommended barcodes. Hence, to differentiate the unclassified species, 39 morphological characteristics were investigated, in which 16 useful characteristics were selected for efficient classification. Finally, the 16 selected morphological useful traits efficiently differentiated all the Vicia species. In conclusion, a combination of barcoding loci together with morphological characteristics of this study efficiently discriminated all the Korean Vicia species.

ACS Style

Seahee Han; Raveendar Sebastin; Xiaohan Wang; Kyung Jun Lee; Gyu-Taek Cho; Do Yoon Hyun; Jong-Wook Chung. Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics. Frontiers in Plant Science 2021, 12, 1 .

AMA Style

Seahee Han, Raveendar Sebastin, Xiaohan Wang, Kyung Jun Lee, Gyu-Taek Cho, Do Yoon Hyun, Jong-Wook Chung. Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics. Frontiers in Plant Science. 2021; 12 ():1.

Chicago/Turabian Style

Seahee Han; Raveendar Sebastin; Xiaohan Wang; Kyung Jun Lee; Gyu-Taek Cho; Do Yoon Hyun; Jong-Wook Chung. 2021. "Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics." Frontiers in Plant Science 12, no. : 1.

Journal article
Published: 07 January 2021 in Antioxidants
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Plant extracts have gained more attention as natural therapeutic agents against inflammation characterized by an overproduction of several inflammatory mediators such as reactive oxygen species and pro-inflammatory cytokines. Although Abeliophyllum distichum Nakai is generally known for its ornamental value, recent pharmacological research has demonstrated its potential therapeutic properties. Thus, to further evaluate the applicability of A. distichum in the food, cosmetic, and medical industries, we identified the phytochemicals in three organ extracts (fruits: AF, branches: AB, leaves: AL) of A. distichum and determined their antioxidant and anti-inflammatory activities. Using UPLC-ESI-Q-TOF-MS, a total of 19 compounds, including dendromoniliside D, forsythoside B, isoacteoside, isomucronulatol 7-O-Glucoside, plantamajoside, and wighteone were identified in the A. distichum organ extracts. AB exhibited a strong reducing power, an oxygen radical antioxidant capacity, and radical scavenging values compared with other samples, whereas AL exhibited the best anti-inflammatory properties. Gene expression, western blot, and molecular docking analyses suggested that the anti-inflammatory effect of AL was mediated by its ability to suppress lipopolysaccharide (LPS)-induced production of reactive oxygen species and/or inhibit LPS-stimulated activation of extracellular signal-regulated protein kinases (ERK1/2) in RAW264.7 cells. Collectively, these results indicate that AL is a potential source of phytochemicals that could be used to treat inflammation-associated diseases.

ACS Style

Tong-Kewn Yoo; Won Tae Jeong; Jun Gu Kim; Hyo Seong Ji; Min-A Ahn; Jong-Wook Chung; Heung Bin Lim; Tae Kyung Hyun. UPLC-ESI-Q-TOF-MS-Based Metabolite Profiling, Antioxidant and Anti-Inflammatory Properties of Different Organ Extracts of Abeliophyllum distichum. Antioxidants 2021, 10, 70 .

AMA Style

Tong-Kewn Yoo, Won Tae Jeong, Jun Gu Kim, Hyo Seong Ji, Min-A Ahn, Jong-Wook Chung, Heung Bin Lim, Tae Kyung Hyun. UPLC-ESI-Q-TOF-MS-Based Metabolite Profiling, Antioxidant and Anti-Inflammatory Properties of Different Organ Extracts of Abeliophyllum distichum. Antioxidants. 2021; 10 (1):70.

Chicago/Turabian Style

Tong-Kewn Yoo; Won Tae Jeong; Jun Gu Kim; Hyo Seong Ji; Min-A Ahn; Jong-Wook Chung; Heung Bin Lim; Tae Kyung Hyun. 2021. "UPLC-ESI-Q-TOF-MS-Based Metabolite Profiling, Antioxidant and Anti-Inflammatory Properties of Different Organ Extracts of Abeliophyllum distichum." Antioxidants 10, no. 1: 70.

Journal article
Published: 24 December 2020 in Animals
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The amaranth plants showed high potential feed value as forage for ruminants. An in-depth study of this plant, particularly in cattle, will help extend its utilization as an alternative protein and fiber feed source in cattle feeding. In this study, the nutrient compositions of three different species of amaranth, Amaranthus caudatus L., Amaranthus cruentus L., and Amaranthus hypochondriacus L.—two varieties for each species, A.ca 74, A.ca 91, A.cu 62, A.cu 66, A. hy 30, and A. hy 48—were evaluated. The in vitro technique was used to evaluate the fermentation characteristics such as total gas production, total volatile fatty acids (VFA) concentration, pH, and ammonia concentration of the rumen fluid. Moreover, the effective degradabilities of dry matter (EDDM) and crude protein (EDCP) of the amaranth forages were determined through in situ bag technique. The amaranth forages: A. caudatus, A. cruentus, and A. hypochondriacus showed better nutritive value than the locally produced forages in Chungcheong province of Korea. The CP of the amaranth ranged from 11.95% to 14.19%, and the neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents ranged from 45.53% to 70.88% and 34.17% to 49.83%, respectively. Among the amaranth varieties, A. hypochondriacus 48 showed the most excellent ruminant feed nutrient quality (CP, 14.19%; NDF, 45.53%; and ADF, 34.17%). The effective degradabilities of dry matter (EDDM; 33–56%) and crude protein EDCP (27–59%) of the amaranth were lower compared to other studies, which could be due to the maturity stage at which the forages were harvested. Nonetheless, A. hypochondriacus 48 showed the highest EDDM (56.73%) and EDCP (59.09%). The different amaranth species did not differ greatly in terms of total VFA concentration or molar proportions, total gas production, or ammonia-N concentration. The high nutrient composition, and highly effective degradability of dry matter and crude protein, coupled with the favorable fermentation characteristics, suggest that the amaranth forages showed good to excellent feed quality for cattle.

ACS Style

Kim Margarette C. Nogoy; Jia Yu; Young Gyu Song; Shida Li; Jong-Wook Chung; Seong Ho Choi. Evaluation of the Nutrient Composition, In Vitro Fermentation Characteristics, and In Situ Degradability of Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hypochondriacus in Cattle. Animals 2020, 11, 18 .

AMA Style

Kim Margarette C. Nogoy, Jia Yu, Young Gyu Song, Shida Li, Jong-Wook Chung, Seong Ho Choi. Evaluation of the Nutrient Composition, In Vitro Fermentation Characteristics, and In Situ Degradability of Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hypochondriacus in Cattle. Animals. 2020; 11 (1):18.

Chicago/Turabian Style

Kim Margarette C. Nogoy; Jia Yu; Young Gyu Song; Shida Li; Jong-Wook Chung; Seong Ho Choi. 2020. "Evaluation of the Nutrient Composition, In Vitro Fermentation Characteristics, and In Situ Degradability of Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hypochondriacus in Cattle." Animals 11, no. 1: 18.

Communication
Published: 01 December 2020 in Molecules
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We used ultraperformance liquid chromatography coupled with a photodiode-array detector and electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-PDA/ESI-Q-TOF/MS) to rapidly and accurately quantify 17 phenolic compounds. Then, we applied this method to the seed and leaf extracts of two Amaranthus species to identify and quantify phenolic compounds other than the 17 compounds mentioned above. Compounds were eluted within 30 min on a C18 column using a mobile phase (water and acetonitrile) containing 0.1% formic acid, and the specific wavelength and ion information of the compounds obtained by PDA and ESI-Q-TOF/MS were confirmed. The proposed method showed good linearity (r2 > 0.990). Limits of detection and quantification were less than 0.1 and 0.1 μg/mL, respectively. Intra- and interday precision were less than 2.4% and 1.8%, respectively. Analysis of amaranth seed and leaf extracts using the established method showed that the seeds contained high amounts of 2,4-dihydroxybenzoic acid and kaempferol, and leaves contained diverse phenolic compounds. In addition, six tentatively new phenolic compounds were identified. Moreover, seeds potentially contained 2,3-dihydroxybenzaldehyde, a beneficial bioactive compound. Thus, our method was an efficient approach for the qualitative and quantitative analysis of phenolic compounds, and could be used to investigate phenolic compounds in plants.

ACS Style

Won Tea Jeong; Jun-Hyoung Bang; Seahee Han; Tae Kyung Hyun; Hyunwoo Cho; Heung Bin Lim; Jong-Wook Chung. Establishment of a UPLC-PDA/ESI-Q-TOF/MS-Based Approach for the Simultaneous Analysis of Multiple Phenolic Compounds in Amaranth (A. cruentus and A. tricolor). Molecules 2020, 25, 5674 .

AMA Style

Won Tea Jeong, Jun-Hyoung Bang, Seahee Han, Tae Kyung Hyun, Hyunwoo Cho, Heung Bin Lim, Jong-Wook Chung. Establishment of a UPLC-PDA/ESI-Q-TOF/MS-Based Approach for the Simultaneous Analysis of Multiple Phenolic Compounds in Amaranth (A. cruentus and A. tricolor). Molecules. 2020; 25 (23):5674.

Chicago/Turabian Style

Won Tea Jeong; Jun-Hyoung Bang; Seahee Han; Tae Kyung Hyun; Hyunwoo Cho; Heung Bin Lim; Jong-Wook Chung. 2020. "Establishment of a UPLC-PDA/ESI-Q-TOF/MS-Based Approach for the Simultaneous Analysis of Multiple Phenolic Compounds in Amaranth (A. cruentus and A. tricolor)." Molecules 25, no. 23: 5674.

Journal article
Published: 26 November 2020 in Agronomy
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Panax ginseng C. A. Mey., a perennial herb belonging to the family Araliaceae, is a valuable medicinal plant with distinctive biological characteristics. However, comprehensive analyses of the mitochondrial genome (mitogenome) are lacking. In this study, we sequenced the complete mitogenome of ginseng based on long-read data from the Nanopore sequencing platform. The mitogenome was assembled into a “master circle” form of 464,705 bp and contained 72 unique genes. The genome had three large repeat regions, and 10.42% of the sequences were mitogenome sequences of plastid origin (MTPTs). In total, 278 variants (213 SNPs and 65 InDels) were discovered, most of which were identified in intergenic regions. The MTPT regions were mutational hotspots, harboring 74.5% of the variants. The ginseng mitogenome showed a higher mutation rate than that of the chloroplast genome, and this pattern is uncommon in plants. In addition, 10 Kompetitive allele-specific PCR (KASP) markers were developed from 10 SNPs, excluding those in MTPT regions. These markers accurately identified the genotypes of 59 Korean ginseng accessions and elucidated mitogenome diversity. These results provide insight into organellar genomes and genetic diversity in ginseng. Moreover, the complete mitogenome sequence and 10 KASP markers will be useful for ginseng research and breeding.

ACS Style

Woojong Jang; Hyun Oh Lee; Jang-Uk Kim; Jung-Woo Lee; Chi-Eun Hong; Kyong-Hwan Bang; Jong-Wook Chung; Ick-Hyun Jo. Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.). Agronomy 2020, 10, 1868 .

AMA Style

Woojong Jang, Hyun Oh Lee, Jang-Uk Kim, Jung-Woo Lee, Chi-Eun Hong, Kyong-Hwan Bang, Jong-Wook Chung, Ick-Hyun Jo. Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.). Agronomy. 2020; 10 (12):1868.

Chicago/Turabian Style

Woojong Jang; Hyun Oh Lee; Jang-Uk Kim; Jung-Woo Lee; Chi-Eun Hong; Kyong-Hwan Bang; Jong-Wook Chung; Ick-Hyun Jo. 2020. "Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.)." Agronomy 10, no. 12: 1868.

Journal article
Published: 09 November 2020 in Journal of Fungi
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Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.

ACS Style

Chang Pyo Hong; Suyun Moon; Seung-Il Yoo; Jong-Hyun Noh; Han-Gyu Ko; Hyun A. Kim; Hyeon-Su Ro; Hyunwoo Cho; Jong-Wook Chung; Hwa-Yong Lee; Hojin Ryu. Functional Analysis of a Novel ABL (Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes. Journal of Fungi 2020, 6, 272 .

AMA Style

Chang Pyo Hong, Suyun Moon, Seung-Il Yoo, Jong-Hyun Noh, Han-Gyu Ko, Hyun A. Kim, Hyeon-Su Ro, Hyunwoo Cho, Jong-Wook Chung, Hwa-Yong Lee, Hojin Ryu. Functional Analysis of a Novel ABL (Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes. Journal of Fungi. 2020; 6 (4):272.

Chicago/Turabian Style

Chang Pyo Hong; Suyun Moon; Seung-Il Yoo; Jong-Hyun Noh; Han-Gyu Ko; Hyun A. Kim; Hyeon-Su Ro; Hyunwoo Cho; Jong-Wook Chung; Hwa-Yong Lee; Hojin Ryu. 2020. "Functional Analysis of a Novel ABL (Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes." Journal of Fungi 6, no. 4: 272.

Research article
Published: 21 September 2020 in Microscopy Research and Technique
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Seed macro‐ and micro‐morphology were analyzed to evaluate their capacity to discriminate species in the genus Vicia (Fabaceae). To assess the interspecific variation of the taxa in the genus Vicia, 41 accessions were obtained from the USDA‐ARS germplasm collection in the USA and 19 accessions were collected from Korea. Seed morphological characteristics such as shape, color, mottling, finish, length, width, diameter, hilum shape, hilum color, hilum length, and lens distance from the hilum were examined under a stereomicroscope. Testa texture characteristics such as testa pattern, papillae type, density, height, ribbing, surface deposits, and peaks topped with wax were examined under scanning electron microscopy. Various gross‐morphological traits of seeds of Vicia species have been analyzed and compared. The present study revealed significant variation in testa traits. Testa were papillose and papillose with mounds, the latter being observed only in Vicia lathyroides. The present study revealed 20 key traits that could be used to diagnose Vicia species and classify them.

ACS Style

Seahee Han; Raveendar Sebastin; Kyung Jun Lee; Xiaohan Wang; Myoung‐Jae Shin; Seong‐Hoon Kim; Sookyeong Lee; Jung‐Ro Lee; Gyu‐Taek Cho; Do Yoon Hyun; Jong‐Wook Chung. Interspecific variation of seed morphological and micro‐morphological traits in the genus Vicia (Fabaceae). Microscopy Research and Technique 2020, 84, 337 -357.

AMA Style

Seahee Han, Raveendar Sebastin, Kyung Jun Lee, Xiaohan Wang, Myoung‐Jae Shin, Seong‐Hoon Kim, Sookyeong Lee, Jung‐Ro Lee, Gyu‐Taek Cho, Do Yoon Hyun, Jong‐Wook Chung. Interspecific variation of seed morphological and micro‐morphological traits in the genus Vicia (Fabaceae). Microscopy Research and Technique. 2020; 84 (2):337-357.

Chicago/Turabian Style

Seahee Han; Raveendar Sebastin; Kyung Jun Lee; Xiaohan Wang; Myoung‐Jae Shin; Seong‐Hoon Kim; Sookyeong Lee; Jung‐Ro Lee; Gyu‐Taek Cho; Do Yoon Hyun; Jong‐Wook Chung. 2020. "Interspecific variation of seed morphological and micro‐morphological traits in the genus Vicia (Fabaceae)." Microscopy Research and Technique 84, no. 2: 337-357.

Journal article
Published: 05 March 2020 in Antioxidants
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Black soybean (Glycine max L.) has been used as a traditional medicine because its seed coat contains various natural phenolic compounds such as anthocyanins. The objective of this study was to reveal the genetic variation in the agricultural traits, phytochemicals, and antioxidant activity of 172 Korean black soybean landraces (KBSLs) and establish a relationship among them. The evaluation of three agricultural traits (days to 50% flowering, maturity, and 100-seed weight), six phytochemicals (delphinidin-3-glucoside, cyaniding-3-glucoside, petunidin-3-glucoside, daidzin, glycitin, and genestin), and four antioxidant activities (2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid)(ABTS), ferric-reducing antioxidant power (FRAP), and the total polyphenol content (TPC) of 172 KBSLs were analyzed in 2012 and 2015. The agricultural traits, phytochemicals, and antioxidant activities of the 172 KBSLs showed wide variation among the accessions and years. In correlation analysis, the agricultural traits and phytochemicals showed positive and negative correlations with phytochemicals and antioxidant activity, respectively. The principal component analyses result indicated that phytochemicals accounted for most of the variability in the KBSLs. In clustering analysis, the 172 KBSLs were classified into four clusters. These results could lead to expanding the knowledge of the agricultural traits, phytochemicals, and antioxidant activity of the KBSLs, which are valuable materials for the development of new soybean varieties.

ACS Style

Kyung Jun Lee; Da-Young Baek; Gi-An Lee; Gyu-Taek Cho; Yoon-Sup So; Jung-Ro Lee; Kyung-Ho Ma; Jong-Wook Chung; Do Yoon Hyun. Phytochemicals and Antioxidant Activity of Korean Black Soybean (Glycine max L.) Landraces. Antioxidants 2020, 9, 213 .

AMA Style

Kyung Jun Lee, Da-Young Baek, Gi-An Lee, Gyu-Taek Cho, Yoon-Sup So, Jung-Ro Lee, Kyung-Ho Ma, Jong-Wook Chung, Do Yoon Hyun. Phytochemicals and Antioxidant Activity of Korean Black Soybean (Glycine max L.) Landraces. Antioxidants. 2020; 9 (3):213.

Chicago/Turabian Style

Kyung Jun Lee; Da-Young Baek; Gi-An Lee; Gyu-Taek Cho; Yoon-Sup So; Jung-Ro Lee; Kyung-Ho Ma; Jong-Wook Chung; Do Yoon Hyun. 2020. "Phytochemicals and Antioxidant Activity of Korean Black Soybean (Glycine max L.) Landraces." Antioxidants 9, no. 3: 213.

Research article
Published: 02 March 2020 in Mycobiology
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In this study, the genetic diversity and the population structure of 77 wild strains and 23 cultivars of Lentinula edodes from Korea were analyzed using 20 genomic SSRs, and their genetic relationship was investigated. The tested strains of L. edodes were divided into three sub-groups consisting of only wild strains, mainly wild strains and several cultivars, and mainly cultivars and several wild strains by distance-based analysis. Using model-based analysis, L. edodes strains were divided into two subpopulations; the first one consisting of only wild strains and the second one with mainly cultivars and several wild strains. Moreover, AMOVA analysis revealed that the genetic variation in the cultivars was higher than that in the wild strains. The expected and observed heterozygosity and values indicating the polymorphic information content of L. edodes cultivars from Korea were also higher than that of the wild strains. Based on these results, we presume that the cultivars in Korea have developed by using numerous strains from other countries. In conclusion, the usage of wild strains for the development of new cultivars could improve the adaptability of L. edodes to biotic and abiotic stress.

ACS Style

Hwa-Yong Lee; Suyun Moon; Hyeon-Su Ro; Jong-Wook Chung; Hojin Ryu. Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes. Mycobiology 2020, 48, 115 -121.

AMA Style

Hwa-Yong Lee, Suyun Moon, Hyeon-Su Ro, Jong-Wook Chung, Hojin Ryu. Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes. Mycobiology. 2020; 48 (2):115-121.

Chicago/Turabian Style

Hwa-Yong Lee; Suyun Moon; Hyeon-Su Ro; Jong-Wook Chung; Hojin Ryu. 2020. "Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes." Mycobiology 48, no. 2: 115-121.

Research note
Published: 27 September 2019 in Mycobiology
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We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (MAF) and the average number of alleles (NA) were 0.50 and 5.47, respectively. The average number of genotypes (NG), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson’s correlation coefficient showed that MAF was negatively correlated with NG (−0.683), NA (−0.600), HO (−0.584), and PIC (−0.941). NG, NA, HO, and PIC were positively correlated with other polymorphic parameters except for MAF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

ACS Style

Hyejin An; Ick-Hyun Jo; Youn-Lee Oh; Kab-Yeul Jang; Won-Sik Kong; Jwa-Kyung Sung; Yoon-Sup So; Jong-Wook Chung. Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus). Mycobiology 2019, 47, 527 -532.

AMA Style

Hyejin An, Ick-Hyun Jo, Youn-Lee Oh, Kab-Yeul Jang, Won-Sik Kong, Jwa-Kyung Sung, Yoon-Sup So, Jong-Wook Chung. Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus). Mycobiology. 2019; 47 (4):527-532.

Chicago/Turabian Style

Hyejin An; Ick-Hyun Jo; Youn-Lee Oh; Kab-Yeul Jang; Won-Sik Kong; Jwa-Kyung Sung; Yoon-Sup So; Jong-Wook Chung. 2019. "Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)." Mycobiology 47, no. 4: 527-532.

Journal article
Published: 07 August 2019 in PeerJ
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Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb in European and Asian countries. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated species. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. In the present study, we developed polymorphic SSR markers based on whole-genomesequence data of Glycyrrhiza lepidota. Then, based on the sequence information, the polymorphic SSR markers were developed. The SSR markers were applied to 23 Glycyrrhiza individual plants. We also evaluated the phylogenetic relationships and interspecies transferability among samples. The genetic diversity analysis using these markers identified 2-23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11-0.91, 0-0.90, 0.17-0.94, and 0.15-0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The reported markers represent a valuable resource for the genetic characteri z ation of Glycyrrhiza spp. for theanalysis of its genetic variability, and as a tool for licorice transferability. This is the first intraspecific study in a collection of Glycyrrhiza spp. germplasm using SSR markers.

ACS Style

Jun Hyoung Bang; Chi Eun Hong; Sebastin Raveendar; Kyong Hwan Bang; Kyung Ho Ma; Soonwook Kwon; Hojin Ryu; Ick Hyun Jo; Jong-Wook Chung. Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. PeerJ 2019, 7, e7479 .

AMA Style

Jun Hyoung Bang, Chi Eun Hong, Sebastin Raveendar, Kyong Hwan Bang, Kyung Ho Ma, Soonwook Kwon, Hojin Ryu, Ick Hyun Jo, Jong-Wook Chung. Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. PeerJ. 2019; 7 ():e7479.

Chicago/Turabian Style

Jun Hyoung Bang; Chi Eun Hong; Sebastin Raveendar; Kyong Hwan Bang; Kyung Ho Ma; Soonwook Kwon; Hojin Ryu; Ick Hyun Jo; Jong-Wook Chung. 2019. "Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species." PeerJ 7, no. : e7479.

Preprint
Published: 29 April 2019
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Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers. Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.

ACS Style

Jun Hyoung Bang; Chi Eun Hong; Sebastin Raveendar; Kyong Hwan Bang; Kyung Ho Ma; Soon Wook Kwon; Hojin Ryu; Ick Hyun Jo; Jong Wook Chung. Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. 2019, 1 .

AMA Style

Jun Hyoung Bang, Chi Eun Hong, Sebastin Raveendar, Kyong Hwan Bang, Kyung Ho Ma, Soon Wook Kwon, Hojin Ryu, Ick Hyun Jo, Jong Wook Chung. Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. . 2019; ():1.

Chicago/Turabian Style

Jun Hyoung Bang; Chi Eun Hong; Sebastin Raveendar; Kyong Hwan Bang; Kyung Ho Ma; Soon Wook Kwon; Hojin Ryu; Ick Hyun Jo; Jong Wook Chung. 2019. "Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species." , no. : 1.

Mitogenome announcement
Published: 25 November 2018 in Mitochondrial DNA Part B
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Desarmillaria tabescens is one of the most important edible, medicinal, and phytopathogenic basidiomycetes. The complete mitochondrial genome of this species was determined using next-generation sequencing technology. This mitogenome is a circular molecule of 93,439 bp with a GC content of 29.28% and contains 15 protein-coding, two rRNA (rnl and rns), and 24 tRNA genes. Phylogenetic analysis revealed that D. tabescens is genetically closest to Agrocybe aegerita. Desarmillaria tabescens mitogenome can contribute to our understanding of the phylogeny and evolution of this species.

ACS Style

Hwa-Yong Lee; Suyun Moon; Chang-Duck Koo; Jong-Wook Chung; Hojin Ryu. The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens. Mitochondrial DNA Part B 2018, 4, 33 -34.

AMA Style

Hwa-Yong Lee, Suyun Moon, Chang-Duck Koo, Jong-Wook Chung, Hojin Ryu. The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens. Mitochondrial DNA Part B. 2018; 4 (1):33-34.

Chicago/Turabian Style

Hwa-Yong Lee; Suyun Moon; Chang-Duck Koo; Jong-Wook Chung; Hojin Ryu. 2018. "The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens." Mitochondrial DNA Part B 4, no. 1: 33-34.

Journal article
Published: 23 October 2018 in Plant Genetic Resources: Characterization and Utilization
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Licorice (Glycyrrhiza glabra) is an important medicinal herb and has long been used in traditional medicine for the treatment of several diseases worldwide. Understanding the genetic diversity within Glycyrrhiza species is important for the efficient conservation of these medicinal herbs. In this study, we have developed 20 polymorphic chloroplast microsatellite (cpSSR) markers using the chloroplast genome of G. lepidota. The cpSSR markers were tested on a total of 27 Glycyrrhiza individual plants. The number of alleles per locus ranged from two to eight among the Glycyrrhiza accessions. Overall, the Shannon index (I) for each cpSSR ranged from 0.315 to 1.694, the diversity indices (h) were 0.140–0.793 and the unbiased diversity indices (uh) were 0.145–0.825. In addition, the cpSSR markers were successfully divided and classified the 27 Glycyrrhiza individuals into four groups. The cpSSR markers developed in this study could be used in the assessment of genetic diversity and rapid identification of Glycyrrhiza species.

ACS Style

Kyung Jun Lee; Sebastin Raveendar; Ji Seon Choi; Jinsu Gil; Jeong Hoon Lee; Yoon-Sup So; Jong-Wook Chung. Development of chloroplast microsatellite markers for identification of Glycyrrhiza species. Plant Genetic Resources: Characterization and Utilization 2018, 17, 95 -98.

AMA Style

Kyung Jun Lee, Sebastin Raveendar, Ji Seon Choi, Jinsu Gil, Jeong Hoon Lee, Yoon-Sup So, Jong-Wook Chung. Development of chloroplast microsatellite markers for identification of Glycyrrhiza species. Plant Genetic Resources: Characterization and Utilization. 2018; 17 (1):95-98.

Chicago/Turabian Style

Kyung Jun Lee; Sebastin Raveendar; Ji Seon Choi; Jinsu Gil; Jeong Hoon Lee; Yoon-Sup So; Jong-Wook Chung. 2018. "Development of chloroplast microsatellite markers for identification of Glycyrrhiza species." Plant Genetic Resources: Characterization and Utilization 17, no. 1: 95-98.

Research article
Published: 02 October 2018 in Mycobiology
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The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

ACS Style

Hwa-Yong Lee; Sebastin Raveendar; Hyejin An; Youn-Lee Oh; Kab-Yeul Jang; Won-Sik Kong; Hojin Ryu; Yoon-Sup So; Jong-Wook Chung. Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus). Mycobiology 2018, 46, 421 -428.

AMA Style

Hwa-Yong Lee, Sebastin Raveendar, Hyejin An, Youn-Lee Oh, Kab-Yeul Jang, Won-Sik Kong, Hojin Ryu, Yoon-Sup So, Jong-Wook Chung. Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus). Mycobiology. 2018; 46 (4):421-428.

Chicago/Turabian Style

Hwa-Yong Lee; Sebastin Raveendar; Hyejin An; Youn-Lee Oh; Kab-Yeul Jang; Won-Sik Kong; Hojin Ryu; Yoon-Sup So; Jong-Wook Chung. 2018. "Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus)." Mycobiology 46, no. 4: 421-428.

Journal article
Published: 01 September 2018 in Plant Breeding and Biotechnology
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ACS Style

Sebastin Raveenadar; Gi-An Lee; Jung-Ro Lee; Kyung Jun Lee; Sok-Young Lee; Gyu-Taek Cho; Kyung-Ho Ma; Jong-Wook Chung. DNA Barcodes for the Assessment of Phylogenetic Relationships Based on CpDNA and NrDNA Regions in Vigna Species. Plant Breeding and Biotechnology 2018, 6, 285 -292.

AMA Style

Sebastin Raveenadar, Gi-An Lee, Jung-Ro Lee, Kyung Jun Lee, Sok-Young Lee, Gyu-Taek Cho, Kyung-Ho Ma, Jong-Wook Chung. DNA Barcodes for the Assessment of Phylogenetic Relationships Based on CpDNA and NrDNA Regions in Vigna Species. Plant Breeding and Biotechnology. 2018; 6 (3):285-292.

Chicago/Turabian Style

Sebastin Raveenadar; Gi-An Lee; Jung-Ro Lee; Kyung Jun Lee; Sok-Young Lee; Gyu-Taek Cho; Kyung-Ho Ma; Jong-Wook Chung. 2018. "DNA Barcodes for the Assessment of Phylogenetic Relationships Based on CpDNA and NrDNA Regions in Vigna Species." Plant Breeding and Biotechnology 6, no. 3: 285-292.

Mitogenome announcement
Published: 26 June 2018 in Mitochondrial DNA Part B
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Little millet, Panicum sumatrense Roth ex Roem. & Schult., is an important cultivated species under the tribe Paniceae, sub-family Panicoideae and family Poaceae. In this study, for the first time we sequenced the complete chloroplast (cp) genome of P. sumatrense to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence of P. sumatrense is 139,384 bp in length with 38.6% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (22,723 bp) separated by a small single-copy region (12,583 bp) and a large single-copy region (81,355 bp). The P. sumatrense cp genome encodes 125 unique genes, which include 91 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 20 genes were duplicated in the inverted repeat region. This newly determined cp genome (P. sumatrense) could be valuable information for the breeding programs of this cereal crops in the family Poaceae.

ACS Style

Raveendar Sebastin; Gi-An Lee; Kyung Jun Lee; Myoung-Jae Shin; Gyu-Taek Cho; Jung-Ro Lee; Kyung-Ho Ma; Jong-Wook Chung. The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae). Mitochondrial DNA Part B 2018, 3, 719 -720.

AMA Style

Raveendar Sebastin, Gi-An Lee, Kyung Jun Lee, Myoung-Jae Shin, Gyu-Taek Cho, Jung-Ro Lee, Kyung-Ho Ma, Jong-Wook Chung. The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae). Mitochondrial DNA Part B. 2018; 3 (2):719-720.

Chicago/Turabian Style

Raveendar Sebastin; Gi-An Lee; Kyung Jun Lee; Myoung-Jae Shin; Gyu-Taek Cho; Jung-Ro Lee; Kyung-Ho Ma; Jong-Wook Chung. 2018. "The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae)." Mitochondrial DNA Part B 3, no. 2: 719-720.