Article
Genetics & Heredity
Kenta Shirasawa, Akihiro Itai, Sachiko Isobe
Summary: A study analyzing the genome sequence of a Japanese pear was conducted to support its breeding and genetic research. A total of 17 chromosome-scale sequences were established, and a large number of protein-encoding genes were predicted through de novo assembly of long sequence reads.
Article
Biotechnology & Applied Microbiology
Niu Yanfei, Su Tai, Wu Chunhua, Deng Jia, Yang Fazhong
Summary: This study sequenced, assembled, and annotated the chloroplast genome of A. transsectum. The complete cp genome contains 131 genes and is similar in size and gene composition to the cp genomes of seven other Ranunculaceae species. Phylogenetic analysis showed that A. transsectum is closely related to certain Aconitum species.
Article
Biochemistry & Molecular Biology
Yuan Gao, Guohui Shen, Guohui Yuan, Zhihui Tian
Summary: In this study, we assembled and compared the complete chloroplast genome sequences of Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens. The results showed minor differences in genome structure, repetitive sequences, and protein-encoding genes among the three species. The phylogenetic tree analysis based on chloroplast genomes revealed the genetic relationships of barnyard grass species in the genus Echinochloa.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Huijie Han, Rui Qiu, Yefei Liu, Xinyue Zhou, Cuiping Gao, Yongzhen Pang, Yan Zhao
Summary: Chloroplast genomes of Agropyron genus plants show a typical quadripartite structure and contain conserved genetic information, making them valuable for species taxonomy and evolution studies. Phylogenetic analysis revealed the genetic relationships among the studied species, with potential molecular markers identified for taxonomic purposes.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Chenxin Li, Chaonan Cai, Yutian Tao, Zhongshuai Sun, Ming Jiang, Luxi Chen, Junmin Li
Summary: The study sequenced 27 complete chloroplast genomes of 11 wild Fragaria species and analyzed the variation among them, revealing higher variability in non-coding regions compared to coding regions. Five variable loci suitable for DNA barcoding of Fragaria species were identified. Phylogenetic analyses based on the whole cp genomes supported the clustering of species into two groups, with different geographic distributions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Na Duan, Lili Deng, Ying Zhang, YanCai Shi, Bingbing Liu
Summary: This study reported three new Heteroplexis chloroplast genomes, which showed high conservation and provided valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of the Aster genus. Phylogenetic analyses did not support the monophyly of the Heteroplexis genus, suggesting that the five species might be subsumed into the Aster genus.
Article
Plant Sciences
Yifei Wang, Fang Wen, Xin Hong, Zhenglong Li, Yaolei Mi, Bo Zhao
Summary: In this study, the complete chloroplast genomes of twelve Paraboea species were sequenced and analyzed, revealing the genomic structure and composition, as well as potential molecular markers. In the phylogenetic tree, all Paraboea species formed a distinct clade, confirming their monophyly. Additionally, genes related to photosynthesis and protein synthesis were found to play crucial roles in the adaptability of Paraboea to diverse karst environments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Virology
Ji-Yeon Hyeon, Guillermo R. Risatti, Zeinab H. Helal, Holly McGinnis, Maureen Sims, Amelia Hunt, David H. Chung, Junwon Kim, Julia Desiato, Dong-Hun Lee
Summary: Whole genome sequencing and genetic characterization of rabies viruses detected in bats submitted to the Connecticut Veterinary Medical Diagnostic Laboratory (CVMDL) during 2018-2019 revealed the presence of RABV in different bat species. Phylogenetic analysis showed the genetic relationships of the detected RABV variants, providing valuable data for future investigations on RABV in North America. Continued surveillance and genome sequencing of bat RABV are necessary to monitor virus evolution and transmission.
Article
Genetics & Heredity
Qianqian Li, Xiang Chen, Dongfeng Yang, Pengguo Xia
Summary: This study sequenced the chloroplast genomes of 19 species of Pleione and compared their complete structure and sequence characteristics. The results showed that the chloroplast genomes exhibited a conserved tetrad structure and encoded a similar set of genes. The chloroplast sequence differences were found to be smaller in coding regions and greater in non-coding regions.
Article
Veterinary Sciences
Ji-Yeon Hyeon, Zeinab H. Helal, Allison Appel, Natalie Tocco, Amelia Hunt, Dong-Hun Lee, Guillermo R. Risatti
Summary: This study discovered West Nile virus (WNV) in an American crow from Connecticut and an alpaca from Massachusetts. The sequencing of the WNVs and their phylogenetic analysis revealed that they belong to lineage 1 and suggest that vector-host feeding preferences may drive viral transmission. The obtained sequences and phylogenetic relationships will serve as valuable reference data for future investigations on WNVs.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Bin Zhu, Fang Qian, Yunfeng Hou, Weicheng Yang, Mengxian Cai, Xiaoming Wu
Summary: Eruca sativa is an important edible vegetable with potential medicinal properties due to antibacterial activity of its seed oil. The complete chloroplast genome of E. sativa shares similarities with other Brassicaceae species, and protein-coding genes show purifying selection pressure, suggesting evolutionary closeness with important Brassica species. This may allow transfer of beneficial alleles from E. sativa to improve other Brassica species.
Article
Plant Sciences
Zhengying Cao, Linyi Yang, Yaxuan Xin, Wenbin Xu, Qishao Li, Haorong Zhang, Yuxiang Tu, Yu Song, Peiyao Xin
Summary: This study conducted comparative genomic and phylogenetic analyses on seven Neocinnamomum taxa, revealing the genetic structure and evolutionary characteristics of these species. The chloroplast genome of Neocinnamomum has a size range of 150,753-150,956 bp and contains 128 annotated genes. The study identified 31 preferred codons and three highly variable regions. The results of this study will serve as a reference for molecular marker development and phylogenetic research in Neocinnamomum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Yuying Huang, Jing Li, Zerui Yang, Wenli An, Chunzhu Xie, Shanshan Liu, Xiasheng Zheng
Summary: The study analyzed the plastomes of ten Ficus species, revealing their similar genome structure but with variation in inverted repeat regions. The comparative analysis showed low sequence variability and suggested eight variable regions as potential molecular markers. Phylogenetic analysis grouped the species into three clades based on subgenera, supporting the Berg classification system. The study contributes to understanding genetic diversity and species evolution of Ficus, providing valuable information for taxonomic and phylogenetic studies.
Article
Biotechnology & Applied Microbiology
Lei Yang, Ozodbek Abduraimov, Komiljon Tojibaev, Khabibullo Shomurodov, Yuan-Ming Zhang, Wen-Jun Li
Summary: This study investigates the plastome features and phylogenetic relationships of Ferula and related genera. The results show that the plastomes have similar characteristics and potential molecular markers. The study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ferula.
Article
Plant Sciences
Xiaomin Wang, Shengyi Bai, Zhaolei Zhang, Fushun Zheng, Lina Song, Lu Wen, Meng Guo, Guoxin Cheng, Wenkong Yao, Yanming Gao, Jianshe Li
Summary: In this study, the chloroplast genomes of 29 tomato germplasms were sequenced and analyzed to compare and understand their phylogenetic relationships. The analysis revealed highly conserved characteristics among the cp genomes, including structure, gene and intron number, inverted repeat regions, and repeat sequences. Candidate SNP markers for future studies were selected based on highly polymorphic SNP loci. The phylogenetic tree showed that the cp genomes of tomatoes were clustered into two major clades, with S. pimpinellifolium and S. lycopersicum showing a close genetic relationship. Only rps15 gene exhibited the highest average K-A/K-S ratio in the analysis of adaptive evolution, indicating strong positive selection. This study provides valuable information for further research on phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Ho Yong Chung, So Youn Won, Yoon-Kyung Kim, Jung Sun Kim
PLANT BIOTECHNOLOGY REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Pil Joong Chung, Hoyong Chung, Nuri Oh, Joohee Choi, Seung Woon Bang, Se Eun Jung, Harin Jung, Jae Sung Shim, Ju-Kon Kim
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Entomology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, In-Woo Kim, Sathishkumar Natarajan, Karpagam Veerappan, Minchul Seo, Junhyung Park, Jae Sam Hwang
Summary: The research analyzed antimicrobial peptides in locusts, predicted promising peptides with antimicrobial effects, and found that they were non-toxic, suggesting their potential as drug candidates.
JOURNAL OF ASIA-PACIFIC ENTOMOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, Mi-Ae Kim, Sathishkumar Natarajan, Karpagam Veerappan, Seong Hyun Kim, Junhyung Park, Jae Sam Hwang
Summary: This study immunized the giant meal worm and predicted numerous novel antimicrobial peptides from the transcriptome data. Some of these peptides showed potential antimicrobial activity and could be candidates for the development of antimicrobial agents.
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
(2021)
Article
Genetics & Heredity
Hyemin Lim, Hyunju Hwang, Taelim Kim, Soyoung Kim, Hoyong Chung, Daewoo Lee, Soorin Kim, Soochul Park, Woosuk Cho, Hyeonso Ji, Gangseob Lee
Summary: PsGAPDH plays a crucial role in rice plants' adaptation to salt stress. The analysis of transcriptome profiles revealed that PsGAPDH-OX promoted seedling growth and germination rates under salt stress conditions.
Article
Entomology
Kang-Woon Lee, Jae-Goo Kim, Karpagam Veerappan, Hoyong Chung, Sathishkumar Natarajan, Ki-Young Kim, Junhyung Park
Summary: Research extracted antimicrobial peptides from high-altitude red spotted apollo butterflies, identifying a promising candidate with antimicrobial activity against bacteria causing periodontitis.
Article
Forestry
Tae-Lim Kim, Hoyong Chung, Karpagam Veerappan, Wi Young Lee, Danbe Park, Hyemin Lim
Summary: The research investigated the effects of elevated atmospheric CO2 on the metabolism, growth, and transcriptome of poplar. Differences in gene expression were identified in poplar trees grown under different CO2 concentrations, providing valuable information for future gene discovery and tree improvement strategies in the face of increasing CO2 levels.
Article
Microbiology
Kwangmin Kim, Karpagam Veerappan, Nahyun Woo, Bohyeon Park, Sathishkumar Natarajan, Hoyong Chung, Cheolmin Kim, Junhyung Park
Summary: The study investigated the impact of Ulmus macrocarpa Hance extract (UME) on human gut microbiota in healthy adults. The results showed that the microbial response to UME supplementation was personalized, with no significant differences in species richness and abundance. However, there was an increase in specific bacterial species and functional enrichment of bacterial genes related to bile acid biosynthesis in the UME group. This preliminary study suggests that UME supplementation may enhance host immunity by modulating gut microbiota, but further larger-scale clinical studies are needed for confirmation.
JOURNAL OF MICROBIOLOGY
(2021)
Review
Plant Sciences
Karpagam Veerappan, Sathishkumar Natarajan, Hoyong Chung, Junhyung Park
Summary: Fleshy fruits, particularly those from the genus Prunus, are highly demanded due to their diverse stone/drupe fruit varieties. Peach varieties have unique palatable qualities, but shorter post-harvest life due to excessive softening, which has led to studies focusing on the molecular mechanisms and genetic basis of the softening process.
Article
Biochemistry & Molecular Biology
Kang-Woon Lee, Michael Immanuel Jesse Denison, Karpagam Veerappan, Sridhar Srinivasan, Bohyeon Park, Sathishkumar Natarajan, Hoyong Chung, Junhyung Park
Summary: This study utilized transcriptome sequencing to analyze differentially expressed genes (DEGs) during the metamorphic development of Parnassius bremeri. The results revealed that multiple genes are involved in cuticle development and melanin biosynthetic pathway during larval development. Pathway analysis indicated the involvement of signaling pathways such as Wnt, hedgehog, and Notch signaling pathways in the developmental stages of P. bremeri. Additionally, sensory receptors were activated during the larval to adult transition stage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Md Ataul Islam, Dawood Babu Dudekula, V. P. Subramanyam Rallabandi, Sridhar Srinivasan, Sathishkumar Natarajan, Hoyong Chung, Junhyung Park
Summary: This study screened the PubChem database and used molecular docking and machine learning to identify potential CYP3A5 molecules for therapeutic applications in cardiovascular diseases. In silico pharmacokinetics and toxicity assessments showed that five molecules had acceptable profiles. Molecular dynamics simulations revealed the dynamic behavior of the molecules in CYP3A5 and binding free energy calculations confirmed their high binding affinity. Further in vitro and in vivo validations are needed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Tae-Lim Kim, Hyemin Lim, Hoyong Chung, Karpagam Veerappan, Changyoung Oh
Summary: This study investigated the physiological response and transcriptome changes of Pinus densiflora grown in an environment with elevated CO2 concentration. The results showed that nonstructural carbohydrates increased, chlorophylls decreased, and antioxidant activity increased at elevated CO2 concentration. Differences in the transcriptomes were also observed, with genes related to glycolysis/gluconeogenesis and starch/sucrose metabolism showing different expression patterns at different levels of elevated CO2 concentration.
Article
Forestry
Tae-Lim Kim, Michael Immanuel Jesse Denison, Hyemin Lim, Hoyong Chung, Changyoung Oh
Summary: This study comprehensively analyzed 17 phosphofructokinase genes in Eastern Cottonwood, including their gene structure, conserved domains, evolutionary relationships, and expression patterns. Quantitative PCR analysis demonstrated that all 17 phosphofructokinase genes were induced in various tissues and developmental stages of P. deltoides. This genome-wide analysis provides insights into PFK and PFP genes and establishes a foundation for future investigations into the role of genes in P. deltoids.
Article
Biochemistry & Molecular Biology
Jeon Hwang-Bo, Karpagam Veerappan, Hyunhye Moon, Tae-Hoon Lee, Kang-Woon Lee, Junhyung Park, Hoyong Chung
Summary: Atopic dermatitis is a chronic inflammatory skin disease that requires continuous treatment. This study found that a peptide called parnassin can alleviate atopic dermatitis by modulating the immune system, with fewer side effects. It could be a potential candidate drug for the treatment of atopic dermatitis.
