Article
Biodiversity Conservation
Meile Sun, Xiangrong Ren, Ya Liu, Jing Yang, Jingtao Hui, Yukun Zhang, Yanhua Cui, Jun Zhang, Guocang Lin, Yan Li
Summary: In this study, the genetic structure of 57 rose cultivars and one wild species with different scents was evaluated through whole genome re-sequencing. The study revealed that the genetic background of roses is complex and can be divided into three main clusters. Genes related to fatty acid derivatives, terpenoids, and benzenoids/phenylpropanoids showed positive selection in rose cultivars with strong fragrance.
Article
Genetics & Heredity
Caihui Wang, Bo Liu, Min Chen, Junhao Ning, Xia Lu, Chunde Wang
Summary: Treating fertilized eggs with 20 mM EMS for 3 hours induced 9 times more mutations in scallop genomes, with mutations in MFS and Tubulin potentially related to fast growth in large-sized scallops, and mutations in Homeobox and SOCs potentially associated with slow growth in small-sized scallops. EMS shows promise in accelerating the selection of economically important traits in molluscs.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Jinxing Du, Shengjie Li, Jiaqi Shao, Hongmei Song, Peng Jiang, Caixia Lei, Junjie Bai, Linqiang Han
Summary: This study used whole-genome re-sequencing to analyze the genetic characteristics and diversity of Florida and Northern largemouth bass. A simple PCR-based method for germplasm identification of largemouth bass was established, which has practical implications for germplasm protection, management, and hybridization breeding.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Xinyu Xu, Bihua Chen, Juan Zhang, Siren Lan, Shasha Wu
Summary: This study evaluated the genomic characteristics of Gardenia jasminoides by re-sequencing wild and cultivated materials. The results showed that Gardenia jasminoides has rich genetic diversity and identified numerous SNPs and other gene variations. Additionally, the study further explored gene variations in the biosynthetic pathway of the main medicinal substances in Gardenia jasminoides.
Article
Agronomy
Huanran Yuan, Weilong Yang, Jianing Zou, Mingxing Cheng, Fengfeng Fan, Ting Liang, Yajie Yu, Ronghua Qiu, Shaoqing Li, Jun Hu
Summary: InDels are valuable molecular markers for genetic research, gene mapping, genetic diversity analysis, marker-assisted breeding, and phylogenetics. High-density long InDel markers have great potential to study functional diversity, species variation, and map-based cloning. InDel markers exhibit excellent polymorphisms between rice varieties and can be used to classify varieties and identify recombinant inbred lines.
Article
Agronomy
Xiaochun Wei, Md Abdur Rahim, Yanyan Zhao, Shuangjuan Yang, Henan Su, Zhiyong Wang, Saleh Ahmed Shahriar, Jundang Li, Zhiyuan Yang, Yuxiang Yuan, Xiaowei Zhang
Summary: This study investigated the genetic characteristics of late-bolting Chinese cabbage through genetic analysis and whole genome re-sequencing. It identified a gene that controls the late-bolting trait and discovered multiple genetic variations within the candidate interval. Additionally, three potential candidate genes were found. These findings are of great importance for marker-assisted breeding of Chinese cabbage.
Article
Genetics & Heredity
Chujie Chen, Bo Zhu, Xiangwei Tang, Bin Chen, Mei Liu, Ning Gao, Sheng Li, Jingjing Gu
Summary: By analyzing the patterns of genome-wide ROH, we found that both ancient and recent inbreeding events had varying degrees of impact on different horse breeds. However, recent inbreeding events were rare, especially among indigenous horse breeds. Therefore, the ROH-based genomic inbreeding coefficient can help monitor the level of inbreeding. Through our study on the Thoroughbred population, we identified 24 ROH islands containing 72 candidate genes associated with artificial selection traits. Our findings provide insight into horse breed characteristics and future breeding strategies.
Article
Medical Laboratory Technology
Matthijs Vynck, Friedel Nollet, Lode Sibbens, Helena Devos
Summary: The study suggests that screening at least 40 biallelic markers is necessary to achieve enough informative markers. There is room for optimization in current chimerism assays, and more effective assays can be designed through support of the introduced simulation framework.
CLINICA CHIMICA ACTA
(2022)
Article
Multidisciplinary Sciences
Yawo Mawunyo Nevame Adedze, Xia Lu, Yingchun Xia, Qiuyue Sun, Chofong G. Nchongboh, Md. Amirul Alam, Menghua Liu, Xue Yang, Wenting Zhang, Zhijun Deng, Wenhu Li, Longting Si
Summary: This study identified a panel of novel InDel polymorphic markers using whole-genome re-sequencing data from parents of cucumber hybrid varieties, demonstrating their effectiveness in hybrid seed purity testing.
SCIENTIFIC REPORTS
(2021)
Article
Veterinary Sciences
Dini Hu, Jianming Yang, Yingjie Qi, Boling Li, Kai Li, Kai Meng Mok
Summary: This study investigated the differences in microbial community composition and structure in Przewalski's horses before and after anthelmintic treatment, showing changes in archaea, bacteria, eukaryota, and viruses. The treatment altered the populations of functional microbes related to immunity and digestion, as well as increasing the abundance of phages which were sensitive to treatment. Pathogens related to clinical diseases in horses also increased post-treatment, while overall intestinal microbiota function remained unchanged but with shifted microbial populations.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Abdul Latif Khan, Sajjad Asaf, Lubna, Ahmed Al-Rawahi, Ahmed Al-Harrasi
Summary: Salvadora persica, a species with economic and medicinal importance, has been sequenced for its complete chloroplast genome for the first time. Comparison with other related species revealed unique features in terms of genome size and encoded genes.
Article
Agriculture, Dairy & Animal Science
Xilong Kang, Ming Wang, Chuang Meng, Ang Li, Xinan Xiao, Zhiming Pan
Summary: Salmonella is prevalent in the duck production chain, with S.Typhimurium being the dominant serotype. The spread of Salmonella across different stages of the production chain poses a potential threat to consumer health. However, the resistance of Salmonella in the duck production chain is low.
Article
Biochemistry & Molecular Biology
Christopher James O'Grady, Vignesh Dhandapani, John K. Colbourne, Dagmar Frisch
Summary: Whole genome sequencing is crucial for studying genome variation in natural populations, and large dormant eggbanks of aquatic invertebrates provide valuable information on genomic processes over centuries. An optimized workflow for whole genome amplification (WGA) has been developed to address limited DNA amounts in single eggs, allowing successful downstream whole genome sequencing of historical eggs. Comparison of two WGA kits showed high genome coverage breadth in samples, with high recovery of genomic positions with single nucleotide polymorphisms for genotyping, and even obtaining 100% coverage of mitochondrial genomes from the oldest isolates. Mitochondrial DNA serves as an additional source for evolutionary studies of these populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
James Friel, Aureliano Bombarely, Carmen Dorca Fornell, Francisco Luque, Ana Maria Fernandez-Ocana
Summary: Olive, a tree species of great economic and cultural importance in the Mediterranean region, has numerous cultivars that can be characterized using different genetic methods. Both whole-genome sequencing (WGS) and genotype by sequencing (GBS) yield similar results in olive genotyping, with GBS being a cost-effective option for characterizing genetic relationships between different accessions. The study also suggests that variants from GBS and WGS datasets can be combined, enabling the reuse of publicly available data.
Article
Biotechnology & Applied Microbiology
Chongqing Wang, Huan Qin, Chun Zhao, Li Yang, Tingting Yu, Yuxin Zhang, Xiang Luo, Qinbo Qin, Shaojun Liu
Summary: The study characterized the ovaries of autotetraploid Carassius auratus (4nRR) and diploid Carassius auratus red var. (RCC) using Illumina sequencing platform, revealing key genes related to oogenesis. Whole-genome re-sequencing showed a large number of SNPs and InDels variations in 4nRR. Genes involved in ubiquitin-mediated proteolysis, calcium transport, and meiosis play crucial roles in oogenesis in 4nRR.
MARINE BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jennifer Im, Heui-Soo Kim
Article
Biochemistry & Molecular Biology
Jennifer Im, Woo Ryung Kim, Hee-Eun Lee, Ahran Kim, Do-Hyung Kim, Yung Hyun Choi, Hee-Jae Cha, Suhkmann Kim, Heui-Soo Kim
Article
Biochemistry & Molecular Biology
Ahran Kim, Dahye Yoon, Yunjin Lim, Heyong Jin Roh, Suhkmann Kim, Chan-Il Park, Heui-Soo Kim, Hee-Jae Cha, Yung Hyun Choi, Do-Hyung Kim
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Hyunsu Kim, Kyung-Wan Baek, Eun-Ji Ko, Nguyen Thanh Luan, Yunjin Lim, Heyong Jin Roh, Nameun Kim, Do-Hyung Kim, Ahran Kim, Yung Hyun Choi, Suhkmann Kim, Heui-Soo Kim, Mee Sun Ock, Hee-Jae Cha
Article
Multidisciplinary Sciences
Hee-Eun Lee, Sang-Je Park, Jae-Won Huh, Hiroo Imai, Heui-Soo Kim
Summary: Transposable elements (TEs) are DNA sequences that make up a significant portion of the human genome and generate microRNAs (miRNAs), some of which are associated with cancer. The well-known hsa-miRNA-625 is derived from long interspersed nuclear elements (LINEs), and its expression varies among different species. Analysis of the 3' UTR of GATAD2B revealed the impact of different numbers and locations of canonical binding sites on gene expression, while NF-kappa B was found to induce enhancer activity of hsa-miRNA-625-5p by sharing binding sites.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Seyoung Mun, Songmi Kim, Wooseok Lee, Keunsoo Kang, Thomas J. Meyer, Bok-Ghee Han, Kyudong Han, Heui-Soo Kim
Summary: This study conducted de novo whole-genome sequencing of a Korean individual, revealing 182 TE-associated structural variation insertions and 89 TASV deletions in their genome. These variations resulted in significant alterations compared to the reference genome, highlighting the role of TEs in driving structural variations in human individual genomes.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
A-Reum Lee, Hyunsu Kim, Kyung-Yoon Jeon, Eun-Ji Ko, Ahran Kim, Nameun Kim, HyeongJin Roh, Yoonhang Lee, Jiyeon Park, Do-Hyung Kim, Yung Hyun Choi, Suhkmann Kim, Heui-Soo Kim, Mee Sun Ock, Hee-Jae Cha
Summary: Olive flounder is a major cultured fish species in Asia, but mass mortality caused by various pathogens leads to significant economic losses. Protein expression patterns in the gills and spleens of olive flounder varied depending on infectious agents, indicating the need for tailored measures for disease prevention and treatment in farmed fish.
Article
Biochemistry & Molecular Biology
Cheol Park, Won Sup Lee, Se-Il Go, Sang-Ho Jeong, Jiyun Yoo, Hee-Jae Cha, Young-Joon Lee, Heui-Soo Kim, Sun-Hee Leem, Hye Jung Kim, Gon Sup Kim, Soon-Chan Hong, Yung Hyun Choi
Summary: The study found that enhanced expression of the ERH gene can augment the anticancer efficacy of anthocyanins in gastric cancer cells, potentially through increased expression of pro-apoptotic proteins and elevated ROS levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eun-Ji Ko, Mee-Sun Ock, Yung-Hyun Choi, Juan L. Iovanna, Seyoung Mun, Kyudong Han, Heui-Soo Kim, Hee-Jae Cha
Summary: HERV-K env gene affects tumorigenic characteristics, including cell proliferation, migration, and tumor colonization through NUPR1 related pathway, as shown by knockout experiments in colorectal cancer cell lines using CRISPR-Cas9 system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eun-Ji Ko, Hyunsu Kim, A-Reum Lee, Kyung-Yoon Jeon, Ahran Kim, Do-Hyung Kim, Chan-Il Park, Yung Hyun Choi, Suhkmann Kim, Heui-Soo Kim, Mee Sun Ock, Hee-Jae Cha
Summary: The protein expression patterns in spleens of rock bream after infection by RBIV or mixed infection were investigated. Proteins related to oxygen transport and energy generation were up-regulated in infected spleens, while proteins involved in structure and cell movement were down-regulated. Infection triggered energy generation and oxygen transport, but decreased cell migration and structural changes in the spleen.
Article
Food Science & Technology
So Young Kim, Hee-Jae Cha, Hyun Hwangbo, Cheol Park, Hyesook Lee, Kyoung Seob Song, Jung-Hyun Shim, Jeong Sook Noh, Heui-Soo Kim, Bae-Jin Lee, Suhkmann Kim, Gi-Young Kim, You-Jin Jeon, Yung Hyun Choi
Summary: The study demonstrated that fermented extract of sea tangle (FST) could protect MC3T3-E1 cells from H2O2-induced damage by maintaining mitochondrial function, eliminating ROS, and activating the Nrf2/HO-1 antioxidant pathway.
Article
Biochemistry & Molecular Biology
Eun-Ji Ko, Kyoung Seob Song, Mee Sun Ock, Yung Hyun Choi, Suhkmann Kim, Heui-Soo Kim, Hee-Jae Cha
Summary: The study revealed significantly increased expression of HERV-K and HERV-R Env proteins in various cancer tissues, with expression patterns varying among individuals and cancer types. The correlations between HERV-Env expression and clinical investigations varied, indicating the potentially significant role of endogenous retroviral Env proteins in cancer progression.
Article
Biology
Da Hye Kwon, Gi-Young Kim, Hee-Jae Cha, Suhkmann Kim, Heui-Soo Kim, Hye-Jin Hwang, Yung Hyun Choi
Summary: Nargenicin A1 exhibits inhibitory effects on inflammation and oxidative stress in LPS-stimulated macrophages and zebrafish models by reducing the release of pro-inflammatory mediators and the generation of oxidative stress molecules through various pathways.
Article
Tropical Medicine
Cheol Park, Da Hye Kwon, Hyesook Lee, Su Hyun Hong, Gi-Young Kim, Hee-Jae Cha, Do-Hyung Kim, Suhkmann Kim, Heui-Soo Kim, Hye-Jin Hwang, Yung Hyun Choi
Summary: The study showed that ethanol extracts of Chondracanthus tenellus can enhance immunomodulatory properties by activating the TLR4/NF-kappa B signaling pathway, leading to increased production of immunomodulatory mediators and cytokines. This suggests that EECT has the potential to enhance immune activity.
ASIAN PACIFIC JOURNAL OF TROPICAL BIOMEDICINE
(2021)
Article
Tropical Medicine
Eun Ok Choi, Hyesook Lee, Cheol Park, Gi-Young Kim, Hee-Jae Cha, Suhkmann Kim, Heui-Soo Kim, You-Jin Jeon, Hye Jin Hwang, Yung Hyun Choi
ASIAN PACIFIC JOURNAL OF TROPICAL BIOMEDICINE
(2020)
Article
Agriculture, Dairy & Animal Science
Adrian Lopez-Catalina, Valentin Costes, Ramon Peiro-Pastor, Helene Kiefer, Oscar Gonzalez-Recio
Summary: Epigenetic marks can explain part of the phenotypic variance in animal breeding models. Nanopore sequencing shows high correlation with bisulphite sequencing in identifying DNA methylation marks. Different sequencing methods highlight differentially methylated genes and positions of economic interest in animal breeding.
