Article
Microbiology
Tao Sun, Yixuan Zhang, Hao Jiang, Kai Yang, Shiyu Wang, Rui Wang, Sha Li, Peng Lei, Hong Xu, Yibin Qiu, Dafeng Sun
Summary: In this study, the whole genome of Naematelia aurantialba was sequenced and analyzed for the first time. Genes and gene clusters related to polysaccharides and other active substances were identified, and the relationship between N. aurantialba and other fungi was revealed.
Review
Biotechnology & Applied Microbiology
Shanshan Zhang, Wenzhong Yang, Jian Chen, Chuanguang Zhang, Siqi Zhang, Lanjing Gao
Summary: Scleroderma yunnanense is a popular edible mushroom in Yunnan Province, China, with significant ecological and economic implications. This study presents the first genome assembly and annotation of S. yunnanense, identifying functional genes involved in secondary metabolite and carbohydrate production pathways.
Article
Plant Sciences
Abhisek Chakraborty, Shruti Mahajan, Manohar S. Bisht, Vineet K. Sharma
Summary: This study sequenced the genome and transcriptome of Syzygium cumini, also known as jambolan or jamun. The genome analysis revealed the tetraploid and highly heterozygous nature of S. cumini, as well as the adaptive evolution of genes involved in secondary metabolism pathways and stress tolerance mechanisms. These findings provide insights into the medicinal properties of S. cumini.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Jianyun Tao, Xuelian Bai, Mingyuan Zeng, Mengshi Li, Zhe Hu, Yunfen Hua, Huawei Zhang
Summary: This study focused on the genomic features and SM biosynthetic potential of the endophytic fungus Alternaria sp. SPS-2 derived from Echrysantha chrysantha Lindl. The results indicated the presence of numerous potential bioactive SMs biosynthetic gene clusters in strain SPS-2, highlighting its importance for further exploration.
Article
Immunology
Kamila Romanowski, Benjamin Sobkowiak, Jennifer L. Guthrie, Victoria J. Cook, Jennifer L. Gardy, James C. Johnston
Summary: By combining WGS data with patient-level information, the timing of secondary TB among contacts of active TB patients in British Columbia, Canada can be calculated.
CLINICAL INFECTIOUS DISEASES
(2021)
Review
Biology
Yifei Pei, Liang Leng, Wei Sun, Baocai Liu, Xue Feng, Xiwen Li, Shilin Chen
Summary: Advancements in genomics have accelerated the research on medicinal plants. The development of herbgenomics has promoted the deciphering of the genetic code of medicinal plants. Whole genome sequences of 123 medicinal plants have been published, with a majority being diploid species. Research on medicinal plant genomes is being conducted worldwide, and the establishment of a research platform for model medicinal plants is advocated.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Genetics & Heredity
Yuanchao Liu, Huiping Hu, Manjun Cai, Xiaowei Liang, Xiaoxian Wu, Ao Wang, Xiaoguang Chen, Xiangmin Li, Chun Xiao, Longhua Huang, Yizhen Xie, Qingping Wu
Summary: The study on the genome of Russula griseocarnosa revealed its genetic characteristics such as gene count, RNA prediction, and carbohydrate-active enzymes (CAZymes). The analysis showed that R. griseocarnosa has similar CAZyme distribution to other ectomycorrhizal fungi, but may have some differences in effector proteins.
Article
Biotechnology & Applied Microbiology
Chengcai Yan, Haiting Hao, Hongzu Feng, Zhe Wang, Shuaishuai Sha, Meng Li, Lan Wang, Zhensheng Kang
Summary: This study reports the genome-scale assembly and annotation of C. pullmanensis, a pathogenic fungus that infects populus and walnut trees. The obtained genome consists of 13 contigs with a genome size of 56.72 Mb and 10,474 putative coding genes. Comparative genomics analysis reveals similarities between C. pullmanensis and other Ascomycetes fungal strains.
Article
Microbiology
Qiang Wu, Huan Liu, Yixin Shi, Wanting Li, Jia Huang, Feifei Xue, Yongnan Liu, Gaoqiang Liu
Summary: This study characterized the genome of Ganoderma lingzhi, a genus of edible and medicinal mushrooms. The researchers identified a wide range of carbohydrate-active enzymes and characterized genes involved in sexual recognition and the biosynthesis of a key bioactive metabolite. Additionally, they discovered novel transcripts and genes with the possibility of alternative splicing. These resources provide valuable tools for studying the biology, genetics, and secondary metabolic pathways of G. lingzhi.
Review
Biochemistry & Molecular Biology
Yuxi Guo, Xuefeng Chen, Pin Gong
Summary: Studies have shown that polysaccharides from edible and medicinal fungus have antiviral capabilities, but the relationship between fungus type, polysaccharide structural characteristics, and mechanisms of action is still unclear. This review focuses on discussing the types of antiviral EMFs, the structural characteristics of polysaccharides, and their antiviral mechanisms to provide a theoretical basis for better clinical utilization of polysaccharides as antiviral agents.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Microbiology
Qianliang Ming, Xiuning Huang, Yimo He, Lingyue Qin, Yu Tang, Yanxia Liu, Yuting Huang, Hongwei Zhang, Peng Li
Summary: Endophytic fungi are a rich source of natural products with vast chemical diversity. In this study, the whole genome of an endophyte, Dactylonectria alcacerensis CT-6, was sequenced for the first time. Genomic analysis revealed numerous unknown biosynthetic gene clusters for secondary metabolites in D. alcacerensis CT-6. This study provides a foundation for further exploration of the chemical constituents of D. alcacerensis CT-6 using genome-mining strategies.
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Review
Plant Sciences
Qi-Qing Cheng, Yue Ouyang, Zi-Yu Tang, Chi-Chou Lao, Yan-Yu Zhang, Chun-Song Cheng, Hua Zhou
Summary: This article discusses the importance and widespread application of medicinal plant genome research with the development of sequencing technology, providing important guidance and support for breeding, evolutionary history, herbal synthesis, etc. in medicinal plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Food Science & Technology
Ruolin Hou, Xin Liu, Xiaoping Wu, Mingfeng Zheng, Junsheng Fu
Summary: The study demonstrated that AAM has therapeutic effects on ethanol-induced liver damage in both in vitro and in vivo models, suggesting its potential as a treatment for alcoholic liver injury.
FOOD SCIENCE AND HUMAN WELLNESS
(2021)
Article
Biochemistry & Molecular Biology
Fei Zheng, Qi An, Ge Meng, Xue-Jun Wu, Yu-Cheng Dai, Jing Si, Bao-Kai Cui
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2017)
Article
Mycology
Xiao-Hong Ji, Shuang-Hui He, Jia-Jia Chen, Jing Si, Fang Wu, Li-Wei Zhou, Josef Vlasak, Xue-Mei Tian, Yu-Cheng Dai
Article
Engineering, Chemical
Hong-Fei Ma, Ge Meng, Bao-Kai Cui, Jing Si, Yu-Cheng Dai
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2018)
Article
Plant Sciences
Lin Zhu, Xing Ji, Jing Si, Bao-Kai Cui
Article
Plant Sciences
Hai-Jiao Li, Meng Zhou, Jing Si
Article
Biochemistry & Molecular Biology
Jing Si, Ge Meng, Yi Wu, Hong-Fei Ma, Bao-Kai Cui, Yu-Cheng Dai
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2019)
Article
Mycology
Xing Ji, Dong-Mei Wu, Chang-Ge Song, Shun Liu, Jing Si, Bao-Kai Cui
MYCOLOGICAL PROGRESS
(2019)
Article
Mycology
Bao-Kai Cui, Hai-Jiao Li, Xing Ji, Jun-Liang Zhou, Jie Song, Jing Si, Zhu-Liang Yang, Yu-Cheng Dai
Article
Mycology
Qian Chen, Fang Wu, Xiao-Hong Ji, Jing Si, Li-Wei Zhou, Xue-Mei Tian, Josef Vlasak, Yu-Cheng Dai
Article
Microbiology
Lin Zhu, Jie Song, Jun-Liang Zhou, Jing Si, Bao-Kai Cui
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Mycology
Xing Ji, Dong-Mei Wu, Shun Liu, Jing Si, Bao-Kai Cui
Article
Microbiology
Jing Si, Hongfei Ma, Yongjia Cao, Baokai Cui, Yucheng Dai
Summary: This study introduces a valuable laccase, ThLacc-S, which efficiently metabolizes endocrine disrupting chemicals and has high specific activity. The enzyme maintains stability in a wide temperature range and pH range, making it a promising green catalyst for various biotechnological and industrial applications.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Mycology
L. F. Fan, X. H. Ji, J. Si
Article
Materials Science, Paper & Wood
Qi An, Hong-Fei Ma, Mei-Ling Han, Jing Si, Yu-Cheng Dai
Article
Biotechnology & Applied Microbiology
Zutan Li, Bingbing Jin, Jingya Fang
Summary: In this study, we propose MetaAc4C, an advanced deep learning model for accurate identification of N4-acetylcytidine (ac4C) sites using pre-trained BERT and various optimization techniques. By adapting generative adversarial networks to address data imbalance and augmenting training RNA samples, our model outperforms existing methods in terms of ACC, MCC, and AUROC.