Article
Agriculture, Multidisciplinary
He-nan Su, Yu-xiang Yuan, Shuang-juan Yang, Xiao-chun Wei, Yan-yan Zhao, Zhi-yong Wang, Liu-yue Qin, Zhi-yuan Yang, Liu-jing Niu, Lin Li, Xiao-wei Zhang
Summary: In this study, PacBio RS II SMRT sequencing was used to analyze the full-length transcriptomes of a clubroot-resistant Chinese cabbage variety. The results identified a large number of genes related to clubroot resistance, providing valuable resources for basic research on clubroot resistance in Chinese cabbage.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Plant Sciences
Lina Shang, Yonghong Zhou, Shiqi Wen, Ke Wang, Yang Li, Meihua Zhang, Hongju Jian, Dianqiu Lyu
Summary: Potato is one of the most important tuber food crops, but cultivated potatoes are susceptible to high temperature, affecting yield. This study identified differentially expressed genes in potato under heat stress and revealed their involvement in temperature signaling, phytohormone, and protein modification. Furthermore, genes related to photoperiodic tuberization, tuber formation, and earliness in potato were identified and verified. The findings of this study provide valuable resources for understanding heat stress response in potato and developing heat-tolerant potato varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Tingyu Ma, Han Gao, Dong Zhang, Wei Sun, Qinggang Yin, Lan Wu, Tianyuan Zhang, Zhichao Xu, Jianhe Wei, Yanyan Su, Yuhua Shi, Dandan Ding, Ling Yuan, Gangqiang Dong, Liang Leng, Li Xiang, Shilin Chen
Summary: Artemisinin is the most effective ingredient in treating malaria, making it important to study the genetic regulation of Artemisia annua. This study found that alternative splicing in the artemisinin biosynthetic pathway is influenced by light, potentially regulating sesquiterpenoid biosynthesis. The analysis provided valuable insights into the complexity of transcriptome and proteome in plant alternative splicing.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Food Science & Technology
Antoon Lievens, Valentina Paracchini, Danilo Pietretti, Linda Garlant, Alain Maquet, Franz Ulberth
Summary: The EU General Food Law aims to prevent fraudulent practices and food adulteration. A broadly applicable approach using digital PCR for detecting the substitution of biological materials has been presented, with scalable and rapid characteristics. The analysis of Saffron samples across the European market using DNA accounting and verification by NGS analysis has demonstrated the effectiveness of the method.
Article
Engineering, Marine
Guang Yang, Zhendong Qin, Zhijie Lu, Rishen Liang, Lijuan Zhao, Gan Pan, Li Lin, Kai Zhang
Summary: This study investigated the molecular basis of gonadal development in M. rosenbergii by transcriptome sequencing of male and female gonadal samples, providing valuable genomic resources for future research and practical aquaculture.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Lili Xiang, Xiaofen Liu, Yanna Shi, Yajing Li, Weidong Li, Fang Li, Kunsong Chen
Summary: The research found that CmbHLH2 and CmbHLH2.1 play important roles in flower color alteration in 'Jimba' chrysanthemums, with the former playing a predominant role in the process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Yong Shi, Heng Xia, Xiaoting Cheng, Libin Zhang
Summary: This study explored the miRNA expression profiles in leaf and flower tissues of Osmanthus fragrans, identifying 106 conserved miRNAs and 88 novel miRNAs, with 133 differentially expressed miRNAs. The potential target genes of miRNAs and related metabolic pathways were predicted, illustrating the regulatory role of miR858 in flavonoid synthesis in O. fragrans.
Article
Genetics & Heredity
Jing Luo, Ruirui Li, Xintong Xu, Hairui Niu, Yujie Zhang, Caiyun Wang
Summary: This study analyzed the sequencing data of L. oriental 'Siberia' to identify highly upregulated transcription factors and key genes involved in flower senescence in lilies. Overexpression of LoNAC29 and LoSAG39 was found to accelerate flower senescence, providing new insights into the molecular mechanisms underlying flower senescence. The study also generated better sequence data for future research in lilies.
Article
Biochemistry & Molecular Biology
Naima Ahmed Fahmi, Heba Nassereddeen, Jaewoong Chang, Meeyeon Park, Hsinsung Yeh, Jiao Sun, Deliang Fan, Jeongsik Yong, Wei Zhang
Summary: AS-Quant is a robust program for identifying alternative splicing events from RNA-seq data. It outperforms other widely used tools by calculating read coverage, categorizing event types, and generating short read coverage plots. The significant alternative splicing events identified by AS-Quant were validated using RT-PCR experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemical Research Methods
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Summary: Alternative splicing (AS), a key pathway for transcriptional regulation, has been shown to be associated with complex diseases. Computational approaches for detecting disease-associated AS events have been developed. This review discusses the metrics used for characterizing AS events quantitatively. It also reviews and discusses three types of methods for detecting disease-associated splicing events: differential splicing analysis, aberrant splicing detection, and splicing-related network analysis. Additionally, methods for detecting genetic variants that potentially regulate splicing are described. Experimental comparisons are conducted to illustrate the performance of each method. The limitations of these methods are discussed, as well as potential ways to address them. This review aims to provide a systematic understanding of computational approaches for analyzing disease-associated splicing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agriculture, Dairy & Animal Science
Huan Li, Changhua Sun, Yunlong Li, Hongyan Sun
Summary: This study characterized the genome-wide alternative splicing events in RIP2 overexpression/knockdown and wild-type chicken macrophages using high-throughput RNA sequencing. Differential expression of alternative splicing genes were identified and their involvement in important pathways was revealed. This research provides a theoretical basis for the gene network related to RIP2.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Horticulture
Yeeun Kang, Suk-Woo Jang, Hee Ju Lee, Derek W. Barchenger, Seonghoe Jang
Summary: The study identified lettuce heat shock protein genes that respond early to heat stress, providing potential candidates for breeding heat-tolerant lettuce cultivars.
Article
Biotechnology & Applied Microbiology
Cheng-Yan Mou, Qiang Li, Zhi-Peng Huang, Hong-Yu Ke, Han Zhao, Zhong-Meng Zhao, Yuan-Liang Duan, Hua-Dong Li, Yu Xiao, Zhou-Ming Qian, Jun Du, Jian Zhou, Lu Zhang
Summary: This study generated a full-length transcriptome of oriental river prawn muscle using the PacBio Sequel platform, and identified 6,599 error-corrected isoforms. Transcriptome structural analysis revealed thousands of alternative splicing and polyadenylation events. This study provides valuable information for understanding the genomic structure and improving the genome annotation of oriental river prawn.
Article
Biotechnology & Applied Microbiology
Pooja Gupta, Trisha Chattopadhyay, Bibekanand Mallick
Summary: Deregulated expression of miRNAs and genes involved in key processes and pathways, including apoptosis, epithelial-mesenchymal transition, endocytosis, and vascular endothelial growth factor signaling, may play a crucial role in the oncogenesis and progression of TSCC, with miR-128-3p targeting MAP2K7 identified as a potential tumor suppressor.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Plant Sciences
Hui Jiang, Ying Li, Mingbao Luan, Siqi Huang, Lining Zhao, Guang Yang, Gen Pan
Summary: In this study, the authors used single-molecule real-time sequencing to investigate cannabis female and induced male flowers. They identified 48 long non-coding RNAs and 8202 transcripts annotated as transcription factors. They also discovered the gene CER1 which may play a role in cannabis male flower development and validated two alternative splicing events.
Article
Pathology
Jing Li, Jin Liang Ping, Bo Ma, Ying Rong Chen, Li Qin Li
PATHOLOGY RESEARCH AND PRACTICE
(2017)
Article
Pathology
Jing Li, Jin Liang Ping, Bo Ma, Ying Rong Chen, Li Qin Li
PATHOLOGY RESEARCH AND PRACTICE
(2017)
Article
Immunology
Li Qin Li, Hui Lian Huang, Jin Liang Ping, Wei Xu, Jing Li, Li Cheng Dai
Review
Oncology
Liqin Li, Heng Li
CANCER BIOLOGY & THERAPY
(2013)
Article
Pathology
Li Qin Li, Li Shan Min, Qun Jiang, Jin Liang Ping, Jing Li, Li Cheng Dai
PATHOLOGY RESEARCH AND PRACTICE
(2012)
Article
Biochemistry & Molecular Biology
Li-qin Li, Xia-li Li, Chun-hua Fu, Chun-fang Zhao, Long-jiang Yu
PROCESS BIOCHEMISTRY
(2013)
Article
Horticulture
Yuxiang Wang, Liqin Li, Youping Sun, Xin Dai
Article
Biotechnology & Applied Microbiology
Xuting Xu, Limin Xu, Huilian Huang, Jing Li, Shunli Dong, Lili Jin, Zhihong Ma, Liqin Li
BIOMED RESEARCH INTERNATIONAL
(2020)
Article
Plant Sciences
Jing Chen, Guifen Zhou, Yan Dong, Xiaodong Qian, Jing Li, Xuting Xu, Huilian Huang, Limin Xu, Liqin Li
Summary: This study used iTRAQ technology to analyze protein expression profiles of saffron under cold stress and a normal environment, revealing the important roles of sucrose/starch biosynthesis pathways in floral development. Under cold stress, saffron non-flowering buds showed significantly decreased sucrose contents, while starch contents remained unchanged.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Cell Biology
Zhongzhou Su, Yingze Ye, Chengen Shen, Sheng Qiu, Yao Sun, Siping Hu, Xiaoxing Xiong, Yuntao Li, Liqin Li, Hongfa Wang
Summary: This review highlights the role of ncRNAs in the pathophysiological processes of ischemic stroke and their potential as diagnostic biomarkers and therapeutic targets.
OXIDATIVE MEDICINE AND CELLULAR LONGEVITY
(2022)
Article
Biochemistry & Molecular Biology
Li-Qin Li, Chun-Hua Fu, Chun-Fang Zhao, Juan Xia, Wen-Juan Wu, Long-Jiang Yu
ZEITSCHRIFT FUR NATURFORSCHUNG SECTION C-A JOURNAL OF BIOSCIENCES
(2009)