Article
Evolutionary Biology
Ming-Rui Li, Ning Ding, Tianyuan Lu, Jing Zhao, Zhen-Hui Wang, Peng Jiang, Si-Tong Liu, Xin-Feng Wang, Bao Liu, Lin-Feng Li
Summary: Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains underinvestigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome, and proteome data sets. Our genome-wide comparative analyses revealed that although the ginseng species complex was recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation, and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypomethylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hypermethylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Genetics & Heredity
Elena Kuzmin, John S. Taylor, Charles Boone
Summary: Gene duplication is common across species, and the retention of duplicated genes may involve mechanisms such as functional redundancy, divergence, neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Additionally, duplication may also be retained due to structural and functional entanglement. Advances in human gene editing have provided new tools to study the contributions of these factors to duplicate gene retention and genome evolution.
TRENDS IN GENETICS
(2022)
Article
Genetics & Heredity
Jiaqi You, Zhenping Liu, Zhengyang Qi, Yizan Ma, Mengling Sun, Ling Su, Hao Niu, Yabing Peng, Xuanxuan Luo, Mengmeng Zhu, Yuefan Huang, Xing Chang, Xiubao Hu, Yuqi Zhang, Ruizhen Pi, Yuqi Liu, Qingying Meng, Jianying Li, Qinghua Zhang, Longfu Zhu, Zhongxu Lin, Ling Min, Daojun Yuan, Corrinne E. Grover, David D. Fang, Keith Lindsey, Jonathan F. Wendel, Lili Tu, Xianlong Zhang, Maojun Wang
Summary: This study investigates the genetic regulation of fiber development in allotetraploid cotton and highlights the potential for fiber quality improvement. The findings provide insights into the dynamics of gene regulation during fiber development in polyploid plants.
Article
Biotechnology & Applied Microbiology
Dongdong Ge, Jiuhua Jiang, Xiaohui An, Longjie Wang, Ting Pan, Kang Liu, Jing Sun, Delin Hong
Summary: This study identified XB3 family genes in cotton related to plant immunity and stress responses, which showed differential expression patterns under different stress conditions and hormonal stimuli. Silencing some of these genes significantly impacted cotton resistance to Verticillium wilt. Interacting proteins of GhXB32A and GhXB32D were functionally enriched in abiotic and biotic stress responses, as well as photosynthesis. XB3 family genes have potential as stress resistance genes for cotton improvement.
Article
Horticulture
Qunyun Tan, Zhengjin He, Shiyong Mei, Jifang Zhang
Summary: CCT genes play important roles in flowering, plant growth, development, and response to abiotic stresses in R. sativus. This study identified a total of 58 CCT genes in R. sativus and classified them into three groups. The expansion of the CCT gene families was mainly due to segmental duplication, with one subgenome retaining more CCT genes. Tissue-specific expression and promoter cis-elements analysis showed the potential role of RsCCT genes in controlling flowering. RsCCT genes also exhibited response to several abiotic stresses. These findings provide essential information for further functional studies of RsCCT genes.
Article
Plant Sciences
Guohui Li, Muhammad Aamir Manzoor, Guoyu Wang, Cunwu Chen, Cheng Song
Summary: This study investigated the KNOX gene family in the Dendrobium huoshanense genome using bioinformatics methods. Phylogenetic relationship and promoter analysis revealed the potential roles of these genes in plant development and stress responses. qRT-PCR experiments confirmed the differential expression of DhKNOX genes under different treatments.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Xu Hu, Jiangshan Hao, Ling Pan, Tao Xu, Longzhou Ren, Yu Chen, Minqiang Tang, Li Liao, Zhiyong Wang
Summary: This study identified a large number of tandem duplicated genes in the genome of seashore paspalum and analyzed their evolution and expression. The results showed that these duplicated genes are related to salt stress adaptation and could be used as a reference for salt resistance research in other grasses and crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Manu Maya Magar, Hui Liu, Guijun Yan
Summary: This study identified and analyzed the AP2/ERF superfamily genes in bread wheat and discovered candidate genes associated with heat stress response. The findings of this study provide important information and a foundation for heat tolerance breeding in wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Madiha Zaynab, Yasir Sharif, Zhaoshi Xu, Sajid Fiaz, Rashid Al-Yahyai, Hamad. A. Yadikar, Najla Amin T. Al Kashgry, Sameer H. Qari, Monther Sadder, Shuangfei Li
Summary: In this study, 30 DUF668 genes were identified in the soybean genome, distributed across fifteen chromosomes. Phylogenetic analysis classified these genes into three groups. Gene structure analysis showed that some of these genes lacked introns. Subcellular localization results indicated that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane.
Article
Biochemistry & Molecular Biology
Faiza Ali, Yonghui Li, Fuguang Li, Zhi Wang
Summary: This study identified 237 CBS genes in cotton and categorized them into four groups through phylogenetic analysis. The expansion of the GhCBS gene family was mainly attributed to whole-genome or segmental with dispersed duplication events. Transcriptomic data and qRT-PCR validation revealed the critical role of some GhCBS genes in ovule development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Taiyi Yang, Hengrui Li, Liangwu Li, Wanling Wei, Yuanhang Huang, Faqian Xiong, Maogui Wei
Summary: This study identified and characterized six MeAMY genes and ten MeBAM genes in the cassava genome. It found that MeAMY1, MeAMY2, MeAMY5, and MeBAM3 are critical genes in response to drought stress and observed changes in starch metabolism in cassava under drought stress. These findings provide fundamental knowledge for understanding the starch metabolism functions of cassava under drought stress and offer new perspectives on the mechanism of how cassava survives and develops under drought.
Article
Plant Sciences
Weirong Luo, Zhenxiang Zhao, Hongzhi Chen, Wenhong Ao, Lin Lu, Junjun Liu, Xinzheng Li, Yongdong Sun
Summary: In this study, the CmoDELLA gene family in pumpkin was investigated in terms of their physical and chemical properties, gene structure, cis-regulatory elements, and expression patterns. Seven CmoDELLA genes were identified in pumpkin, and their proteins were relatively unstable and mainly formed by alpha-helix and random coil. Cis-regulatory elements analysis indicated that CmoDELLA genes play a critical role in regulating plant growth and development, as well as responding to stress in pumpkin. The expression patterns under different abiotic stresses suggested that CmoDELLA genes mediate the stress response of pumpkin to NaCl, waterlogging, and cold, but with varied functions.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Yixiu Yao, Li Jia, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao, Guozhi Zhou, Jia Liu, Jiahong Yu, Peng Zhang, Yuhe Yin, Weiping Diao, Hongjian Wan
Summary: This study identified and analyzed the members of the CCO gene family in pepper and other plants using bioinformatics methods. A total of 158 CCO genes were found, which were further divided into two groups. Results from RNA-seq and qRT-PCR experiments showed that CaCCO genes in pepper responded to H2O2 and other abiotic stresses, indicating their important roles in plant stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Qi Zhang, Caidie Zhang, Zhenyuan Pan, Hairong Lin, Zhibo Li, Xinhe Hou, Jinshan Liu, Xinhui Nie, Yuanlong Wu
Summary: This study identified the WNK subfamily in Gossypium hirsutum and investigated their expression patterns under biotic and abiotic stresses. Several GhWNKs were found to play important roles in the response of cotton to Verticillium dahliae. Additionally, a homoeologous expression bias was discovered within GhWNKs in upland cotton.
Article
Plant Sciences
Xinsheng Wang, Huidan Guo, Zhi Jin, Yina Ding, Meng Guo
Summary: In this study, 25 ClBBX genes were identified and classified into five clades based on their conserved domains and phylogenetic relationships. Most of the ClBBXs might be localized in the nuclei or cytoplasm. Hormonal and stress-responsive cis elements were discovered in ClBBX promoters, indicating their involvement in stress and hormone signaling pathways. The different expression patterns and significant response to hormonal and abiotic stress suggest potential functional interactions among ClBBXs.
Article
Plant Sciences
Shaowei Dong, Vincent Lau, Richard Song, Matthew Ierullo, Eddi Esteban, Yingzhou Wu, Teeratham Sivieng, Hardeep Nahal, Allison Gaudinier, Asher Pasha, Rose Oughtred, Kara Dolinski, Mike Tyers, Siobhan M. Brady, Ruth Grene, Bjorn Usadel, Nicholas J. Provarta
Article
Clinical Neurology
Kaiyun Yang, Yosef Ellenbogen, Shaowei Dong, Jeehyun Kim, Ramiro Larrazabal, Amadeo R. Rodriguez, Almunder R. Algird, Doron D. Sommer, Kesava Reddy
ACTA NEUROCHIRURGICA
(2020)
Article
Biochemistry & Molecular Biology
Xiaoshi Ma, Jinan Guo, Kaisheng Liu, Lipeng Chen, Dale Liu, Shaowei Dong, Jinquan Xia, Qiaoyun Long, Yongjian Yue, Pan Zhao, Fengyan Hu, Zhangang Xiao, Xinghua Pan, Kefeng Xiao, Zhiqiang Cheng, Zunfu Ke, Zhe-Sheng Chen, Chang Zou
Review
Pharmacology & Pharmacy
Zi-Ning Lei, Zhuo-Xun Wu, Shaowei Dong, Dong-Hua Yang, Litu Zhang, Zunfu Ke, Chang Zou, Zhe-Sheng Chen
PHARMACOLOGY & THERAPEUTICS
(2020)
Article
Oncology
Nan Li, Kaisheng Liu, Shaowei Dong, Ling Ou, Jieling Li, Minshan Lai, Yue Wang, Yucheng Bao, Huijie Shi, Xiao Wang, Shaoxiang Wang
FRONTIERS IN ONCOLOGY
(2020)
Article
Oncology
Shao-wei Dong, Rong Li, Zhiqiang Cheng, Dong-cheng Liu, Jinquan Xia, Jing Xu, Shixuan Li, Jian Wang, Yongjian Yue, Yingrui Fan, Yundi Cao, Lingyun Dai, Jigang Wang, Pan Zhao, Xin Wang, Zhangang Xiao, Chen Qiu, Guang-suo Wang, Chang Zou
Summary: This study utilized whole exome sequencing to analyze mutations in multiple pulmonary nodules, revealing a positive correlation between the number of mutations or mutated genes and the degree of malignancy. The mutated genes in the nodules were found to be associated with cell proliferation and survival related signaling pathways.
FRONTIERS IN ONCOLOGY
(2021)
Article
Pharmacology & Pharmacy
Feiyuan Liu, Qiaoyun Long, Hui He, Shaowei Dong, Li Zhao, Chang Zou, Weiqing Wu
Summary: In this study, a classifier model was established by combining FIT results and other demographic and clinical features to enhance the sensitivity of identifying colorectal neoplasia. The top six features mostly related to CRC include age, gender, history of intestinal adenoma or polyposis, smoking history, gastrointestinal discomfort symptom, and fruit eating habit. The LR algorithm was used to generate the model, achieving an AUC score of 0.92 and an NMSE score of 0.076 in separating normal individuals from participants with colorectal neoplasia.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Pharmacology & Pharmacy
Zhenwei Su, Shaowei Dong, Shan-Chao Zhao, Kaisheng Liu, Yao Tan, Xingyu Jiang, Yehuda G. Assaraf, Bo Qin, Zhe-Sheng Chen, Chang Zou
Summary: Chemotherapy is powerful in eliminating malignant cells, but its efficacy is often hindered by drug resistance. Nanomedicine, focusing on targeted drug delivery to tumor tissues using nano-sized formulations, shows promise in improving treatment outcomes, minimizing adverse effects, and overcoming cancer drug resistance. This approach involves strategies such as passive and active targeted delivery, delivering multidrug combinations, and multimodal combination therapy to pave the way for effective cancer treatment and holds great potential in overcoming drug resistance.
DRUG RESISTANCE UPDATES
(2021)
Article
Pharmacology & Pharmacy
L. Li, C. Zou, S. Dong, Z-X Wu, C. R. Ashby, Z-S Chen, C. Qiu
Summary: Lurbinectedin has demonstrated significant antitumor efficacy and tolerable adverse effects in treating SCLC patients. It is efficacious in platinum-sensitive and platinum-resistant SCLC patients, as well as those with SCLC relapse after second-line treatment.
Article
Pharmacology & Pharmacy
Z-X Wu, J. Li, S. Dong, L. Lin, C. Zou, Z-S Chen
Summary: Non-small cell lung cancer (NSCLC) is a highly lethal cancer globally, and tyrosine kinase inhibitors (TKIs) have become a standard treatment in combating NSCLC by inhibiting specific molecular targets in cancer cells. Tepotinib, as a MET TKI, has shown durable clinical response in NSCLC patients, leading to approvals in Japan and breakthrough therapy designation and accelerated approval in the U.S., making it a promising candidate for NSCLC patients.
Review
Biochemistry & Molecular Biology
Huibin Song, Dongcheng Liu, Shaowei Dong, Leli Zeng, Zhuoxun Wu, Pan Zhao, Litu Zhang, Zhe-Sheng Chen, Chang Zou
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2020)
Article
Biology
Carina Steliana Carianopol, Aaron Lorheed Chan, Shaowei Dong, Nicholas J. Provart, Shelley Lumba, Sonia Gazzarrini
COMMUNICATIONS BIOLOGY
(2020)