Article
Plant Sciences
Octavio Martinez, Magda L. Arce-Rodriguez, Fernando Hernandez-Godinez, Christian Escoto-Sandoval, Felipe Cervantes-Hernandez, Corina Hayano-Kanashiro, Jose J. Ordaz-Ortiz, M. Humberto Reyes-Valdes, Fernando G. Razo-Mendivil, Ana Garces-Claver, Neftali Ochoa-Alejo
Summary: This study compared the gene expression profiles of domesticated and wild chili pepper ancestors during fruit development, revealing significant differences in cell cycle gene expression between them, possibly driven by selection pressures during domestication. Domesticated genotypes showed higher gene expression levels and earlier peaks.
Article
Biochemistry & Molecular Biology
Yuanyuan Li, Chenyu Zhang, Chunlei Ma, Liang Chen, Mingzhe Yao
Summary: In this study, tea leaf-color mutants were studied using transcriptome and biochemical analysis, and it was found that the reduced chlorophyll content might be caused by the activation of genes related to chlorophyll degradation, along with a reduction in flavonoid biosynthesis and an accumulation of glutamate. These findings provide new insights into the molecular mechanisms underlying leaf-color bud mutation in tea plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lulu Zhang, Canbin Chen, Fangfang Xie, Qingzhu Hua, Zhike Zhang, Rong Zhang, Jianye Chen, Jietang Zhao, Guibing Hu, Yonghua Qin
Summary: A novel WRKY transcription factor, HmoWRKY40, was found in pitaya, which activates the promoter of HmoCYP76AD1 involved in betalain biosynthesis. The results provide new insights into the regulatory networks of betalain biosynthesis in pitaya.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Fabio Gomez-Cano, Yi-Hsuan Chu, Mariel Cruz-Gomez, Hesham M. Abdullah, Yun Sun Lee, Danny J. Schnell, Erich Grotewold
Summary: Predicting transcription factors (TFs) associated with Camelina lipid metabolism using gene expression datasets. Identified DNA-binding sites and predicted target genes for 16 TFs using DNA affinity purification followed by sequencing. These TFs may play important roles in seed fatty acid elongation and triacylglycerol synthesis and degradation.
Article
Biochemistry & Molecular Biology
Matin Miryeganeh, Hidetoshi Saze
Summary: Mangrove trees, with their high adaptability to difficult coastal conditions, serve as an interesting model system for understanding stress tolerance in plants. This study utilized RNA-Seq to characterize the leaf transcriptome of the Bruguiera gymnorhiza species and compared gene expression profiles between populations growing under different levels of stress, providing valuable insights into plant adaptations. Genes related to salt and osmotic stress showed elevated expression levels in trees growing in high salinity conditions, suggesting potential targets for future research on salt resistance in mangroves and other woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell & Tissue Engineering
Yuan-chi Teng, Alfredo Leonardo Porfirio-Sousa, Giulia Magri Ribeiro, Marcela Corso Arend, Lindolfo da Silva Meirelles, Elizabeth Suchi Chen, Daniela Santoro Rosa, Sang Won Han
Summary: This study investigated the gene expression profiles of pericytes during early stages of limb ischemia, showing that ischemia triggered proliferation, migration, and upregulation of myogenesis-related transcripts. The transcriptomic analysis also revealed that pericytes induced or upregulated the expression of cytokines with effects on endothelial cells, leukocyte chemoattraction, or the activation of inflammatory cells. These findings provide insights into skeletal muscle pericyte biology under ischemic conditions and may be beneficial for developing novel pericyte-based therapies.
STEM CELL RESEARCH & THERAPY
(2021)
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Qiaozhen Li, Jing Chen, Jianyu Liu, Hailong Yu, Lujun Zhang, Chunyan Song, Yu Li, Ning Jiang, Qi Tan, Xiaodong Shang, Yunfu Gu
Summary: This study collected Lentinula edodes fruiting bodies at different developmental stages, characterized their polysaccharides, and used transcriptomic analysis to uncover some of the mechanisms behind polysaccharide biosynthesis. The study predicted the molecular mechanisms behind changes in polysaccharide yield, providing insights into the biosynthetic pathway and candidate genes for regulating polysaccharide biosynthesis in L. edodes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shisi Xing, Dan Deng, Wen Wen, Wei Peng
Summary: This study investigated the differences in gene expression in the female midgut between mated and virgin Drosophila suzukii. The results showed that mating had significant effects on metabolism and immune system in the midgut, which may contribute to supplying the female with nutrients and energy required for egg production.
Article
Horticulture
Hui Li, Yibo Bai, Yaxin Yang, Huan Zheng, Xianbin Xu, Haoran Li, Wu Wang, Jianmin Tao
Summary: Teinturier grapevine cultivars, characterized by red pulp berries, showed inhibited anthocyanin accumulation under bagging treatment, while rapid accumulation of malvidin, cyanidin, and delphinidin derivatives was observed after exposure to light. Transcriptomic analysis revealed that genes associated with light-responsive factors, transcription factors, and structural genes were significantly up-regulated under bag removal treatment. These findings provide insights into the molecular mechanism of light-induced anthocyanin biosynthesis in teinturier grapes.
SCIENTIA HORTICULTURAE
(2023)
Article
Multidisciplinary Sciences
Qian Li, Lili Gu, Jiaxing Song, Chenjian Li, Yanhui Zhang, Yuxiang Wang, Yongzhen Pang, Bo Zhang
Summary: Medicago falcata, a leguminous forage crop, has been found to exhibit increased activities of antioxidant enzymes and soluble sugar content when challenged with PEG-6000. Transcriptome analysis revealed differential expression of 706 genes, with enrichment in various pathways including phenylpropanoid biosynthesis and glycolysis/gluconeogenesis, indicating their involvement in drought response. qPCR confirmed seven differentially expressed genes to be associated with drought response in M. falcata, providing valuable insights for future molecular studies and genetic breeding of legume crops.
Article
Plant Sciences
Qian Li, Wenbo Jiang, Zhihu Jiang, Wenxuan Du, Jiaxing Song, Zhiquan Qiang, Bo Zhang, Yongzhen Pang, Yuxiang Wang
Summary: Medicago falcata is a legume forage grass with strong drought resistance. In this study, transcriptome analysis and WGCNA analysis identified key transcription factor genes related to drought response in M. falcata. Overexpression of the selected MfERF053 gene in Arabidopsis enhanced drought and salt resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Hua Liu, Xiaoxi Chen, Haixia Chen, Jie Lu, Dongliang Chen, Chang Luo, Xi Cheng, Yin Jia, Conglin Huang
Summary: Chrysanthemum dichrum, an important wild species in the Asteraceae family, has been relatively understudied due to a lack of genetic information. Through transcriptome and metabolome analyses, this study identified abundant metabolites in the leaves, flower buds, and blooming flowers of C. dichrum, providing valuable genetic and metabolic information for future research on the molecular mechanisms in this species.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Weijian Huang, Meng Li, Huangwei Zhang, Juyou Wu, Jim M. Dunwell, Shaoling Zhang
Summary: By analyzing agronomic traits and sequencing data, the differences between cultivated and wild grapes and peaches were compared in terms of fruit size, flavor, resistance, and color. Cultivated varieties showed advantages in fruit size, sugar content, and sugar-acid ratio. Wild varieties had utility value in terms of resistance. The study identified differentially expressed genes in cultivated and wild grapes and peaches, with some common genes between them.
SCIENTIFIC REPORTS
(2023)
Article
Biology
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
Summary: scBalance is an integrated sparse neural network framework that incorporates adaptive weight sampling and dropout techniques to handle noise and imbalanced datasets, achieving high classification accuracy for both rare and major cell types.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Guibing Hu, Junting Feng, Xu Xiang, Jiabao Wang, Jarkko Salojarvi, Chengming Liu, Zhenxian Wu, Jisen Zhang, Xinming Liang, Zide Jiang, Wei Liu, Liangxi Ou, Jiawei Li, Guangyi Fan, Yingxiao Mai, Chengjie Chen, Xingtan Zhang, Jiakun Zheng, Yanqing Zhang, Hongxiang Peng, Lixian Yao, Ching Man Wai, Xinping Luo, Jiaxin Fu, Haibao Tang, Tianying Lan, Biao Lai, Jinhua Sun, Yongzan Wei, Huanling Li, Jiezhen Chen, Xuming Huang, Qian Yan, Xin Liu, Leah K. McHale, William Rolling, Romain Guyot, David Sankoff, Chunfang Zheng, Victor A. Albert, Ray Ming, Houbin Chen, Rui Xia, Jianguo Li
Summary: By studying the genome of lychee, it was found that lychee had undergone two independent domestication events in Yunnan and Hainan, China. The maturity differences between early-maturing and late-maturing lychee cultivars may be regulated by gene deletions. This research is important for understanding the domestication history of lychee and improving lychee and related crops.
Review
Plant Sciences
Yanqing Zhang, Muhammad Waseem, Zaohai Zeng, Jing Xu, Chengjie Chen, Yuanlong Liu, Jixian Zhai, Rui Xia
Summary: MicroRNAs (miRNAs) such as miR482/2118 are small noncoding RNAs of 21-24 nucleotides in length, widely distributed across the plant kingdom. They play essential roles in disease resistance and plant reproduction, with distinct functions in different plant species.
Article
Genetics & Heredity
Canbin Chen, Fangping Li, Fangfang Xie, Jiaxuan Chen, Qingzhu Hua, Jianye Chen, Zhijiang Wu, Zhike Zhang, Rong Zhang, Jietang Zhao, Guibing Hu, Yonghua Qin
Summary: Pitaya, a novel fruit with a delicious taste and superior horticulture ornamental value, has diverse uses in agricultural produce, processed foods, industrial and medicinal products. It also serves as an excellent plant material for biological research. A comprehensive database of pitaya has been constructed, providing genomic, gene expression, miRNA, metabolite, and proteomic data from different pitaya cultivars. The database also includes videos on flowering process and planting tutorials. These valuable data will significantly facilitate future studies on pitaya genetics, breeding, and function research.
Article
Plant Sciences
Fangfang Xie, Canbin Chen, Jiaxuan Chen, Yuanju Yuan, Qingzhu Hua, Zhike Zhang, Jietang Zhao, Guibing Hu, Jianye Chen, Yonghua Qin
Summary: This study examined the sugar and organic acid metabolism in pulp of yellow-peel pitayas and identified genes involved in these processes. The results highlighted the changes in sugar and organic acid contents during fruit development stages and revealed the key genes related to sugar and organic acid metabolism in pitayas. This study provides new insights for regulating the quality of pitayas.
Article
Biochemistry & Molecular Biology
Canbin Chen, Fangfang Xie, Kamran Shah, Qingzhu Hua, Jiayi Chen, Zhike Zhang, Jietang Zhao, Guibing Hu, Yonghua Qin
Summary: This study reports the characterization and function of 70 WRKY genes in pitaya. It is found that HmoWRKY42 acts as a transcriptional repressor and regulates pitaya betalain biosynthesis by inhibiting the transcription of HmocDOPA5GT1. These findings provide a foundation for future research on the regulation and functions of the HuWRKY gene family.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Jiakun Zheng, Chengjie Chen, Guanliang Li, Peike Chen, Yuanlong Liu, Rui Xia
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Fangfang Xie, Canbin Chen, Jiayi Chen, Jiaxuan Chen, Qingzhu Hua, Kamran Shah, Zhike Zhang, Jietang Zhao, Guibing Hu, Jianye Chen, Yonghua Qin
Summary: In this study, a 1R-MYB gene named HuMYB132 was identified in red-pulp pitaya. It was found to positively regulate the synthesis of betalain in pitaya by promoting the transcriptional activities of HuADH1, HuCYP76AD1-1, and HuDODA1. This research provides new insights into the regulation of betalain biosynthesis in pitaya.
Article
Plant Sciences
Dan Wang, Lei Chen, Yabing Yang, Farhat Abbas, Yaqi Qin, Hanle Lu, Biao Lai, Zichen Wu, Bing Hu, Yonghua Qin, Huicong Wang, Jietang Zhao, Guibing Hu
Summary: Anthocyanins, health-promoting compounds with strong antioxidant properties, accumulate in the pericarp but not in the aril of litchi fruit. Metabolome and transcriptome analyses revealed that a block in cyanidin glycosylation is responsible for the deficiency of anthocyanin biosynthesis in the aril. Additionally, 9 candidate genes, including LcMYB1, were identified to play a significant role in regulating anthocyanin biosynthesis. This study provides insights into the molecular mechanism of tissue-specific anthocyanin accumulation and will contribute to the development of new red-fleshed litchi germplasm.
PHYSIOLOGIA PLANTARUM
(2023)
Correction
Biochemical Research Methods
Yaqi Qin, Dan Wang, Jiaxin Fu, Zhike Zhang, Yonghua Qin, Guibing Hu, Jietang Zhao
Correction
Plant Sciences
Canbin Chen, Fangfang Xie, Qingzhu Hua, Noemi Tel-Zur, Lulu Zhang, Zhike Zhang, Rong Zhang, Jietang Zhao, Guibing Hu, Yonghua Qin
Article
Plant Sciences
Jianmei Zeng, Jiayi Chen, Kamran Shah, Fangfang Xie, Canbin Chen, Jiaxuan Chen, Jietang Zhao, Guibing Hu, Zhike Zhang, Yonghua Qin
Summary: In this study, 16 HuSPL genes were identified from the pitaya genome, which were distributed unevenly among nine chromosomes. It was found that these genes could be targeted by Hmo-miR156/157b and exhibited differential expression patterns during fruit maturation. HuSPL12 could inhibit the expression of HuWRKY40 by binding to its promoter and interact with HuMYB1, HuMYB132, or HuWRKY42, which are responsible for betalain biosynthesis.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Biochemistry & Molecular Biology
Jiayi Chen, Fangfang Xie, Kamran Shah, Canbin Chen, Jianmei Zeng, Jiaxuan Chen, Zhike Zhang, Jietang Zhao, Guibing Hu, Yonghua Qin
Summary: In this study, 165 HubHLH genes were identified, and their functions related to betalain biosynthesis in pitaya were revealed. HubHLH159 gene showed high expression level in red-pulp pitaya, and promoted betalain biosynthesis by activating the expression of HuADH1, HuCYP76AD1-1, and HuDODA1.
Article
Plant Sciences
Sha Li, Yaqi Qin, Shiqi Jing, Dan Wang, Zhike Zhang, Yonghua Qin, Guibing Hu, Jietang Zhao
Summary: Agrobacterium rhizogenes-mediated hairy root culture is a useful method for gene function analysis and plant secondary metabolite production. In this study, red litchi hairy roots were successfully obtained by transforming with A. rhizogenes-mediated LcMYB1. Anthocyanin profiling and transcriptome analysis revealed significant changes in metabolites and gene expression associated with flavonoid biosynthesis. Key structural genes in anthocyanin biosynthesis were identified, while genes involved in lignin production were down-regulated, indicating a competition between flavonoids and lignin in the phenylpropanoid pathway. Several transcription factors were also found to play a role in regulating anthocyanin biosynthesis in litchi hairy roots. These findings provide insights into the molecular mechanisms of anthocyanin accumulation in litchi hairy roots regulated by LcMYB1.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Forestry
Jun-Wen Yi, Han-Tao Ge, Farhat Abbas, Jie-Tang Zhao, Xu-Ming Huang, Gui-Bing Hu, Hui-Cong Wang
Summary: The level of glucose is negatively correlated with fruit abscission in litchi. Furthermore, LcHXK1 is identified as a key regulator in fruit abscission through its function as a hexose sensor.
Article
Biochemistry & Molecular Biology
Tong Ning, Chengjie Chen, Ganjun Yi, Houbin Chen, Yudi Liu, Yanjie Fan, Jing Liu, Shule Chen, Sixuan Wei, Zexuan Li, Yehuan Tan, Zhenting He, Chunxiang Xu
Summary: This study reveals the dynamic changes of HG in banana fruit development and ripening, as well as its correlation with fruit expansion, peel firmness, and epitope levels of antibodies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)