Article
Biochemistry & Molecular Biology
Bingyu Cai, Yixian Xie, Yufeng Chen, Miaomiao Cao, Junting Feng, Yuqi Li, Liu Yan, Yongzan Wei, Yankun Zhao, Jianghui Xie, Wei Wang
Summary: Plant height is an important agronomic trait associated with yield and resistance to stresses. In this study, the popular banana cultivar 'Brazilian banana' and its dwarf mutant were compared to identify genes related to plant height. The analysis revealed several differentially expressed genes and identified key genes in the signaling pathways of gibberellic acid and indole acetic acid that regulate plant height development in banana.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shuang Qiu, Chen Zhong, Bo Zhao, Guangyue Li, Jinhua Wang, Shah Jehan, Jialiang Li, Xudong Zhao, Dangdang Li, Guangchao Sui
Summary: Ellagic acid induced G1 phase arrest and promoted apoptosis of HCC cells by activating the p21 gene and downregulating the MCM2-7 genes, respectively. The findings of this study provide valuable insights for the development of novel therapeutic strategies for HCC patients.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(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
Biochemistry & Molecular Biology
Lei He, Nan Meng, Simone D. Castellarin, Yu Wang, Qi Sun, Xiang-Yi Li, Zhi-Gang Dong, Xiao-Ping Tang, Chang-Qing Duan, Qiu-Hong Pan
Summary: The involvement of ABA in promoting free norisoprenoids and NAA in enhancing total norisoprenoid accumulation highlights their potential roles in regulating norisoprenoids in grape berries. These findings provide insights into managing norisoprenoids in vineyards in response to changing environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Hiroki Ura, Sumihito Togi, Yo Niida
Summary: This study compared the advantages and disadvantages of three RNA-Seq library preparation methods and found that TruSeq detected transcripts and splicing events better than the other methods, accurately measuring gene expression levels and splicing events. TeloPrime had higher coverage at the transcription start site, while SMARTer performed better than TeloPrime in terms of the number of detected transcripts and splicing events among the studied full-length double-stranded cDNA methods.
Article
Horticulture
Yanli Yao, Mingwei Li, Wenqiu Lin, Shenghui Liu, Qingsong Wu, Qiong Fu, Zhuying Zhu, Yuyao Gao, Xiumei Zhang
Summary: Watercore is a physiological disorder in pineapples that affects fruit quality and storage life. This study, using transcriptome analysis, revealed the molecular mechanism of watercore for the first time and identified key genes related to this disorder.
Article
Agriculture, Dairy & Animal Science
Zahra Pezeshkian, Seyed Ziaeddin Mirhoseini, Shahrokh Ghovvati, Esmaeil Ebrahimie
Summary: This study aimed to investigate the transcriptome of breast muscle tissue in male turkeys with high and low feed efficiency. The results showed that high feed efficiency turkeys increased the expression of genes related to amino acid biosynthesis, while low feed efficiency turkeys increased the expression of genes related to the immune response. Furthermore, key genes associated with feed efficiency may serve as potential biomarkers for genetic selection in turkeys.
Article
Plant Sciences
Keyvan Esmaeilzadeh-Salestani, Masoud Tohidfar, Rahele Ghanbari Moheb Seraj, Banafsheh Khaleghdoust, Indrek Keres, Hashem Marawne, Evelin Loit
Summary: This study compares the effects of organic and mineral nitrogen fertilizers on gene activity in barley. The results show that mineral nitrogen fertilizer treatment leads to a higher number of differentially expressed genes compared to organic nitrogen fertilizer treatment. Pathways related to amino acid synthesis and ribosomal activities are upregulated in mineral fertilizer treatment, while pathways related to starch and sucrose metabolism and carotenoid biosynthesis are downregulated. Organic nitrogen fertilizer treatment enriches pathways related to phenylpropanoid biosynthesis and plant-pathogen interaction. These findings provide insights into the genetic regulation of barley growth in field conditions and can guide the development of sustainable cropping practices and low nitrogen input varieties.
Article
Agriculture, Multidisciplinary
Songyu Liu, Bingqi Shan, Xiaomiao Zhou, Wenping Gao, Yaran Liu, Baoqing Zhu, Lei Sun
Summary: This study investigates the regulation of monoterpenoid biosynthesis in grapes by analyzing the monoterpenoid profiles and transcriptome data of four grape hybrids. Candidate genes and transcription factors related to monoterpenoid biosynthesis are identified, enhancing our understanding of this process.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Desalegn D. Serba, Xiaoxi Meng, James Schnable, Elfadil Bashir, J. P. Michaud, P. V. Vara Prasad, Ramasamy Perumal
Summary: The study used RNA-Seq technology to analyze the effects of sugarcane aphid on moderately resistant and susceptible genotypes, revealing transcriptome differences between the two genotypes at multiple time points after infestation by SCA. The resistant genotype exhibited differential expression of several gene clusters during SCA infestation, while the susceptible genotype showed a series of down-regulated genes on the basis of the resistant genotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Wei Zhang, Mengsi Xu, Juanjuan Wang, Shiyin Wang, Xinhua Wang, Jingquan Yang, Lei Gao, Shangquan Gan
Summary: Using RNA sequencing, this study analyzed the transcriptome profiles of tail fat tissues in Altay sheep and Xinjiang fine wool sheep, revealing significant differences in gene expression related to fat metabolism between the two breeds. Pathway analysis showed that the majority of differentially expressed genes were enriched in pathways related to fat metabolism. Additionally, some genes were involved in multiple pathways.
FRONTIERS IN GENETICS
(2021)
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
Agriculture, Dairy & Animal Science
Jitka Kyselova, Ladislav Tichy, Zuzana Sztankoova, Jirina Markova, Katerina Kavanova, Monika Beinhauerova, Michala Muskova
Summary: This study explores the potential role of immune genes in the fight against caseous lymphadenitis (CL) in sheep. By investigating the blood transcriptome, the study provides new insights into the disease course and host-pathogen interaction, which can help prevent the spread of incurable diseases and improve animal breeding for bacterial resistance.
Article
Plant Sciences
Pawandeep Singh Kohli, Lekha T. Pazhamala, Balaji Mani, Jitendra Kumar Thakur, Jitender Giri
Summary: Root hairs are extensions of root epidermal cells that increase in length and density under low phosphorus availability. This study explores the genes involved in root hair development and response to low phosphorus in chickpea, an important leguminous crop. The findings reveal that genes related to root hair initiation and cellular differentiation are upregulated, and genes involved in cell wall synthesis, cytoskeleton/vesicle transport, and ethylene biosynthesis are also upregulated in root hairs. In addition, genes related to low phosphorus responses, such as lipid and/or pectin P remobilization and acid phosphatases, are induced in root hairs. The study also highlights the preferential enrichment of processes involved in symbiotic interactions in root hairs. Overall, root hairs exhibit a multifaceted response to low phosphorus, involving molecular changes in epidermal cell differentiation and root hair initiation, as well as tip growth and various low phosphorus responses in elongated root hairs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Veterinary Sciences
Yujie Zhang, Ningbo Zhang, Lin Liu, Yan Wang, Jinyi Xing, Xiuling Li
Summary: This study examined the effects of folic acid on gene expression in the liver of broilers using RNA-seq technology. Different doses of folic acid were found to regulate gene expression levels, providing valuable insights into the molecular mechanisms of folic acid in liver lipid metabolism regulation.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Yunpeng Gai, Lei Li, Bing Liu, Haijie Ma, Yanan Chen, Fang Zheng, Xuepeng Sun, Mingshuang Wang, Chen Jiao, Hongye Li
Summary: This study identifies the crucial role of bZIP transcription factors in fungal morphogenesis, abiotic stress response, and pathogenesis in phytopathogenic fungus Alternaria alternata. The findings expand our understanding of how microbial pathogens utilize these genes to cope with environmental stresses and achieve successful infection in the host plant.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ziyue Wen, Jingrui Wang, Chen Jiao, Wenyong Shao, Zhonghua Ma
Summary: Fusarium head blight (FHB), caused by F. graminearum, is a destructive disease for cereal crops, particularly wheat. Fludioxonil, a phenylpyrrole fungicide, has been registered for FHB control in China due to its excellent activity against F. graminearum. In this study, six fludioxonil-resistant isolates were identified from wheat fields in three provinces of China. These resistant isolates exhibited fitness defects and reduced glycerol accumulation compared to sensitive isolates. Importantly, there was no cross-resistance observed between fludioxonil and other fungicides. The mutations in different domains of FgOS1, FgOS2, or FgOS4 were found in the resistant isolates. This study provides valuable insights into the biological and molecular characteristics of field isolates of fludioxonil-resistant F. graminearum, which can contribute to the development of effective strategies for FHB control.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Plant Sciences
Zi-Ming Ren, Dong Zhang, Chen Jiao, Dan-Qing Li, Yun Wu, Xiu-Yun Wang, Cong Gao, Ye-Fan Lin, Yong-Ling Ruan, Yi-Ping Xia
Summary: In this study, the metabolic characteristics and regulatory pathways involved in vegetative propagation (VP) in Lycoris bulb were investigated. The researchers found that high expression or activity of cell wall invertase (CWIN) is associated with bulblet initiation in high-regeneration species, while a high hexose-to-sucrose ratio supports cell division in the next phase of bulblet formation. These findings provide a sugar-mediated model for the regulation of VP in Lycoris bulb.
Article
Agriculture, Multidisciplinary
Li Wang, Song-lin Zhang, Chen Jiao, Zhi Li, Chong-huai Liu, Xi-ping Wang
Summary: This study sequenced the genomes of grape cultivars with and without seeds, and identified key genes and mechanisms involved in seedlessness. The findings provide valuable resources for future functional studies and grape breeding.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Plant Sciences
Lin Guo, Chunyue Wang, Jin Chen, Ye Ju, Fen Yu, Chen Jiao, Zhangjun Fei, Yulong Ding, Qiang Wei
Summary: Bamboo differentiates between a cell division zone and a cell elongation zone during rapid growth. The cell wall and organelles such as chloroplasts are more developed in the cell elongation zone, while hydrogen peroxide and stomata are concentrated in this zone. Hormone levels, including gibberellin, auxin, cytokinin, and brassinosteroid, are higher in the cell division zone, whereas salicylic acid and jasmonic acid levels are higher in the cell elongation zone. Transcriptome analysis reveals differential gene expression, with cell division and primary metabolism genes being upregulated in the cell division zone, and photosynthesis, cell wall growth, and secondary metabolism genes being significantly upregulated in the cell elongation zone. Overexpression of the transcription factor BmMYB83 promotes cell wall lignification.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Biochemistry & Molecular Biology
Chaofan Zhang, Chen Jiao, Xuepeng Sun, Xiaolong Li
Summary: This study conducted a comprehensive analysis of the MYB superfamily in 437 different plant species to explore its evolutionary contributions to species diversification, trait formation, and environmental adaptation. The research revealed major changes in gene copy number and genomic context within subclades and proposed the role of transposable element insertion in promoting sub-/neo-functionalization of MYB genes. It emphasizes the importance of lineage-/tissue-specific characterization to understand trait variability and environmental adaptation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Min Xu, Qiang Gao, Mengwei Jiang, Wenling Wang, Juan Hu, Xiaojun Chang, Dinggao Liu, Yuwei Liang, Yifan Jiang, Fei Chen, Chuhao Li, Haoran Huang, Feng Chen, Fan Li, Robert N. Trigiano, Jihua Wang, Chen Jiao, Xiaofan Zhou, Liangsheng Zhang
Summary: Jasminum sambac is a well-known plant known for its attractive fragrance and its flowers are used to produce scented tea. This study provides insights into the genetic basis of aromatic volatile production and salicylic acid and jasmonate accumulation in J. sambac under non-stress conditions through comprehensive comparative genomic, transcriptomic, and metabolomic analyses. The findings offer valuable genomic resources for further utilization of natural products.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Wenyong Shao, Kewei Sun, Tianling Ma, Huixian Jiang, Matthias Hahn, Zhonghua Ma, Chen Jiao, Yanni Yin
Summary: SUMOylation plays crucial roles in multiple biological processes in eukaryotic organisms. This study reveals the regulatory functions of SUMOylation in low-temperature survival and oxidative DNA damage tolerance during infection in B. cinerea. SUMOylated BcSsb affects the stability of microtubules and consequently mycelial growth at low temperature, while SUMOylated BcRad18 modulates the mono-ubiquitination of pcna involved in oxidative DNA damage response during infection.
Article
Agronomy
Bei Liu, Xingxing Liang, Jinchao Kong, Chen Jiao, Hongye Li, Yunpeng Gai
Summary: In this study, the genetic structure and diversity of Colletotrichum gloeosporioides, the dominant species causing citrus anthracnose, were analyzed using the Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. A total of 19 GAPDH haplotypes were identified, with the main haplotype (haplotype 5) distributed widely among isolates from different Citrus species and locations. The genetic differentiation index (Fst) revealed significant genetic differentiation between populations from different regions and host species. The results suggest that genetic differentiation in C. gloeosporioides is mainly influenced by gene mutation, recombination, or migration within native populations rather than natural selection caused by geography or host variety.
Article
Biochemistry & Molecular Biology
Ju-Chen Chia, Jiapei Yan, Maryam Rahmati Ishka, Marta Marie Faulkner, Eli Simons, Rong Huang, Louisa Smieska, Arthur Woll, Ryan Tappero, Andrew Kiss, Chen Jiao, Zhangjun Fei, Leon Kochian, Elsbeth Walker, Miguel Pineros, Olena K. Vatamaniuk
Summary: Arabidopsis OPT3 transports Cu and Fe into phloem companion cells and plays a role in systemic signaling of Cu and Fe deficiencies.
Article
Plant Sciences
Yuxin Shen, Zhengrui Qin, Gaojie Ren, Pingchuan Deng, Wanquan Ji, Chen Jiao, Liang Wu
Summary: Alternative splicing mediated by SCL33, SCL33L, and miR156 is involved in phase transitions in Brachypodium, regulating intron assembly and miR156 targets in growth transitions.
Article
Agronomy
Yunpeng Gai, Qichen Niu, Jinchao Kong, Lei Li, Xingxing Liang, Yuwei Cao, Xianqi Zhou, Xuepeng Sun, Haijie Ma, Mingshuang Wang, Neeraj Shrivastava, Hongye Li, Chen Jiao
Summary: A comparative transcriptome analysis was performed to study the gene expression patterns of Alternaria alternata during infection of citrus. Significant gene expression differences were found between the early and late stages of infection. Several novel genes related to plant-pathogen interaction were identified. RT-qPCR analysis confirmed the expression patterns of selected genes from the peroxisome pathway.
Article
Agronomy
Lei Li, Rongjie Wang, Xingxing Liang, Yunpeng Gai, Chen Jiao, Meiqin Wang
Summary: The present study provides a comprehensive overview of Bacillus velezensis strain Htq6 and its potential applications in plant disease control. The study conducted genomic analysis and transcriptome analysis to better understand the strain's biological control mechanism and response to pathogens. The results show promise for the development of an effective biocontrol agent for various plant diseases.
Article
Microbiology
Wen Wang, Tao Xiong, Yating Zeng, Wenwen Li, Chen Jiao, Jianping Xu, Hongye Li
Summary: This study conducted an extensive survey of Phyllosticta species across 11 citrus-producing provinces in southern China and identified five Phyllosticta species with pathogenicity on different citrus species. The findings have important implications for the control and management of Citrus Black Spot and related diseases.
Article
Agronomy
Xingxing Liang, Qichen Niu, Jinchao Kong, Xiaoyan Zhao, Bin Zhang, Lei Li, Chen Jiao, Yunpeng Gai
Summary: Antioxidant molecules play a crucial role in regulating redox homeostasis in fungi. This study identified a component called AaBemA involved in the regulation of the antioxidant system in Alternaria alternata. Loss-of-function analysis revealed the importance of AaBemA in response to oxidative stress. The study also revealed the interaction of multiple genes in the antioxidant system and their role in oxidative stress response.