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
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
Plant Sciences
Lin Chen, Maomao Yun, Zhenqiang Cao, Zhaojun Liang, Wenrui Liu, Min Wang, Jinqiang Yan, Songguang Yang, Xiaoming He, Biao Jiang, Qingwu Peng, Yu'e Lin
Summary: This study evaluated the changes in male flower development in cucumber under normal and heat stress conditions. It was found that heat stress led to decreased pollen fertility, abnormal tapetum and microspores, and significant changes in gene expression related to carbohydrate metabolism. Additionally, a co-expression network analysis revealed specific hub genes associated with heat stress response.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Forough Joudaki, Ahmad Ismaili, Seyed Sajad Sohrabi, Seyedeh Zahra Hosseini, Danial Kahrizi, Hadi Ahmadi
Summary: The current research achieved de novo transcriptome assembly of Gall oak using RNA sequencing technique, generating 89,335 unigenes, among which 6,928 unigenes showed significant differential expression between leaves and root tissues. Gene ontology examination revealed enrichment in cellular processes and enzyme activity. KEGG enrichment analysis displayed a high proportion of unigenes related to metabolic pathways and biosynthesis of secondary metabolites. Additionally, 39 families of transcription factors were identified, with C2H2, bZIP, bHLH, and ERF having the highest frequency. This transcriptome study provides a valuable reference for future functional and comparative studies in the absence of a reference genome and serves as a scientific resource for Q.infectoria.
Article
Plant Sciences
Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai, Yuhua Wang
Summary: The study identified a 92-gene core transcriptome of Camellia sinensis flower development by analyzing three different developmental stages of three different cultivars. Results revealed the involvement of endogenous hormone changes and gene expression related to synthesis and signal transduction during flower development. The study also showed that key genes such as MYC, FT, SOC1, and LFY play important roles in regulating the flowering process of C. sinensis through a complex hormone regulation network.
Article
Biochemistry & Molecular Biology
Hexuan Wang, Yahui Yang, Yiyao Zhang, Tingting Zhao, Jingbin Jiang, Jingfu Li, Xiangyang Xu, Huanhuan Yang
Summary: This research conducted transcriptome sequencing of early flower buds and flowers from both a late-flowering and an early-flowering tomato material, identifying 49 candidate genes related to flowering time and flower development. Predictions were made on the early flowering of the early-maturing material based on the expression patterns of these candidate genes, with a focus on their involvement in hormone regulation. The study provides a foundation for future functional verification and a more comprehensive exploration of the molecular mechanisms of tomato flowering time.
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
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
Plant Sciences
Yangang Lan, Lin Wu, Min Wu, Huanlong Liu, Yameng Gao, Kaimei Zhang, Yan Xiang
Summary: In this study, a transcriptome analysis of moso bamboo shoots during early elongation stages revealed key candidate genes regulating plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways. The cytokinin-signaling pathway was continuously active in the three successive elongation stages, indicating its importance in moso bamboo growth. Additionally, key genes involved in sugar, starch metabolism, and energy conversion were found to play essential roles in energy production and substrate synthesis during shoot growth.
PHYSIOLOGIA PLANTARUM
(2021)
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
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
Multidisciplinary Sciences
Carla A. Goncalves, Michael Larsen, Sascha Jung, Johannes Stratmann, Akiko Nakamura, Marit Leuschner, Lena Hersemann, Rashmiparvathi Keshara, Signe Perlman, Lene Lundvall, Lea Langhoff Thuesen, Kristine Juul Hare, Ido Amit, Anne Jorgensen, Yung Hae Kim, Antonio del Sol, Anne Grapin-Botton
Summary: This study established a single-cell transcriptome atlas of human fetal pancreas and developed a tool for identifying cell-cell interactions. By establishing a pancreas culture system, it was found that progenitors expanded in 3-dimensions are transcriptionally closer to the fetal pancreas.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Annapurna Bhattacharjee, Prabhakar Lal Srivastava, Onkar Nath, Mukesh Jain
Summary: OsHOX24 mediates regulation of desiccation stress response in rice through binding to multiple target genes involved in various biological processes, such as plant development and abiotic stress responses. The involvement of OsHOX24 in complex regulatory networks is indicated by the enrichment of cis-regulatory motifs representing binding sites of other transcription factors.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Juhi Bansal, Khushboo Gupta, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: The study presents a draft genome assembly of Oryza coarctata, predicting protein-coding genes and identifying miRNAs and target transcripts related to salinity and submergence stress responses. Additionally, whole genome bisulphite sequencing analysis reveals the influence of methylation status on gene expression.
PHYSIOLOGIA PLANTARUM
(2021)
Review
Plant Sciences
Kunchapu Chennakesavulu, Harshita Singh, Prabodh Kumar Trivedi, Mukesh Jain, Shri Ram Yadav
Summary: The review highlights the principles and functional importance of CRISPR-Cas9 in plant genome editing, emphasizing recent advancements like CRISPR-Cpf1, base editing, and prime editing. These technologies have the potential to improve stress tolerance in crops, essential for enhancing food security and agricultural practices globally.
PLANT CELL REPORTS
(2022)
Review
Biotechnology & Applied Microbiology
Vikram Singh, Mukesh Jain
Summary: CRISPR-based imaging methods play a crucial role in studying the localization, interaction, and coordinated regulation of chromatin, genomic loci, RNAs, and proteins. These methods, utilizing various tools and technologies, have significantly improved the efficiency and clarity of imaging, offering insights into chromatin organization and dynamics, RNA visualization, and protein imaging for genome biology research.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: Drought stress affects plant growth and yield in chickpea. Genome diversity and selective alleles in different genotypes of crop plants may influence agronomic traits, including drought stress response. DNA polymorphisms were found in genes related to stress response, highlighting their importance in engineering drought tolerance in chickpea.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Developmental Biology
Tushar Garg, Zeenu Singh, Kunchapu Chennakesavulu, Khrang Khrang Khunggur Mushahary, Anuj Kumar Dwivedi, Vijina Varapparambathu, Harshita Singh, Raj Suryan Singh, Debabrata Sircar, Divya Chandran, Kalika Prasad, Mukesh Jain, Shri Ram Yadav
Summary: In this study, the researchers investigated the molecular mechanisms controlling the development of shoot-borne adventitious/crown roots in rice. They identified transcription factors from the WUSCHEL-RELATED HOMEOBOX and PLETHORA gene families that play non-redundant and species-specific roles in determining root architecture. The study also revealed the involvement of PLT genes in promoting crown root development through the activation of local auxin biosynthesis genes. Interestingly, the PLT genes from rice were able to rescue lateral root primordia outgrowth defects in Arabidopsis mutants, indicating their conserved role in root primordia outgrowth regardless of their developmental origin. This research provides a molecular framework for understanding the tissue transdifferentiation during root primordia establishment and the evolution of transcription regulation in acquiring species-specific function.
Article
Biotechnology & Applied Microbiology
Mukesh Jain, Juhi Bansal, Mohan Singh Rajkumar, Naveen Sharma, Jitendra P. Khurana, Paramjit Khurana
Summary: In this study, a high-quality genome sequence of a cultivated Indian mulberry was obtained using multiple technologies. It identified repetitive DNA and a large number of protein-coding genes supported by transcript evidence. Comparative analysis with other plant genomes revealed species-specific genes in the mulberry genome. Transcriptome profiling showed tissue-specific and differential expression of these genes across different accessions and implicated in various biological processes.
Article
Plant Sciences
Nidhi Kandhol, Mukesh Jain, Durgesh Kumar Tripathi
Summary: This review discusses the role and mechanisms of nanoparticles in helping plants cope with drought, highlighting their importance in addressing global water scarcity issues in agriculture.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Zhishuo Zhang, Yi Liu, Qiaoling Yuan, Cheng Xiong, Hao Xu, Bowen Hu, Huan Suo, Sha Yang, Xilin Hou, Fang Yuan, Zhenming Pei, Xiongze Dai, Xuexiao Zou, Feng Liu
Summary: This study identified CabHLH1 as a candidate gene for controlling pollen fertility in pepper. It was found that CabHLH1 regulates the synthesis of anther flavonoids, which affects pollen vigor and fertility. These findings provide important insights into the factors affecting pollen fertility in pepper.
HORTICULTURE RESEARCH
(2022)
Article
Plant Sciences
Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: Integrated transcriptome data analysis identified candidate long non-coding RNAs (lncRNAs) associated with QTLs and involved in miRNA-mediated seed size/weight determination in chickpea seed development. The study provides a comprehensive resource and identifies potential lncRNAs that play important roles in chickpea seed development and seed size/weight determination.
Article
Biology
Mukesh Jain, Juhi Bansal, Mohan Singh Rajkumar, Rohini Garg
Summary: A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Plant Sciences
Rohini Garg, Prasanta K. K. Subudhi, Rajeev K. K. Varshney, Mukesh Jain
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Rama Shankar, Anuj Kumar Dwivedi, Vikram Singh, Mukesh Jain
Summary: Drought stress is a significant threat to rice productivity. This study analyzed the genetic variations between drought-tolerant and drought-sensitive rice cultivars and identified millions of single nucleotide polymorphisms and insertions/deletions. The genetic variations were unevenly distributed throughout the rice genome, with a higher frequency near the transcription start and stop sites. The study also identified cis-regulatory motifs and differentially expressed genes associated with stress-related transcription factors, providing valuable insights into candidate genes for drought stress tolerance in rice.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Plant Sciences
Anuj Kumar Dwivedi, Vikram Singh, Khalid Anwar, Ashwani Pareek, Mukesh Jain
Summary: Drought is a serious threat to rice production caused by climate change. Comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars identified the molecular mechanisms involved in drought tolerance/response. This study characterized the global transcriptome, proteome, and metabolome profiles and integrated them to reveal the role of transporters, translational machinery, aromatic amino acids, soluble sugars, and auxiliary carbohydrate metabolism in drought tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shalini Tiwari, Mukesh Jain, Sneh Lata Singla-Pareek, Prem L. Bhalla, Mohan B. Singh, Ashwani Pareek
Summary: The study found that the salt-tolerant rice genotype Pokkali plays a crucial role in stress response through the regulation of long non-coding RNA (lncRNA). These lncRNAs modulate various cellular processes, including transcriptional regulation, ion homeostasis, and secondary metabolite production. Furthermore, lncRNAs are predicted to bind to stress-responsive transcription factors. Additionally, some lncRNAs are also regulated under other abiotic stresses and phytohormone treatments, indicating possible cross-talk and further functional characterization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xue-Mei Yang, Jing-Hao Zhao, Xiao-Yu Xiong, Zhang-Wei Hu, Ji-Fen Sun, Hao Su, Yan-Jing Liu, Ling Xiang, Yong Zhu, Jin-Lu Li, Sadam Hussain Bhutto, Guo-Bang Li, Shi-Xin Zhou, Chi Li, Mei Pu, He Wang, Zhi-Xue Zhao, Ji-Wei Zhang, Yan-Yan Huang, Jing Fan, Wen-Ming Wang, Yan Li
Summary: The Arabidopsis RPW8.1 gene enhances disease resistance but compromises plant growth. It has been found that RPW8.1 constitutively enhances the expression of WRKY51 transcription factor and activates salicylic acid and ethylene signaling pathways. WRKY51, in turn, suppresses RPW8.1 expression, forming a feedback regulation loop.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Hannes Claeys, Eveline Neyrinck, Lies Dumoulin, Anne Pharazyn, Arne Verstichele, Laurens Pauwels, Michael L. Nuccio, Frederic Van Ex
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Melanie Ormancey, Bruno Guillotin, Camille Ribeyre, Clemence Medina, Nathanael Jariais, Helene San Clemente, Patrice Thuleau, Serge Plaza, Martina Beck, Jean-Philippe Combier
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Edgar Perez-Matas, Diego Hidalgo-Martinez, Elisabeth Moyano, Javier Palazon, Mercedes Bonfill
Summary: In this study, the production of paclitaxel was enhanced by overexpressing the bottleneck genes BAPT and DBTNBT in Taxus baccata cells. The transgenic cells showed significantly higher expression of these genes and improved taxane production compared to the wild type. Transcriptional profiling revealed that the GGPPS, TXS, and DBAT genes were most responsive to DBTNBT overexpression and the dual elicitation treatment.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Biying Dong, Dong Meng, Zhihua Song, Hongyan Cao, Tingting Du, Meng Qi, Shengjie Wang, Jingyi Xue, Qing Yang, Yujie Fu
Summary: This study identified the involvement of the citrate transporter CcMATE35 and the long noncoding RNA CcLTCS in aluminum stress response in pigeon pea. These findings suggest that the modules CcNFYB3-CcMATE35 and CcLTCS-CcCS jointly regulate the efflux and synthesis of citrate to enhance the resistance of pigeon pea under aluminum stress.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Review
Biotechnology & Applied Microbiology
Tien V. Vu, Ngan Thi Nguyen, Jihae Kim, Jong Chan Hong, Jae-Yean Kim
Summary: Prime editing technology uses an extended guide RNA to direct a fusion peptide to a specific location in the genome, enabling precise gene editing. This groundbreaking tool has potential in improving crop varieties, but efficiency limitations exist in certain plants.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Yan Xu, Jinyi Tan, Junxing Lu, Yuelin Zhang, Xin Li
Summary: Sclerotinia sclerotiorum causes white mold in economically important plants, and the discovery of SsGAP1 and SsRAS1/SsRAS2 genes as essential regulators of fungal development and virulence provides potential targets for controlling the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Xiaoyang Chen, Chen Liu, Hailin Wang, Qi Liu, Yaping Yue, Yuhang Duan, Zhaoyun Wang, Lu Zheng, Xiaolin Chen, Yaohui Wang, Junbin Huang, Qiutao Xu, Yuemin Pan
Summary: This study identified a secreted protein, Uv1809, as a key virulence factor in Ustilaginoidea virens-rice interactions. Uv1809 inhibits rice immunity and promotes infection by targeting and enhancing rice histone deacetylase OsSRT2-mediated histone deacetylation. CRISPR-Cas9 edited ossrt2 mutants showed broad-spectrum resistance to rice pathogens, indicating its potential as a genetic resource for breeding disease resistance.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Weishuai Bi, Jing Liu, Yuanyuan Li, Ziwei He, Yongming Chen, Tingting Zhao, Xiangxiu Liang, Xiaodan Wang, Xiangzong Meng, Daolong Dou, Guangyuan Xu
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Shengjie You, Yu Wu, Wen Li, Xiaofeng Liu, Qinlan Tang, Fengkun Huang, Yan Li, Hsihua Wang, Mingchun Liu, Yang Zhang
Summary: In this study, a transcription factor called SlERF.G3-Like in tomato was found to play a role in regulating ethylene synthesis, cell wall degradation, and the flavonoid pathway. The researchers also discovered the interaction between SlERF.G3-Like and the master ripening regulator SlRIN, and increased the production of resveratrol derivatives through genetic manipulation. These findings provide insights into the coordination of fruit maturation and metabolic changes in tomatoes, and have implications for metabolic engineering.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Thomas R. Aalders, Mara de Sain, Fleur Gawehns, Nina Oudejans, Yoran D. Jak, Henk L. Dekker, Martijn Rep, Harrold A. van den Burg, Frank L. W. Takken
Summary: The TPL1 and TPL2 genes in tomato are closely associated with susceptibility to Fusarium wilt disease, and mutating these genes can enhance plant resistance to the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
