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
Plant Sciences
Hai-Xiang Jin, Ming Jiang, Jian-Feng Yang, Zhi-Hao Wu, Long-Long Ma, Cong-Cong Wang, Chen Liang, Xin-Yi Ning, Liang-Fa Ge, Shu Chen
Summary: This study collected a novel biotype of Zoysia japonica, YueNong-9 (YN-9), and conducted comprehensive research on its characteristics. The results showed that YN-9 exhibited longer leaves, higher cold tolerance, and increased chlorophyll content compared to the popular Z. japonica cultivar LanYin-3 (LY-3) in Southern China.
Article
Horticulture
Yuqin Liang, Changzhi Han, Liu Yun, Yang Yang, Yanpo Cao
Summary: Anthocyanin pigments in purple asparagus spears fade under high temperature conditions, which is attributed to the reduced expression of genes related to anthocyanin biosynthesis. Metabolomic and transcriptomic analyses revealed that high temperatures led to a decrease in anthocyanin metabolites and the downregulation of key genes in the anthocyanin biosynthetic pathway. The redirection of metabolic flux from the anthocyanin branch to the lignin biosynthetic branch under high temperatures restricted anthocyanin synthesis.
SCIENTIA HORTICULTURAE
(2022)
Article
Multidisciplinary Sciences
Mitsuko Kishi-Kaboshi, Tsuyoshi Tanaka, Katsutomo Sasaki, Naonobu Noda, Ryutaro Aida
Summary: In this study, high-coverage transcriptomic data of Chrysanthemum morifolium was obtained using a combination of single-molecule real-time sequencing and RNA-seq technologies with error correction. The dataset was reliable and useful for molecular biology research.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Xu Qian Peng, Yu Jie Ai, Yu Ting Pu, Xiao Jing Wang, Yu Hang Li, Zhong Wang, Wei Bing Zhuang, Bing Jun Yu, Zhi Qi Zhu
Summary: In this study, an integrated metabolite and transcriptome analysis was performed to explore the anthocyanin composition and the specific regulatory network of anthocyanin biosynthesis in colored-leaf poplar. The expression patterns of certain differentially expressed genes in the anthocyanin biosynthesis pathway were strongly correlated with the differential accumulation of anthocyanins. One specific R2R3-MYB subfamily member, Podel.04G021100, showed a similar expression pattern to some structural genes and was strongly correlated with 16 anthocyanin compounds, indicating its potential involvement in the regulation of anthocyanin biosynthesis.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Zhenyu Ma, Chuangqi Wei, Yudou Cheng, Zhonglin Shang, Xiulin Guo, Junfeng Guan
Summary: This study explores the potential regulatory mechanism of anthocyanin biosynthesis in 'Red Zaosu' pear through a comprehensive transcriptome analysis. The results show that PpPIF8 plays a significant role in anthocyanin biosynthesis and promotes the process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yanli Xiang, Thomas Sapir, Pauline Rouillard, Marina Ferrand, Jose M. Jimenez-Gomez
Summary: This study reveals the significant impact of phase changes on photoperiod perception in tomato during domestication, while changes in period have minimal effect.
Article
Plant Sciences
Zhenjie Shi, Xiaoying Han, Guohui Wang, Jing Qiu, Li-jie Zhou, Sumei Chen, Weimin Fang, Fadi Chen, Jiafu Jiang
Summary: Temperature affects anthocyanin synthesis in chrysanthemum, leading to color fading. High-temperature stress induces differential gene expression related to heat shock response and flavonoid pathways, contributing to the fading of flower color. Genes involved in anthocyanin synthesis and heat shock response show differential expression under high-temperature stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yahui Yang, Huanhuan Yang, Yinxiao Tan, Tingting Zhao, Xiangyang Xu, Jingfu Li, Jingbin Jiang
Summary: Inflorescences play a crucial role in fruit yield, with the quality and quantity of inflorescences closely linked to fruit quality and yield. Transcriptome sequencing of cherry tomato and tomato plants identified new genes involved in compound inflorescence development, enriching our understanding of this process. The study provides a theoretical basis for further research on compound inflorescence development in tomatoes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Fenfang Long, Hairong Wu, Huie Li, Weiwei Zuo, Qian Ao
Summary: In this study, MYB genes were identified and analyzed in Rhododendron delavayi, a famous ornamental plant. It was found that two R2R3-MYB genes were key regulators in the formation of red color in this plant, providing references for understanding the transcriptional regulation of red color formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Naveed Ahmad, Kun Zhang, Jing Ma, Mei Yuan, Shuzhen Zhao, Mingqing Wang, Li Deng, Li Ren, Sunil S. Gangurde, Jiaowen Pan, Changle Ma, Changsheng Li, Baozhu Guo, Xingjun Wang, Aiqin Li, Chuanzhi Zhao
Summary: Through bulk RNA-seq analysis, the regulatory mechanism of testa color in peanut was revealed, with a focus on the anthocyanin biosynthetic pathway and the upstream regulatory genes PAL, CHS, and CHI. Additionally, the deepening of testa color was found to be associated with FLS inhibition. This study provides potential candidate genes and strategies for improving peanut varieties with desirable testa color.
Review
Horticulture
Shaohang Li, Yongjun He, Linzhi Li, Dalu Li, Huoying Chen
Summary: This article reviews the positive impact of anthocyanins on plants and human health, as well as the synthesis and regulation mechanisms of anthocyanins in Solanaceous fruit vegetables. It aims to provide a reference for further research on anthocyanin biosynthesis and increasing anthocyanin content in Solanaceous fruit vegetables.
SCIENTIA HORTICULTURAE
(2022)
Article
Forestry
Yun Yang, Mengjiao Chen, Yaxin Liu, Huanhuan Ding, Hongyan Du, Zhiqiang Sun, Jingle Zhu
Summary: The study focused on the differences in metabolites and gene regulation between red and green leaves of Eucommia ulmoides Oliv. Red leaves exhibited lower chlorophyll content and higher anthocyanin content, with up-regulation of flavonoid synthesis pathways. The integrative analysis of transcriptomics and metabolomics indicated the up-regulation of flavonoid metabolism and down-regulation of chlorophyll biosynthesis genes in red leaves, providing insights into the mechanism of red leaf coloration in woody plants.
Article
Microbiology
Peng Wang, Sheng Sun, Kerang Liu, Rong Peng, Na Li, Bo Hu, Lumei Wang, Hehe Wang, Ahmed Jawaad Afzal, Xueqing Geng
Summary: Tomato yellow leaf curl virus (TYLCV) is a significant threat to tomato production worldwide. In this study, we found that exogenous application of salicylic acid (SA), jasmonic acid (JA), or the JA mimetic, coronatine (COR), improved tomato resistance against TYLCV infection. RNA-Seq analysis revealed differentially expressed genes (DEGs) related to cell wall metabolism, hormone signaling, and secondary metabolism pathways in compound treated samples. Silencing SlNPR1 and SlCOI1 genes affected TYLCV levels in tomato plants, with SA signaling being hyper-activated in SlCOI1 silenced plants leading to reduced viral titers, while SINPR1 silencing resulted in a 19-fold increase in viral load. These findings provide valuable insights into SA and JA induced defenses against viral invasion in tomato plants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Jagmohan Singh, Rashmi Aggarwal, Bishnu Maya Bashyal, K. Darshan, Pooja Parmar, M. S. Saharan, Zakir Hussain, Amolkumar U. Solanke
Summary: Research on Chaetomium globosum has shown its potential as a biological control agent against plant pathogens, particularly in combating early blight disease in tomatoes. The study on the induced defense component of C. globosum (Cg-2) revealed its role in modulating hormone signaling pathways and metabolic processes to induce resistance against plant pathogens.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Katja Witzel, Andrea Matros, Uwe Bertsch, Tariq Aftab, Twan Rutten, Eswarayya Ramireddy, Michael Melzer, Gotthard Kunze, Hans-Peter Mock
Summary: The study identified a protein HvHorcH in barley that contributes to salt stress tolerance and accumulates in the root tip. This discovery may provide a new research direction for understanding how plants adapt to saline environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Taketo Okada, Takao Namiki, Takayuki Tohge, Shigehiko Kanaya
Summary: Kampo is a traditional Japanese medicine system validated over millennia in Asia, focusing on preventing and treating disease holistically based on specific diagnosis Sho. This complex medication system can be explained using chemometrics and informatic approaches.
JOURNAL OF NATURAL MEDICINES
(2022)
Article
Plant Sciences
Martine Lemaire-Chamley, Claude Koutouan, Joana Jorly, Julien Assali, Takuya Yoshida, Marilise Nogueira, Takayuki Tohge, Carine Ferrand, Lazaro E. P. Peres, Erika Asamizu, Hiroshi Ezura, Paul D. Fraser, Mohammad-Reza Hajirezaei, Alisdair R. Fernie, Christophe Rothan
Summary: The bZIP transcription factor SlTGA2.2 plays an important role in the growth and maturation of tomato fruits. By targeting the expression of a chimeric repressor, the study found that the repressor affects fruit development and metabolism, prolongs the time to reach maturity, and slows down fruit ripening. This research provides a useful tool for studying the molecular bases of tomato fruit transition to ripening.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Yuting Liu, Alisdair R. Fernie, Takayuki Tohge
Summary: The O-methylation of specialized metabolites in plants is a unique decoration that provides structural and functional diversity. The O-methylation of flavonoids promotes antimicrobial activities and liposolubility. Characterizing the physiology roles of methoxylated flavonoids with flavonoid O-methyltransferases is useful for crop improvement and metabolic engineering.
Article
Agronomy
Kefyalew Negisho, Surafel Shibru, Andrea Matros, Klaus Pillen, Frank Ordon, Gwendolin Wehner
Summary: Genome-wide association studies (GWAS) have enabled the detection of novel quantitative trait loci (QTLs) and the identification of single nucleotide polymorphism (SNP) markers associated with grain biomass and related traits for drought stress tolerance in durum wheat, based on a combination of climate chamber and multiyear and multilocation field experiments.
Article
Plant Sciences
Jay C. Delfin, Yuri Kanno, Mitsunori Seo, Naoki Kitaoka, Hideyuki Matsuura, Takayuki Tohge, Takafumi Shimizu
Summary: AtGH3.10 plays a role in flower development and the wound stress response in Arabidopsis, partially overlapping with AtJAR1.
Article
Multidisciplinary Sciences
Surafel Shibru Teklemariam, Kefyalew Negisho Bayissa, Andrea Matros, Klaus Pillen, Frank Ordon, Gwendolin Wehner
Summary: The genetic diversity of Ethiopian barley, influenced by diverse topography, altitude, climate conditions, soil types, and farming systems, was analyzed. Three genetically distinct clusters were identified, with higher genetic variation within clusters and moderate genetic differentiation between clusters. The weak correlation between geographic distance and genetic differentiation was observed, but certain regions showed a significant association between landraces and genetic clusters.
Article
Plant Sciences
Kefyalew Negisho, Surafel Shibru, Andrea Matros, Klaus Pillen, Frank Ordon, Gwendolin Wehner
Summary: This study aimed to explore the associations between different drought indices and quantitative trait loci (QTLs) to improve the drought tolerance of durum wheat in Ethiopia. Through analysis, potential gene loci were discovered that can increase yield and improve drought tolerance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Nandhakumar Shanmugaraj, Twan Rutten, Ales Svatos, Thorsten Schnurbusch, Hans-Peter Mock
Summary: Sublimation is a preferred method for matrix deposition in high spatial resolution MALDI-MSI, but reproducibility and time are concerns. A lab-made glass sublimator with improved vacuum control and rapid sublimation process was developed in this study. The method produced reproducible matrix crystals of <1 μm on the sample surface and demonstrated its efficiency in MALDI-MSI of barley inflorescence meristems at 15 μm spatial resolution.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Plant Sciences
Leonardo Perez de Souza, Elena Bitocchi, Roberto Papa, Takayuki Tohge, Alisdair R. Fernie
Summary: The process of crop domestication leads to a reduction in gene expression associated with metabolic diversity, particularly in genes involved in specialized metabolism. The reduction in diversity at the metabolite level has been assumed but never adequately assessed and quantified. This study used high coverage metabolomics to investigate metabolic diversity in common bean and found a shift towards lower diversity and specialization in domesticated bean accessions. Molecular networking analysis enabled a broader annotation of metabolites and revealed a metabolic shift from specialized metabolism to central metabolism upon domestication of this crop.
Article
Plant Sciences
Sara Leite Dias, Adriana Garibay-Hernandez, Fabian Leon Brendel, Benjamin Gabriel Chavez, Elena Brueckner, Hans-Peter Mock, Jakob Franke, John Charles D'Auria
Summary: A new method for monitoring specialized metabolites in barley and lupins was developed and validated using fluorescence detection. The method offers accurate and sensitive chromatographic separation and detection, providing an accessible alternative to LC-MS techniques for routine screening.
Review
Plant Sciences
Mutsumi Watanabe, Takayuki Tohge
Summary: Functional genomics approaches have successfully detected key metabolic polymorphisms in plant specialized metabolism through comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters. In recent decades, intra-species specific metabolic polymorphisms, new functionalization of tandem duplicated genes, and metabolic gene clusters have been found as the main factors creating metabolic diversity of specialized metabolites in plants. However, strategic approaches depending on the target metabolic pathways are required for gene identification in plant specialized metabolism. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Plant Sciences
Yue Jing, Mutsumi Watanabe, Fayezeh Aarabi, Alisdair R. Fernie, Monica Borghi, Takayuki Tohge
Summary: This study comprehensively analyzed the responses of four Brassicaceae species to UV-B radiation, revealing a reprogramming of the central metabolic pathway and the production of specific classes of flavonoids with increased protection against UV-B radiation. The activation of the phenylpropanoid-acetate pathway and the increase in phenylacylated-flavonoid glucosides were also observed across species. Interestingly, the expression of acyltransferase genes of the SCPLs protein class was constitutive but downregulated in response to UV-B radiation, possibly independent of the HY5 signaling pathway.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Monica Borghi, Leonardo Perez de Souza, Takayuki Tohge, Jianing Mi, Giovanni Melandri, Sebastian Proost, Marina C. M. Martins, Salim Al-Babili, Harro J. Bouwmeester, Alisdair R. Fernie
Summary: Anthesis is characterized by intense metabolic changes, including high-energy-level metabolism and transport of carbohydrates and amino acids. These changes play a crucial role in flower opening and may promote pollination in crops.
Article
Plant Sciences
Feng Zhu, Sagar Sudam Jadhav, Takayuki Tohge, Mohamed A. Salem, Je Min Li, James J. Giovannoni, Yunjiang Cheng, Saleh Alseekh, Alisdair R. Fernie
Summary: A reliable approach combining comparative transcriptomics and expression QTLs was used to identify 16 candidate genes involved in tomato fruit ripening. One potential ripening regulator, SlWD40, was validated and found to strongly co-express with master regulators and vital TFs. Overexpression and RNAi analysis of SlWD40 confirmed its role as an important ripening regulator. These findings contribute to our understanding of the gene regulatory networks involved in tomato ripening and demonstrate the effectiveness of comparative genomics and transcriptomics in identifying causal genes.