Article
Multidisciplinary Sciences
Satoru Nakagami, Michitaka Notaguchi, Tatsuhiko Kondo, Satoru Okamoto, Takanori Ida, Yoshikatsu Sato, Tetsuya Higashiyama, Allen Yi-Lun Tsai, Takashi Ishida, Shinichiro Sawa
Summary: Parasitic nematodes manipulate host plant signaling to promote infection.
Article
Plant Sciences
Thomas A. DeFalco, Pauline Anne, Sean R. James, Andrew C. Willoughby, Florian Schwanke, Oliver Johanndrees, Yasmine Genolet, Paul Derbyshire, Qian Wang, Surbhi Rana, Anne-Marie Pullen, Frank L. H. Menke, Cyril Zipfel, Christian S. Hardtke, Zachary L. Nimchuk
Summary: This study uncovers a common regulatory mechanism involving a RLCK kinase and a PP2C phosphatase that regulates receptor signaling in both immune responses and plant development.
Article
Plant Sciences
Zahra Zangishei, Maria Luz Annacondia, Heidrun Gundlach, Alena Didriksen, Julien Bruckmuller, Hooman Salari, Kirsten Krause, German Martinez
Summary: The RNA silencing machinery in parasitic plants shows similar evolutionary signatures, and microRNAs reflect the lifestyle of the parasites.
Article
Chemistry, Medicinal
Rui Wang, Zhecheng Zhou, Xiaonan Wu, Xin Jiang, Linlin Zhuo, Mingzhe Liu, Hao Li, Xiangzheng Fu, Xiaojun Yao
Summary: This study proposes a feature-correction-based model for plant SSP recognition, called SE-SSP. The model uses Transformer encoders and a feature correction module to improve prediction performance, and applies contrastive learning strategy to mitigate the problem of sparse samples. Experimental results demonstrate the excellent performance of the proposed model.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Plant Sciences
Catherine Damerval, Carmine Claudot, Martine Le Guilloux, Natalia Conde e Silva, Veronique Brunaud, Ludivine Soubigou-Taconnat, Jose Caius, Etienne Delannoy, Sophie Nadot, Florian Jabbour, Yves Deveaux
Summary: TCP transcription factors are important in developmental processes and hormonal pathways. We studied the TCP genes in the plant species Nigella damascena and found that they are orthologs of TCP genes in Aquilegia coerulea. Phylogenetic analysis and amino acid motif identification suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. There have been independent duplications in core eudicots and Ranunculales, resulting in different numbers of paralogs within TCP gene subclasses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai
Summary: This study reports the chloroplast genome sequences of 11 Cerasus species to investigate the evolution of their plastome. The results reveal the typical quadripartite circular structure of Cerasus chloroplast genomes and the presence of 115 unique genes. Several genes were found to have high nucleotide diversity and more polymorphic sites, including matK, rps16, and rbcL. The phylogenetic analysis sheds light on the relationships between different Cerasus species, providing insights for further research on their phylogenetics and phylogeography.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Min Li, Min Liu, Shi-Yun Hu, Fang-Zhen Luo, Ming-Long Yuan
Summary: This study analyzed the mitogenomes of ten spider species and found that nucleotide composition and codon usage were conserved within the RTA clade, but there was diversity in sequence length and structure in the control region. Most protein-coding genes were undergoing purifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Jie Hu, Xiaotong Hu, Yang Yang, Chunmei He, Jin Hu, Xuelu Wang
Summary: Through studying genetic materials in Arabidopsis, the antagonistic roles of BES1 and WOX4 in regulating cambium activity were identified, providing insight into the dynamic regulation of cambium development.
Article
Agricultural Engineering
Wuqin Xu, Ruisen Lu, Junyou Li, Maoqin Xia, Guangyong Chen, Pan Li
Summary: In this study, we sequenced the complete plastomes of 21 species and cultivars in the Atractylodes genus, revealing the typical quadripartite structure and highly variable regions of the plastomes. Our phylogenetic analysis based on plastid and RAD datasets provides strong support for studying the phylogeography and population genetics of Atractylodes, and the genomic resources accumulated in this study will also be valuable for genetic engineering and germplasm exploration of this important genus.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Qiong Xiao, Xue Pan, Yang Xu, Stacy D. Singer, Guanqun Chen
Summary: This study investigated the evolution and diversity of CCTs in the green lineage and provided insights into the association between the biochemical and structural properties of the enzyme and its function. The findings expanded our understanding of the importance of CCT at the genome-wide level.
Article
Environmental Sciences
Ning Huang, Shuai Chen, Ming He, Qi Song, Lina Hou, Yan Zhao, Shuo Zhao, Miao Miao
Summary: Ciliates, the most complex unicellular eukaryotic organisms, play essential roles in various ecosystems. The research on Euplotes mitochondrial genomes revealed gene rearrangements and codon usage differences among species, indicating salinity as a potential barrier for species distribution. Mitochondrial genes were recommended for distinguishing closely related Euplotes species.
FRONTIERS IN MARINE SCIENCE
(2021)
Review
Biochemical Research Methods
Guanjing Hu, Corrinne E. Grover, Mark A. Arick, Meiling Liu, Daniel G. Peterson, Jonathan F. Wendel
Summary: This study presents an analytical workflow using cotton genus as an example to evaluate various bioinformatic methods at different stages of RNA-seq analysis for understanding polyploid expression evolution. The findings suggest that EAGLE-RC and GSNAP-PolyCat quantification pipelines outperform others, representing homoeolog expression and co-expression divergence well. This work highlights the importance of examining homoeolog read ambiguity to avoid potential artifacts affecting the understanding of duplicate gene expression in polyploids.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Lior Tal, Malathy Palayam, Mily Ron, Aleczander Young, Anne Britt, Nitzan Shabek
Summary: This study reveals the mechanism of perception and signal activation of the plant hormone strigolactones, as well as the key factors regulating strigolactone signaling. Through the study of mutants, the importance of protein conformational switch in the signaling process is demonstrated. Additionally, an organic acid metabolite that can directly trigger the conformational switch is discovered.
Article
Virology
Semmannan Kalaiyarasu, Niranjan Mishra, Saravanan Subramaniam, Dashprakash Moorthy, Shashi Bhusan Sudhakar, Vijendra Pal Singh, Aniket Sanyal
Summary: This study determined the full-genome sequences of three new clades (c, d, and e) of HoBiPeV and performed genetic and evolutionary analyses. It revealed the existence of four main clades (a, c, d, and e) globally, with genetic divergence ranging from 13.0% to 18.2%. The study suggested that HoBiPeV most likely originated in India in 1938, providing new insights into its origin and evolution.
Article
Genetics & Heredity
De Bi, Shiyun Han, Jun Zhou, Maojin Zhao, Sijia Zhang, Xianzhao Kan
Summary: This study provides a comprehensive assessment of codon manipulation in Saxifragales plastid genes, showing a high preference for AT bases and AT-ending codons. Intrafamilial differences in codon bias were detected in three families. Selection was found to play a dominant role in codon usage bias in Saxifragales plastid genes, supported by ENC plots and neutrality analyses. The inferred phylogenetic affinities of Saxifragales were consistent with each other and enhance our understanding of the evolutionary processes in this order.
Article
Biochemistry & Molecular Biology
Cheng Zhang, Theresa Lauster, Wenxin Tang, Anaxi Houbaert, Shanshuo Zhu, Dominique Eeckhout, Ive De Smet, Geert De Jaeger, Thomas B. Jacobs, Tongda Xu, Sabine Mueller, Eugenia Russinova
Summary: In this study, it was found that brassinosteroid (BR) influences Arabidopsis epidermal cell morphogenesis by regulating PLECKSTRIN HOMOLOGY GTPase-ACTIVATING proteins (PHGAPs), thereby connecting the BR and ROP2-GTPase signaling pathways crucial for pavement cell interdigitation.
Article
Plant Sciences
Ren Wang, Ellie Himschoot, Matteo Grenzi, Jian Chen, Alaeddine Safi, Melanie Krebs, Karin Schumacher, Moritz K. Nowack, Wolfgang Moeder, Keiko Yoshioka, Daniel Van Damme, Ive De Smet, Danny Geelen, Tom Beeckman, Jiri Friml, Alex Costa, Steffen Vanneste
Summary: This study evaluates the effects of different auxin analogs on the accumulation of PIN proteins in BFA bodies and their ability to induce Ca2+ responses. The results show that not all auxin analogs can elicit Ca2+ responses and their ability to do so partially correlates with their inhibition of BFA body formation.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Xuejun Tian, Zhen Qin, Yue Zhao, Jingjing Wen, Tianyu Lan, Liyuan Zhang, Fei Wang, Dandan Qin, Kuohai Yu, Aiju Zhao, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Ive De Smet, Huiru Peng, Mingming Xin
Summary: The TaMBF1c gene plays a crucial role in regulating heat stress response in wheat by affecting the translation of specific genes. It is evolutionarily conserved in various wheat species and is closely associated with the translation of heat shock proteins, providing a potential target for improving heat tolerance in wheat breeding programs.
Article
Plant Sciences
Harshita Singh, Zeenu Singh, Tingting Zhu, Xiangyu Xu, Bhairavnath Waghmode, Tushar Garg, Shivani Yadav, Debabrata Sircar, Ive De Smet, Shri Ram Yadav
Summary: The root system of rice, mainly composed of shoot-borne adventitious/crown roots, serves as an excellent model system to study the shoot-to-root trans-differentiation process. This study uncovers global changes in protein and metabolite abundance and protein phosphorylation during crown root development in response to auxin stimulus. It identifies differentially regulated proteins, amino acids, and phosphoproteins, and reveals the involvement of auxin signaling in chromatin conformational change, gene expression, cell cycle regulation, and ethylene biosynthesis. The study also highlights the importance of translational and post-translational regulation in root organogenesis.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Anna C. Ortiz, Ive De Smet, Rosangela Sozzani, Anna M. Locke
Summary: This study investigated the genotypic variation in soybean response to elevated temperature, revealing diverse responses among genotypes. Results showed that long-term elevated air temperature affected gas exchange, chlorophyll fluorescence, yield, and seed composition. The findings highlight the potential for improving soybean heat tolerance through breeding and the importance of efficient selection strategies for stress-tolerant crops.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Hans Motte, Tao Fang, Boris Parizot, Wouter Smet, Xilan Yang, Ward Poelmans, Liam Walker, Maria Njo, George W. Bassel, Tom Beeckman
Summary: This study examined root bifurcation in the lycophyte Selaginella moellendorffii and found that the initial cells in the root meristem are irregular in shape rather than tetrahedral as previously assumed. The study also identified a subset of core meristem genes and suggested the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance. These findings contribute to a better understanding of root formation and development in plants.
Article
Plant Sciences
Brecht Wybouw, Helena E. Arents, Baojun Yang, Jonah Nolf, Wouter Smet, Michael Vandorpe, Max Minne, Xiaopeng Luo, Inge De Clercq, Daniel Van Damme, Matous Glanc, Bert De Rybel
Summary: A forward genetics screen identified the MYB12 transcription factor as a repressor of TMO5/LHW activity in Arabidopsis, regulating cell proliferation rates during root vascular development. Transcriptional networks play a crucial role in integrating internal and external signals for optimal plant growth and development. The MYB12-mediated negative feedback loop restricts TMO5/LHW activity, ensuring optimal cell proliferation rates during root vascular development in response to cytokinin signaling.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Shouguang Huang, Tobias Maierhofer, Kenji Hashimoto, Xiangyu Xu, Sohail M. Karimi, Heike Mueller, Michael A. Geringer, Yi Wang, Joerg Kudla, Ive De Smet, Rainer Hedrich, Dietmar Geiger, M. Rob G. Roelfsema
Summary: This study found that CIPK23 is expressed in Arabidopsis guard cells and enhances stomatal conductance by regulating the activity of multiple ion channel proteins, including the inhibition of SLAC1-type anion channels.
Article
Plant Sciences
Joris Jourquin, Ana Ibis Fernandez, Qing Wang, Ke Xu, Jian Chen, Jan Simura, Karin Ljung, Steffen Vanneste, Tom Beeckman
Summary: GOLVEN peptides regulate lateral root spacing in Arabidopsis by inhibiting auxin accumulation and regulating the expression of auxin response genes. This is achieved through the action of PIN3 and PIN7 auxin export proteins in xylem-pole pericycle cells.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Ke Xu, Joris Jourquin, Xiangyu Xu, Ive De Smet, Ana Fernandez, Tom Beeckman
Summary: During root exploration, roots adapt to different conditions and interact with their environment. Asymmetric molecular patterns guide directional root growth, but the mechanisms of their establishment and dynamic regulation are not well understood. Asymmetric gradients of the phytohormone auxin are established through polarized auxin transporters, mainly during root gravitropism. GOLVEN-ROOT GROWTH FACTOR 1 INSENSITIVE signaling in lateral root cap cells plays a crucial role in root gravitropism by regulating the plasma membrane abundance of PIN-FORMED2 in Arabidopsis.
Review
Plant Sciences
Tingting Zhu, Shao-Li Yang, Ive De Smet
Summary: Climate change-induced temperature fluctuations affect agricultural productivity by causing short-term intense heat waves or long-term heat stress. Plants have developed sophisticated strategies to cope with heat stress. This review focuses on the translocation of molecules and proteins associated with signal transduction, aiming to understand how plant cells decode signals from the environment to trigger an appropriate response.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Plant Sciences
Qing Wang, Hugues De Gernier, Xingliang Duan, Yuanming Xie, Danny Geelen, Ken-ishiro Hayashi, Wei Xuan, Markus Geisler, Kirsten ten Tusscher, Tom Beeckman, Steffen Vanneste
Summary: LR positioning and development are regulated by auxin production, transport, and inactivation. This study demonstrates the impact of GH3-type auxin conjugating enzymes and DAO1 in LR development. The gh3hex mutants exhibit increased LR density due to enhanced initiation and faster progression, with GH3 activities controlling LR formation. GH3-mediated auxin inactivation attenuates LR development by modulating meristem activities and apical meristem size, resulting in accelerated auxin response oscillations and increased LR initiation rates.
Article
Plant Sciences
Hans Motte, Boris Parizot, Wei Xuan, Qian Chen, Steven Maere, Sandra Bensmihen, Tom Beeckman
Summary: This study developed and adapted LRIS in rice, Medicago, and Arabidopsis to perform RNA-sequencing during different developmental stages of lateral root formation. The results provide valuable datasets and insights into the molecular control of lateral root development in multiple plant species.
Editorial Material
Plant Sciences
Marcel Quint, Carolin Delker, Sureshkumar Balasubramanian, Martin Balcerowicz, Jorge J. Casal, Christian Danve M. Castroverde, Meng Chen, Xuemei Chen, Ive De Smet, Christian Fankhauser, Keara A. Franklin, Karen J. Halliday, Scott Hayes, Danhua Jiang, Jae-Hoon Jung, Eirini Kaiserli, S. Vinod Kumar, Daniel Maag, Eunkyoo Oh, Chung-Mo Park, Steven Penfield, Giorgio Perrella, Salome Prat, Rodrigo S. Reis, Philip A. Wigge, Bjorn C. Willige, Martijn van Zanten
TRENDS IN PLANT SCIENCE
(2023)