Article
Biochemistry & Molecular Biology
Jing Yu, Chenguang Zhou, Danning Li, Shuang Li, Ying-Chung Jimmy Lin, Jack P. Wang, Vincent L. Chiang, Wei Li
Summary: In this study, the formation mechanism of tension wood in Populus trichocarpa was analyzed using laser capture microdissection and full transcriptome RNA-sequencing. It was found that PtrLBD39 and PtrLBD22 are key regulatory genes controlling tension wood formation by regulating a set of tension wood-related genes.
PLANT COMMUNICATIONS
(2022)
Article
Plant Sciences
Yang Zhang, Yingying Liu, Xueying Wang, Ruiqi Wang, Xuebing Chen, Shuang Wang, Hairong Wei, Zhigang Wei
Summary: In this study, a plant-specific transcription factor PtrWOX13A was identified and characterized for its role in secondary cell wall formation in Populus trichocarpa. Overexpression of PtrWOX13A resulted in enhanced growth potential and increased secondary cell wall thickness, fiber length, and lignin and hemicellulose contents. PtrWOX13A directly activated its target genes through binding to specific cis-elements in their promoter regions. Furthermore, PtrWOX13A was found to be responsive to gibberellin signaling and could regulate genes involved in GA homeostasis. The discovery of PtrWOX13A's role in secondary cell wall formation and its regulatory functions has important implications for improving wood quality through genetic engineering.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Hui He, Xue-Qin Song, Cheng Jiang, Ying-Li Liu, Dian Wang, Shuang-Shuang Wen, Guo-Hua Chai, Shu-Tang Zhao, Meng-Zhu Lu
Summary: In this study, the researchers investigated the role of PagSAG101a in secondary xylem development. They found that PagSAG101a is primarily expressed in lignified stems and plays a crucial role in regulating plant growth and wood development by controlling cambium cell division activity and secondary cell wall deposition.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Peerapat Khamwachirapithak, David Guillaume-Schoepfer, Pakkanan Chansongkrow, Sarah A. Teichmann, Philip A. Wigge, Varodom Charoensawan
Summary: This study combines ChIP-seq and RNA-seq to investigate the effects of global and local H3 depletion on gene transcription, as well as the interaction between the transcription factor Rap1 and H3. The results provide a working model and testable hypotheses regarding the impact of H3 depletion on transcriptional changes.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Michael F. Nagle, Jialin Yuan, Damanpreet Kaur, Cathleen Ma, Ekaterina Peremyslova, Yuan Jiang, Bahiya Zahl, Alexa Nino de Rivera, Wellington Muchero, Li Fuxin, Steven H. Strauss
Summary: Adventitious rooting (AR) plays a crucial role in tree propagation, breeding, and genetic engineering. However, the genetic basis of AR is not well-characterized. To identify genetic regulators of AR, a genome-wide association study (GWAS) was performed using 1148 Populus trichocarpa genotypes. A computer vision system was developed to measure various traits related to adventitious root development. GWAS analysis revealed 277 unique associations, indicating that genes involved in hormone signaling, cell division, and other root development processes play a role in AR. Numerous genes with unknown functions were also identified as candidates for further analysis.
HORTICULTURE RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Zhijie Chen, Lu Cui, Li Xu, Zheyi Liu, Yumeng Liang, Xuefeng Li, Yanhui Zhang, Yijing Li, Shengwang Liu, Hai Li
Summary: In this study, the chp53 transcriptional regulatory network was comprehensively characterized through analysis of chromatin occupancy and gene expression, providing insights into the underlying mechanisms of chp53's antiviral functions in chickens. The findings also contribute to a better understanding of p53 transcriptional regulatory mechanisms.
Article
Plant Sciences
Huizi Liu, Jinghui Gao, Jiatong Sun, Shuang Li, Baofeng Zhang, Zhuwen Wang, Chenguang Zhou, Daniel Barletta Sulis, Jack P. Wang, Vincent L. Chiang, Wei Li
Summary: Wood formation is regulated by transcriptional regulatory networks, and this study identified a new interaction between PtrMYB074 and PtrWRKY19 in Populus trichocarpa. The study also revealed the involvement of PtrbHLH186 as a direct target gene of the PtrMYB074-PtrWRKY19 complex. Overexpression of PtrbHLH186 resulted in altered plant growth and wood properties. Understanding this regulatory pathway may aid in optimizing wood formation and growth.
Article
Plant Sciences
Huimin Zhao, Yani Niu, Hao Dong, Yaqi Jia, Yucheng Wang
Summary: The study identified two S1Fa-like TF genes, PtS1Fa1 and PtS1Fa2, in Populus trichocarpa. While PtS1Fa1 did not show significant effects, overexpression of PtS1Fa2 increased antioxidant activity and reduced ROS accumulation, playing a crucial role in drought tolerance in the plant.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Xiaokang Fu, Huili Su, Shuai Liu, Xuelian Du, Changzheng Xu, Keming Luo
Summary: The study revealed that the local cytokinin signaling in the secondary phloem regulates cambial activity in a noncell-autonomous manner.
Article
Biochemistry & Molecular Biology
Lijiao Sun, Xinxin Dong, Xingshun Song
Summary: In this study, a new drought regulatory pathway was identified, which promotes lateral root growth and development and improves tolerance to drought stress through the regulation of transcription factor PtrABR1 and target genes PtrYY1, PtrGH3.6, and PtrPP2C44.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Hemeng Wang, Jin-Gui Chen, Ying Chang
Summary: OFPs are a family of plant growth regulators known to play diverse roles in physiological processes, with members like PtOFP1 having been shown to act as a transcriptional repressor. In Populus trichocarpa, 30 PtOFP genes were identified, grouped into four subfamilies, and found to be involved in hormonal responses and cellular processes. Overexpression of PtOFP1 in Arabidopsis enhanced tolerance to drought stress, highlighting its potential as a target for genetic modification in improving stress resistance in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Yingying Liu, Ruiqi Wang, Jiajie Yu, Shan Huang, Yang Zhang, Hairong Wei, Zhigang Wei
Summary: This study systematically investigated the PtrARF gene family and provided comprehensive information on their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics. The expression patterns of PtrARF genes were analyzed, and it was found that certain genes were preferentially expressed in primary stems and participated in different phases of wood formation. Some PtrARF genes showed different responses to exogenous IAA and ABA treatment. Three PtrARF proteins were characterized and their interactions with other proteins were demonstrated. This study lays the foundation for future research on PtrARF genes in tree development and growth, especially wood formation, in response to cellular signaling and environmental cues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Dian Wang, Yan Chen, Wei Li, Quanzi Li, Mengzhu Lu, Gongke Zhou, Guohua Chai
Summary: Research has shown that the formation of wood involves the initiation, proliferation, and differentiation of vascular stem cells, which requires coordination of multiple hormones and peptides. In Populus and Arabidopsis, there is a similar but more complex regulatory network orchestrating vascular cambium development. Future research will focus on the development of vascular cambium in perennial woody plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Ruiqi Wang, Mengxuan Reng, Shuanghui Tian, Cong Liu, He Cheng, Yingying Liu, Huaxin Zhang, Muhammad Saqib, Hairong Wei, Zhigang Wei
Summary: This study utilized miRNA expression profiling to investigate the regulation of miRNA species on lignocellulosic synthesis in Populus trichocarpa stems at three different developmental stages. The results revealed differential expression of miRNAs and their candidate target genes, as well as the involvement of miRNAs in regulating processes such as cell division, wall modification, and lignification. Overall, the findings advance understanding of individual miRNAs and their diverse roles in the dynamic regulation of secondary growth in woody tree species.
G3-GENES GENOMES GENETICS
(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
Microbiology
Andreas N. Schneider, John Sundh, Gorel Sundstrom, Kerstin Richau, Nicolas Delhomme, Manfred Grabherr, Vaughan Hurry, Nathaniel R. Street
Summary: The study compared fungal community information obtained from RNA-Seq and fungal ITS1 DNA amplicon sequencing, revealing both consistency and differences between the two methods in terms of taxonomic and functional insights. It also demonstrated the potential of transcriptomic data to provide biologically informative functional insights, advancing our understanding of the interaction and effect between host plants and their associated microbial communities.
Article
Plant Sciences
Defeng Shen, Rens Holmer, Olga Kulikova, Chanaka Mannapperuma, Nathaniel R. Street, Zhichun Yan, Thomas van der Maden, Fengjiao Bu, Yuanyuan Zhang, Rene Geurts, Kevin Magne
Summary: The study reveals the essential role of PanNODULE ROOT1 in controlling stem secondary growth, with CRISPR-Cas9 mutants altering the expression of key genes related to secondary growth. This suggests that PanNODULE ROOT1 positively contributes to the regulation of stem secondary growth and demonstrates the potential of Parasponia andersonii as a research system for tree-related traits.
Article
Biochemistry & Molecular Biology
Martha Rendon-Anaya, Jonathan Wilson, Saemundur Sveinsson, Aleksey Fedorkov, Joan Cottrell, Mark E. S. Bailey, Dainis Runis, Christian Lexer, Stefan Jansson, Kathryn M. Robinson, Nathaniel R. Street, Par K. Ingvarsson
Summary: Understanding local adaptation in European aspen is crucial due to climate challenges and conservation of genetic resources. Genetic studies reveal a strong genomic mosaicism in Scandinavian trees and an adaptive introgression event in chromosome 10, originating from an Eastern source, possibly Russian, contributing to adaptation in Northern Scandinavia. This study emphasizes the migration-selection balance in shaping adaptive traits.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Nanette Christie, Chanaka Mannapperuma, Raphael Ployet, Karen van der Merwe, Niklas Mahler, Nicolas Delhomme, Sanushka Naidoo, Eshchar Mizrachi, Nathaniel R. Street, Alexander A. Myburg
Summary: Affordable high-throughput DNA and RNA sequencing technologies are enabling genomic analysis of plant and animal populations, allowing for new systems genetics approaches to study complex traits. Developing intuitive tools to browse and analyze resulting large-scale genetic and genomic datasets remains a significant challenge.
BMC BIOINFORMATICS
(2021)
Correction
Biochemistry & Molecular Biology
Martha Rendon-Anaya, Jonathan Wilson, Saemundur Sveinsson, Aleksey Fedorkov, Joan Cottrell, Mark E. S. Bailey, Dainis Rungis, Christian Lexer, Stefan Jansson, Kathryn M. Robinson, Nathaniel R. Street, Par K. Ingvarsson
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shuyu Liu, Lei Zhang, Yupeng Sang, Qiang Lai, Xinxin Zhang, Changfu Jia, Zhiqin Long, Jiali Wu, Tao Ma, Kangshan Mao, Nathaniel R. Street, Par K. Ingvarsson, Jianquan Liu, Jing Wang
Summary: Hybridization and introgression play important roles in shaping the tree of life. This study used whole-genome resequencing data to characterize hybridization patterns and genomic signatures of introgression in Populus species. The results reveal a high frequency of contemporary hybridization and the presence of F1 hybrids. Frequent past introgression is found to be a common feature in the speciation of these Populus species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Alexander Vergara, Julia C. Haas, Tuuli Aro, Paulina Stachula, Nathaniel R. Street, Vaughan Hurry
Summary: The conifer-dominated boreal forest is expected to experience warmer winter air temperatures and reduced snow cover depth and duration due to climate change. Norway spruce exhibits unique mechanisms for cold tolerance, utilizing early response transcription factors and showing delayed response compared to Arabidopsis. Regulatory network analysis identified both conserved transcription factors and species-specific responses in Norway spruce cold stress adaptation.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Forestry
David Castro, Andreas N. Schneider, Mattias Holmlund, Torgny Nasholm, Nathaniel R. Street, Vaughan Hurry
Summary: The study found that early, small-scale nitrogen addition can increase survival rate and needle carbon content of Scots pine seedlings, while also accelerating the rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings.
Article
Plant Sciences
Alok Ranjan, Irene Perrone, Sanaria Alallaq, Rajesh Singh, Adeline Rigal, Federica Brunoni, Walter Chitarra, Frederic Guinet, Annegret Kohler, Francis Martin, Nathaniel R. Street, Rishikesh Bhalerao, Valerie Legue, Catherine Bellini
Summary: This study provides insights into the molecular basis of genotypic differences in adventitious root (AR) development and implicates differential expression of transcription factors as critical players in this process. Comparative transcriptomic analysis reveals higher transcriptional activity in the easy-to-root genotype compared with the difficult-to-root genotype.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Simon R. Law, Alonso R. Serrano, Yohann Daguerre, John Sundh, Andreas N. Schneider, Zsofia R. Stangl, David Castro, Manfred Grabherr, Torgny Nasholm, Nathaniel R. Street, Vaughan Hurry
Summary: Carbon storage and cycling in boreal forests, which are the largest terrestrial carbon store, are influenced by the complex interactions between trees and soil microorganisms. This study developed a metatranscriptomic approach to examine the impact of nutrient enrichment on Norway spruce fine roots and the fungal community structure and function. The findings demonstrate the important role of host-microbe dynamics in mediating the carbon storage potential of boreal soils under changing nutrient conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Shirin Akhter, Karl Johan Westrin, Nathan Zivi, Veronika Nordal, Warren W. Kretzschmar, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, Jens F. Sundstrom
Summary: This study investigates reproductive phase change in the gymnosperm Picea abies using a cone-setting acrocona mutant, revealing the involvement of PaSPL1 gene and miRNAs in regulating the transition shoots.
Article
Plant Sciences
Pasquale Luca Curci, Jie Zhang, Niklas Maehler, Carolin Seyfferth, Chanaka Mannapperuma, Tim Diels, Tom Van Hautegem, David Jonsen, Nathaniel Street, Torgeir R. Hvidsten, Magnus Hertzberg, Ove Nilsson, Dirk Inze, Hilde Nelissen, Klaas Vandepoele
Summary: Cross-species network analysis was used to identify and validate growth regulators in Arabidopsis. The study built leaf growth transcriptional networks in Arabidopsis, maize, and aspen, and predicted new growth regulators using known growth regulators and conserved networks across species. Through literature screening and phenotypic characterization, 34 new potential growth regulators were confirmed. The research findings demonstrate that this network approach is effective in identifying genes involved in plant growth and development.
Article
Multidisciplinary Sciences
Bastian Schiffthaler, Elena van Zalen, Alonso R. Serrano, Nathaniel R. Street, Nicolas Delhomme
Summary: Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. Currently, there is a lack of usable and scalable software tools for performing these analyses. Seidr is a software toolkit that addresses these limitations and provides improved results by creating community networks and utilizing noise corrected network backboning.
Article
Plant Sciences
Janos Urbancsok, Evgeniy N. Donev, Pramod Sivan, Elena van Zalen, Felix R. Barbut, Marta Derba-Maceluch, Jan Simura, Zakiya Yassin, Madhavi L. Gandla, Michal Karady, Karin Ljung, Sandra Winestrand, Leif J. Jonsson, Gerhard Scheepers, Nicolas Delhomme, Nathaniel R. Street, Ewa J. Mellerowicz
Summary: Stem bending in trees induces flexure wood, but its properties and development are poorly understood. This study investigated the effects of low-intensity stem flexing on growth and wood properties in hybrid aspen. The results showed that stem flexing stimulated gelatinous-fiber formation, reduced secondary wall thickness, and changed matrix polysaccharides, leading to improved wood properties. The study also revealed the involvement of various transcriptional and hormonal pathways in the response to stem flexing.
Article
Forestry
Julia C. Haas, Alexander Vergara, Alonso R. Serrano, Sanatkumar Mishra, Vaughan Hurry, Nathaniel R. Street
Summary: Drought stress has significant impacts on seedling establishment, survival, and productivity of plants, particularly coniferous tree species. Norway spruce seedlings show reversible physiological plasticity in response to drought, with changes in shoot water potential and ABA levels. Root and needle transcriptional responses to drought differ, with roots showing more down-regulation of growth-related genes. Comparison with previously studied drought-response genes in Arabidopsis thaliana shows both conservation and divergence in transcriptional response in P. abies, highlighting the importance of profiling both above- and belowground tissues to understand drought response mechanisms in coniferous species.