Article
Plant Sciences
Muhammad Imran, Tengfei Liu, Zheng Wang, Min Wang, Shulin Liu, Xinyan Gao, Anning Wang, Songfeng Liu, Zhixi Tian, Min Zhang
Summary: This study investigates the role of nested miRNA structures in gene silencing in plants, using the Arabidopsis nested miR159a structure as a model. The study demonstrates that the miR159a structure can complement the mir159ab phenotype to different degrees, and a duplex nested structure in the tail end region of the pre-miR159a fold back may have a dominant function in the cleavage of the mature miRNA. Furthermore, the study suggests that a miRNA precursor in plants may encode multiple regulatory small RNAs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Axel J. Giudicatti, Ariel H. Tomassi, Pablo A. Manavella, Agustin L. Arce
Summary: MicroRNAs play crucial roles in various processes in plants and undergo modifications such as trimming and tailing to control the silencing release of targeted-genes, with the loading, slicing activity, and cellular localization of ARGONAUTE 1 (AGO1) being important factors.
Article
Biology
Chao Ma, Qiuju Chen, Shiping Wang, Amnon Lers
Summary: The microRNA miR827 and the transcription regulator GPL alpha are functionally involved in both senescence and phosphate homeostasis, with miR827 playing a role in regulating the expression of GPL alpha. The expression of GPL alpha is induced by phosphate deficiency and overexpression of GPL alpha leads to reduced expression of phosphate transporter genes. The close interactions between senescence and phosphate homeostasis are further emphasized by the functional involvement of miR827 and GPL alpha in both processes.
Article
Biochemistry & Molecular Biology
Syed Muhammad Muntazir Mehdi, Sivakumar Krishnamoorthy, Michal Wojciech Szczesniak, Agnieszka Ludwikow
Summary: The study identified differentially expressed miRNAs in response to ABA treatment in wild-type Arabidopsis and mutant plants. Potential target genes of these miRNAs were identified and validated using psRNATarget and RT-PCR. The target genes of the identified miRNAs were found to be involved in diverse cellular processes, including development and stomatal movement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Taiyun Wang, Yanhua Zheng, Qi Tang, Songxiao Zhong, Wei Su, Binglian Zheng
Summary: Plant hormone brassinosteroids inhibit miRNA-mediated translational repression by negatively regulating the distribution of AGO1 at the endoplasmic reticulum in Arabidopsis thaliana. This affects the protein levels of miRNA target genes. The findings provide new insights into how miRNA-mediated gene silencing is regulated by plant endogenous hormones.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Plant Sciences
Elisa Fasani, Giovanni DalCorso, Gianluca Zorzi, Nicola Vitulo, Antonella Furini
Summary: miRNAs are key players in mineral homeostasis, with differential expression patterns in response to Zn excess in Arabidopsis thaliana and the Zn-hyperaccumulator species Arabidopsis halleri. These differences reflect distinct regulatory pathways in nutrient requirements, response to stresses, and plant growth and development.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Plant Sciences
Xiaomei Wu, Xuewen Wang, Wei Chen, Xunyan Liu, Yibin Lin, Fengfeng Wang, Lulu Liu, Yijun Meng
Summary: Plants have evolved miRNA-mediated gene regulation as a strategy to adapt to variable natural conditions. This study proposes a novel approach to construct a miRNA-miRNA crosstalk network, highlighting the potential of miRNA regulation in environmental adaptation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Muhammed Hamit Ekinci, Doga Selin Kayihan, Ceyhun Kayihan, Yelda Ozden Ciftci
Summary: The alteration of expression levels of cold- and oxidative stress-induced genes related-miRNAs is crucial for the successful development of cryopreservation protocols.
PLANT CELL TISSUE AND ORGAN CULTURE
(2021)
Article
Plant Sciences
Yan-Qin Ma, Zuo-Qian Pu, Qi Meng, Xiao-Min Tan, Liu Yang, Kai-Li Zhang, Ye-Ye Ma, Xuan Huang, Zi-Qin Xu
Summary: The study revealed the important role of SEPALLATA genes in regulating flowering, leaf morphology and floral organ development in Arabidopsis. Two splicing variants, SEP3-2 and SEP3-3, of SEP3 gene were found to be involved in leaf morphogenesis and floral organ development by affecting transcriptional activity. SEP4 genes participate in the development of sepals, petals, stamens, and carpels. These findings demonstrate the diversified functions of SEPALLATA genes.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Yuxi Hu, Chao Feng, Lihua Yang, Patrick P. Edger, Ming Kang
Summary: This study used whole-genome resequencing data from F. nilgerrensis individuals to investigate the genetic diversity, population structure, and genomic basis of local adaptation. The results highlighted the importance of environmental differences in driving genetic variation and identified genetic variations associated with local adaptation.
HORTICULTURE RESEARCH
(2022)
Article
Plant Sciences
Joseph L. Pegler, Jackson M. J. Oultram, Duc Quan Nguyen, Christopher P. L. Grof, Andrew L. Eamens
Summary: Studies have found that under Cd stress, the drb1 mutant exhibits the highest tolerance, while the drb2 mutant is the most sensitive. DRB1 is the primary DRB protein required for six of the seven Cd-responsive miRNAs, while DRB2 is essential for the production of miR396.
Article
Biochemistry & Molecular Biology
Akihiro Ezoe, Kazumasa Shirai, Kousuke Hanada
Summary: Gene duplication is a major mechanism for creating new genes in plants, resulting in duplicated genes with varying degrees of functional diversification. High diversified duplicates from tandem duplications tend to have lineage-specific functions, while low diversified duplicates from whole-genome duplications are related to essential signaling pathways, impacting plant evolution differently.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Uliana K. Kolesnikova, Alison Dawn Scott, Jozefien D. Van de Velde, Robin Burns, Nikita P. Tikhomirov, Ursula Pfordt, Andrew C. Clarke, Levi Yant, Alexey P. Seregin, Xavier Vekemans, Stefan Laurent, Polina Yu Novikova
Summary: A transition to selfing can be advantageous in situations with limited mating partners. This study investigates the evolution of self-compatibility in diploid Siberian Arabidopsis lyrata and its contribution to the formation of allotetraploid Arabidopsis kamchatica. The researchers provide genome assemblies for two self-fertilizing diploid A. lyrata accessions and propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, dating this transition to around 90,000 years ago. They also demonstrate the independent transition to selfing in Siberia and suggest that the selfing of A. kamchatica is mediated by a loss-of-function mutation in a dominant S-allele inherited from A. lyrata.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Qian Ruan, Yizhen Wang, Haoyu Xu, Baoqiang Wang, Xiaolin Zhu, Bochuang Wei, Xiaohong Wei
Summary: In this study, the alfalfa WHY gene family was studied by analyzing the alfalfa genome. The results showed that there are 10 WHY genes in alfalfa, distributed on 10 chromosomes, possibly derived from segmental duplications. Based on phylogenetic analysis, the alfalfa WHY gene family can be divided into four subfamilies, and genes within the same subfamily share similar gene structures. Furthermore, cis-regulatory element analysis revealed the abundance of regulatory elements related to transcription, cell cycle, development, hormone, and stress response in the promoter sequence of the MsWHY genes. Real-time quantitative PCR demonstrated that the expression of MsWHY genes is induced by drought, salt, and methyl jasmonate.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Yue Guo, Jing Liu, Xingna Wang, Ying Li, Xilin Hou, Jianchang Du
Summary: Positive selection genes (PSGs) are enriched in plant hormone signal transduction pathway and the transcription factor family, and show higher expression levels in tissue-specific callus and reproductive tissues. Furthermore, the expression level of PSGs decreases with an increase in retained triplication gene copies, and the methylation levels of PSGs are higher in introns and UTRs, potentially affecting their expression. This study provides insights into the evolutionary forces shaping PSGs in Brassica rapa.
Article
Biochemical Research Methods
Frank Vogt, Gautam Shirsekar, Detlef Weigel
Summary: vcf2gwas is a convenient package that streamlines the traditional GWAS workflow and enhances reproducibility.
Article
Ecology
Or Shalev, Haim Ashkenazy, Manuela Neumann, Detlef Weigel
Summary: Plants are protected not only by their own immunity but also by commensal microbes. In interaction between a pathogenic Pseudomonas strain and naturally co-occurring commensals, non-pathogenic Pseudomonas were found to provide plant protection. Different bacterial genes linked to plant protection in each lineage were discovered through genome-wide association, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection.
Article
Multidisciplinary Sciences
J. Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Agren, Matthew T. Rutter, Charles B. Fenster, Detlef Weigel
Summary: This study challenges the prevailing paradigm that mutations occur randomly by demonstrating that mutations occur less frequently in functionally constrained regions of the genome in Arabidopsis. It also shows that epigenomic and physical features explain the majority of the variance in the genome-wide pattern of mutation bias surrounding genes. The findings suggest that mutation bias is the primary force driving patterns of sequence evolution in natural accessions.
Article
Biotechnology & Applied Microbiology
Adam Nunn, Isaac Rodriguez-Arevalo, Zenith Tandukar, Katherine Frels, Adrian Contreras-Garrido, Pablo Carbonell-Bejerano, Panpan Zhang, Daniela Ramos-Cruz, Katharina Jandrasits, Christa Lanz, Anthony Brusa, Marie Mirouze, Kevin Dorn, Brice Jarvis, John Sedbrook, Donald L. Wyse, Christian Otto, David Langenberger, Peter F. Stadler, Detlef Weigel, M. David Marks, James A. Anderson, Claude Becker, Ratan Chopra
Summary: Thlaspi arvense, a winter annual oilseed crop, is being domesticated to improve ecosystems and agricultural productivity without increasing land use. It is a selfing diploid and a suitable model species for genetics and epigenetics. The study presents a chromosome-level genome assembly and investigates gene structure differences between two highly transformable accessions.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biology
Julia M. Kreiner, George Sandler, Aaron J. Stern, Patrick J. Tranel, Detlef Weigel, John R. Stinchcombe, Stephen Wright
Summary: This study investigates the evolutionary history of herbicide resistance in agricultural fields using genomic data from common waterhemp populations. The researchers find that resistance alleles show strong parallelism in their mutational origins and are influenced by gene flow in their distribution. The age and selection dynamics of resistant lineages vary, indicating heterogeneity in the forces that govern their persistence, including intra- and inter-locus allelic interactions.
Article
Plant Sciences
Katelyn Sageman-Furnas, Markus Nurmi, Meike Contag, Bjoern Ploetner, Saleh Alseekh, Andrew Wiszniewski, Alisdair R. Fernie, Lisa M. Smith, Roosa A. E. Laitinen
Summary: Hybrids between different accessions of Arabidopsis thaliana reveal the consequences of epistatic interactions in plants, showing that a combination of natural alleles of the OUTGROWTH-ASSOCIATED KINASE (OAK) gene regulates growth and development through the integration of hormone and stress signals.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Julieta L. Mateos, Sabrina E. Sanchez, Martina Legris, David Esteve-Bruna, Jeanette C. Torchio, Ezequiel Petrillo, Daniela Goretti, Noel Blanco-Tourinan, Danelle K. Seymour, Markus Schmid, Detlef Weigel, David Alabadi, Marcelo J. Yanovsky
Summary: Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. The proper spliceosome assembly, which requires the methylosome complex, is crucial for efficient pre-mRNA splicing. PICLN, a part of the methylosome complex, plays a key role in regulating pre-mRNA splicing and mediating plant adaptation to environmental conditions.
Article
Multidisciplinary Sciences
Julia M. Kreiner, Sergio M. Latorre, Hernan A. Burbano, John R. Stinchcombe, Sarah P. Otto, Detlef Weigel, Stephen I. Wright
Summary: This study uses genome analysis of the common waterhemp to demonstrate the significant impact of modern agriculture and agricultural intensification on the evolution of agricultural weeds. The strong selection pressure and changes in allele frequency trajectories since the 1960s have influenced the success of this weed in the 21st century, with human-mediated range shifts playing a role.
Article
Cell Biology
Agustin L. Arce, Regina Mencia, Damian A. Cambiagno, Patricia L. Lang, Chang LIu, Hernan A. Burbano, Detlef Weigel, Pablo A. Manavella
Summary: Transposons are mobile elements that are silenced in order to protect genome integrity. In plants, transposable element-derived inverted repeats (IRs) are often found near genes and affect gene expression. However, the molecular mechanisms of this regulation are still unclear in most cases.
Article
Genetics & Heredity
Anjar Tri Wibowo, Javier Antunez-Sanchez, Alexander Dawson, Jonathan Price, Cathal Meehan, Travis Wrightsman, Maximillian Collenberg, Ilja Bezrukov, Claude Becker, Moussa Benhamed, Detlef Weigel, Jose Gutierrez-Marcos
Summary: Clonal propagation is commonly used in commercial plant breeding and biotechnology programs to minimize genetic variation. However, clonal plants often show stable phenotypic changes, known as somaclonal variation. Studies have linked this variation to epigenetic modifications induced during regeneration.
Article
Biotechnology & Applied Microbiology
Sonja Kersten, Fernando A. Rabanal, Johannes Herrmann, Martin Hess, Zev N. Kronenberg, Karl Schmid, Detlef Weigel
Summary: Rapid adaptation of weeds to herbicide applications in agriculture through resistance development, particularly the grass Alopecurus myosuroides, is a common phenomenon. Target-site resistances (TSRs) are important for this adaptive response. In this study, we used PacBio HiFi reads to sequence long-range amplicons and resolved them into haplotypes using the PacBio amplicon analysis (pbaa) algorithm in pools of individuals. We recovered most haplotypes from previously sequenced individuals and found common TSR mutations originating from independent soft sweeps in new populations.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Letter
Biotechnology & Applied Microbiology
Herve Vanderschuren, Patience Chatukuta, Detlef Weigel, Devang Mehta
NATURE BIOTECHNOLOGY
(2023)
Review
Multidisciplinary Sciences
Hernan A. Burbano, Rafal M. Gutaker
Summary: Herbaria serve as valuable sources of genomic data for studying plant evolution, ecology, and diversity. Ancient DNA from herbarium specimens provides insights into past plant communities and genetic changes over time. Integrating herbarium genomics data with other data types can enhance understanding of the evolutionary and ecological processes shaping plant communities.
Article
Biotechnology & Applied Microbiology
Sami Saarenpaeae, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek Severi Lundberg, Detlef Weigel, Stefania Giacomello
Summary: The interactions between microorganisms and their multicellular host are crucial for understanding plant or animal tissues. However, current technology hinders the study of spatial interactions between the host and its colonizing microorganisms. In this study, we introduce spatial metatranscriptomics (SmT), a sequencing-based approach that allows simultaneous characterization of host transcriptome and microbiome at a high spatial resolution. The SmT technique was applied to outdoor-grown Arabidopsis thaliana leaves and revealed tissue-scale hotspots of bacteria and fungi. By analyzing networks, we investigated the spatial interactions between microorganisms from different kingdoms, as well as the host response to microbial hotspots. SmT provides a valuable approach for studying the interplay between host and microbiome.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Thanvi Srikant, Wei Yuan, Kenneth Wayne Berendzen, Adrian Contreras-Garrido, Hajk-Georg Drost, Rebecca Schwab, Detlef Weigel
Summary: A systematic analysis of the requirement for MET1 in different A. thaliana accessions reveals that CG methylation plays a dual role in gene expression. For many genes, CG methylation appears to canalize expression levels, masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.