Article
Plant Sciences
Siarhei A. Dabravolski, Stanislav V. Isayenkov
Summary: Our study elucidates the evolution of the voltage-independent TPK (two-pore K+-channels) family, represented in some species by one pore, K+-inward rectifier (Kir)-like channels. Through a comprehensive investigation of existing databases and modern bioinformatic tools, we have gained insight into the evolutionary origin of TPK family proteins by conducting a detailed phylogenetic inventory of TPK/KCO3 (KCO: potassium channel, outward rectifying) channels across many taxa.
Editorial Material
Multidisciplinary Sciences
Michael Haslam
Summary: Investigating whether orangutans have the capacity to make stone tools, to gain insights into the origin of this behavior.
Editorial Material
Plant Sciences
Kate M. Johnson, Leila R. Fletcher
Summary: The pit membrane thickness and overall lignification degree are the driving factors for drought resistance in Arabidopsis thaliana.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Virology
Mohamed El Sayes, Ahmed Kandeil, Yassmin Moatasim, Ahmed El Taweel, Adam Rubrum, Omnia Kutkat, Mina Nabil Kamel, Rebecca Badra, Ahmed B. Barakat, Pamela P. McKenzie, Rabeh El-Shesheny, Richard J. Webby, Ghazi Kayali, Mohamed Ahmed Ali
Summary: This study characterized the genetic evolution and virological features of H9N2 avian influenza viruses in Egypt, revealing reassortment events and replication capabilities in mammalian cells without clinical signs in poultry and mice.
Article
Plant Sciences
Xu Zhang, Yanxia Sun, Jacob B. Landis, Jun Shen, Huajie Zhang, Tianhui Kuang, Wenguang Sun, Jiao Sun, Bashir B. Tiamiyu, Tao Deng, Hang Sun, Hengchang Wang
Summary: Investigating genetic basis and evolutionary adaptations of alpine plants, this study generated transcriptomic data of five Saussurea species using high-throughput sequencing and de novo assembly. Analysis revealed gene families specific to alpine species and hundreds of genes with signatures of positive selection, providing insights into Saussurea's adaptation to extreme environments of high altitude during the Miocene period.
Article
Chemistry, Multidisciplinary
Zhihengyu Chen, Zhijie Chen, Omar K. Farha, Karena W. Chapman
Summary: Understanding and controlling the structure, chemistry, and defects of nanomaterials is a challenge that has been explored using metal-organic frameworks (MOFs). The study found that the resulting nanoparticle structure, chemistry, and defect concentration depend on the node chemistry of the original MOF. This suggests that MOFs offer new potential control over nanomaterial synthesis under mild reaction conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Plant Sciences
Yanlei Feng, Xiaoguo Xiang, Delara Akhter, Ronghui Pan, Zhixi Fu, Xiaohua Jin
Summary: This study decoded the mitochondrial genomes of Fagales, revealing their dynamic and mosaic characteristics, potentially influenced by independent and unequal transfers of third-party DNA.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Chloe P. Drummond, Tanya Renner
Summary: Plant trait evolution is influenced by mechanisms of genome evolution, and comparative studies using genome sequencing have shed light on the evolution of plant chemical defense. Chemical defense in plants is achieved through defensive compounds, which play important roles in plant physiology.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Plant Sciences
Lisha Zhang, Chenlei Hua, Denis Janocha, Judith Fliegmann, Thorsten Nuernberger
Summary: Plants use both surface resident and intracellular immune receptors to defend against microbial infections. The contribution of these receptors to plant immunity varies in space and time. The discovery of new plant cell surface immune receptors and their microbial ligands reveals a previously unknown complexity of plant surface sensors involved in the detection of specific microbial species. Comparative analyses suggest that plants have a larger number of species-specific surface receptors in addition to a few widely distributed pattern sensors. Leucine-rich repeat surface and intracellular immune receptors are two polymorphic classes whose evolutionary trajectories are linked, indicating their cooperativity in providing full plant immunity.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Energy & Fuels
Jiale Xu, Songtao Wu, Jingdong Liu, Yujie Yuan, Jinggang Cui, Ling Su, Xiaohua Jiang, Jun Wang
Summary: This study focused on the pore evolution of organic-rich shales from the Permian Lucaogou Formation in Junggar Basin, China. The research identified 18 nanometers as the critical pore size boundary that connected different stages of pore evolution, and revealed that different pore size ranges were controlled by different diagenesis processes. The study also showed a three-phase pattern of pore evolution as thermal maturity increases, with different correlations between pore evolution and organic matter maturity in specific pore size ranges.
Article
Multidisciplinary Sciences
Mingzheng Duan, Haiying Bao, Tolgor Bau
Summary: The study presents a high-quality genome assembly for the wild mushroom species Leucocalocybe mongolica (LM) and conducted transcriptome sequencing to analyze its genetic basis. The genome size of LM is 46.0 Mb with 11,599 predicted protein-coding genes, of which 65.7% could be aligned with annotated homologous genes in other species. Phylogenetic analyses supported the distinction of LM from the genus Tricholoma, and transcriptome data indicated the potential role of key metabolic genes in the species' limited wild occurrences and reproductive strategies.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Tianying Lan, Kalle Leppala, Crystal Tomlin, Sandra L. Talbot, George K. Sage, Sean D. Farley, Richard T. Shideler, Lutz Bachmann, Oystein Wiig, Victor A. Albert, Jarkko Salojarvi, Thomas Mailund, Daniela Drautz-Moses, Stephan C. Schuster, Luis Herrera-Estrella, Charlotte Lindqvist
Summary: Research finds that the effective population size of an ancient polar bear lineage experienced a dramatic decline, followed by a modest increase just before its extinction. The ancient polar bear had slightly higher genetic diversity, suggesting severe genetic erosion in modern polar bears during a prolonged bottleneck. The study also suggests the occurrence of a possible ancient introgression event from brown bears dating back over 150,000 years.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Medicine, Research & Experimental
Annamarie E. Allen, Jason W. Locasale
Summary: Plant-based diets, including veganism, are gaining popularity for their sustainability and health benefits. Studies suggest that vegans and vegetarians may have lower risks for certain health conditions, but the underlying mechanisms are still unclear.
EMBO MOLECULAR MEDICINE
(2021)
Article
Multidisciplinary Sciences
Shao-Chen Cheng, Chun-Bing Liu, Xue-Qin Yao, Jing-Yang Hu, Ting-Ting Yin, Burton K. Lim, Wu Chen, Guo-Dong Wang, Cheng-Lin Zhang, David M. Irwin, Zhi-Gang Zhang, Ya-Ping Zhang, Li Yu
Summary: Highly specialized myrmecophagy has independently evolved multiple times in mammalian species of different orders, demonstrating a textbook example of phenotypic evolutionary convergence. Through multi-omic analyses and validating assays, we reveal the complex and diverse interactions between hosts and their gut microbiota, providing adaptive solutions for nutritional and detoxification challenges. This study contributes new insights into the dietary evolution of mammals and the coordination of physiological functions between animal hosts and their gut commensals.
NATIONAL SCIENCE REVIEW
(2023)
Review
Plant Sciences
Lubomir Adamec, Ildiko Matusikova, Andrej Pavlovic
Summary: Carnivorous plants have evolved in response to nutrient-poor environments by capturing and digesting animal prey, which enhances their growth and development. While many aspects of their adaptations have been clarified through recent research, there are still many unknowns remaining.
Review
Plant Sciences
Michael T. Pisias, Harmeet Singh Bakala, Alex C. McAlvay, Makenzie E. Mabry, James A. Birchler, Bing Yang, J. Chris Pires
Summary: Modern agriculture is highly vulnerable to climate change and population expansion due to its reliance on a narrow range of crop species. Crop improvement using plant genetic diversity is one solution, but new approaches like neodomestication and redomestication are being explored. Redomestication focuses on feral crops, which have escaped cultivation and adapted to local environments, but still retain some domestication traits. This review explores the potential of using genome editing techniques to develop novel crops through de novo redomestication, which could be important for global food security.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Evolutionary Biology
Prakash Raj Timilsena, Craig F. Barrett, Alma Pineyro-Nelson, Eric K. Wafula, Saravanaraj Ayyampalayam, Joel R. McNeal, Tomohisa Yukawa, Thomas J. Givnish, Sean W. Graham, J. Chris Pires, Jerrold Davis, Cecile Ane, Dennis W. Stevenson, Jim Leebens-Mack, Esteban Martinez-Salas, Elena R. alvarez-Buylla, Claude W. dePamphilis
Summary: Mycoheterotrophy is a nutritional strategy in plants where they obtain nutrients from soil fungi. The evolution of mycoheterotrophy and loss of photosynthesis has occurred multiple times in plants, especially in monocots. While the reduction of plastomes in mycoheterotrophs is well documented, the evolution of nuclear genomes remains largely unknown.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ricardo De La Pena, Hannah Hodgson, Jack Chun -Ting Liu, Michael J. Stephenson, Azahara C. Martin, Charlotte Owen, Alex Harkess, Jim Leebens-Mack, Luis E. Jimenez, Anne Osbourn, Elizabeth S. Sattely
Summary: Triterpenes with complex scaffold modifications are common in plants, and limonoids are a well-known family responsible for the bitter taste in citrus and the active constituents of neem oil. However, the complete biosynthetic route of limonoids has not been described. This study discovered 22 enzymes involved in the biosynthesis of important limonoids and provided a template for the discovery and reconstitution of triterpene biosynthetic pathways in plants.
Article
Evolutionary Biology
Carrie M. Tribble, Michael R. May, Abigail Jackson-Gain, Rosana Zenil-Ferguson, Chelsea D. Specht, Carl J. Rothfels
Summary: Testing adaptive hypotheses about the evolution of continuous traits in association with developmentally structured discrete traits, while considering other hidden evolutionary forces, is a challenge in evolutionary biology. This study expands existing phylogenetic comparative methods and finds that plants with different underground storage organs (USOs) do not differ in their climatic niche, except for root morphology, where modified roots are associated with lower temperature seasonality. These findings question the generalization of ecological patterns across geophytic taxa, as different USO types may reflect adaptations to different climatic conditions.
SYSTEMATIC BIOLOGY
(2023)
Article
Plant Sciences
Fabian Bratzel, Juraj Paule, Jim Leebens-Mack, Elton M. C. Leme, Rafaela C. C. Forzza, Marcus A. A. Koch, Sascha Heller, Georg Zizka
Summary: A phylogenomic analysis of the Bromelioideae subfamily of the Bromeliaceae family was conducted to understand species relationships and provide a basis for taxonomic treatment and further evolutionary and biogeographical studies. The study used a target-enrichment approach and analyzed nuclear, plastome, and mitogenome data. The resulting phylogenetic framework identified 26 well-supported clades and revealed interesting patterns, such as polyphyletic genera. This research is important for future taxonomic revisions and better understanding the evolutionary processes in this subfamily.
Article
Plant Sciences
Luz A. Triana-Moreno, Agustina Yanez, Li-Yaung Kuo, Carl J. Rothfels, Nelson Tulio L. Pena, Pedro B. Schwartsburd, Michael Sundue
Summary: In this study, a molecular phylogenetic revision of hayscented ferns was conducted. The results showed that hayscented ferns are polyphyletic and a new classification was proposed. Three morphologically distinct clades were identified and a new type species was suggested. Additionally, three new genera were discovered: Microlepia, Mucura, and Sitobolium.
Article
Plant Sciences
Natalie Garrett, Juan Viruel, Nathaniel Klimpert, Marybel Soto Gomez, Vivienne K. Y. Lam, Vincent S. F. T. Merckx, Sean W. Graham
Summary: Thismiaceae species have lost the ability to photosynthesize and instead obtain carbon from soil fungi. This study analyzes the plastid genomes of Thismiaceae and reveals that most gene losses occurred early in their evolution, with occasional inversions and losses of the plastid inverted repeat region. Despite these changes, retained plastid genes are still under strong purifying selection.
AMERICAN JOURNAL OF BOTANY
(2023)
Review
Plant Sciences
Sontosh K. Deb, Patrick P. Edger, J. Chris Pires, Michael R. McKain
Summary: Allopolyploids are formed by hybridization between different evolutionary lineages with genome doubling. Homoeologous chromosomes can undergo recombination immediately after allopolyploid formation and continue over successive generations. Homoeologous exchanges have both negative and positive effects, leading to unbalanced gametes, reduced fertility, novel phenotypic diversity, and the formation of neo-allopolyploids. The causes and consequences of homoeologous exchanges vary across lineages, generations, and genomes. Recent technological advances provide insights into the mechanistic basis of homoeologous exchanges in allopolyploid angiosperms, which have implications for understanding allopolyploid evolution and developing important traits in polyploid crops.
Article
Plant Sciences
Yu Gao, Andrew S. Lipton, Coyla R. Munson, Yingxuan Ma, Kim L. Johnson, Dylan T. Murray, Henrik V. Scheller, Jenny C. Mortimer
Summary: The plant secondary cell wall is a thickened matrix of polysaccharides and lignin. It is an abundant and renewable source for various purposes but accessing the carbon in an economical and sustainable way is challenging. In this study, the researchers aimed to increase the length of galactan chain in the cell wall and found that it enhanced pectin- cellulose contacts and cellulose crystallinity. However, it also disrupted the cell wall architecture.
Article
Plant Sciences
Kim-Kristine Mueller, Lukas Pfeifer, Lina Schuldt, Peter Szovenyi, Sophie de Vries, Jan de Vries, Kim L. Johnson, Birgit Classen
Summary: The composition of plant cell walls has changed significantly during the evolution of tracheophytes, and the cell wall of ferns, as the sister lineage to seed plants, is crucial for understanding evolutionary changes and innovations in seed plants. The study characterizes the arabinogalactan proteins (AGPs) from fern genera Azolla, Salvinia, and Ceratopteris and reveals differences in AGP composition between ferns and seed plants. The findings also highlight the diversity of AGPs across different plant lineages and shed light on the evolution of tracheophytes' cell walls.
Article
Plant Sciences
Yingxuan Ma, Thomas Shafee, Asha M. Mudiyanselage, Julian Ratcliffe, Colleen P. MacMillan, Shawn D. Mansfield, Antony Bacic, Kim L. Johnson
Summary: The role of glycoproteins in cell surface molecules during development and stress is important but poorly understood. FASCICLIN-LIKE ARABINOGALACTAN PROTEINs (FLAs) are a glycoprotein family that affects plant growth and development. They have complex structures comprising globular fasciclin-like (FAS1) domains, intrinsically disordered regions, and glycomotifs for directing glycan addition.
Article
Ecology
William A. Freyman, Matthew G. Johnson, Carl J. Rothfels
Summary: In this paper, we introduce homologizer, a flexible Bayesian method that uses a phylogenetic framework to infer the separation of gene copies into their respective subgenomes across different loci. Through simulation tests, we demonstrate the robustness of homologizer to factors such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data by analyzing a multilocus dataset from the fern family Cystopteridaceae. Lastly, we discuss the potential use of homologizer beyond its core phasing functionality to identify non-homologous sequences.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Lazar Novakovic, Gleb E. Yakubov, Yingxuan Ma, Antony Bacic, Kerstin G. Blank, Arun Sampathkumar, Kim L. Johnson
Summary: DEK1 is a key regulator of plant cell wall that influences the mechanical properties and regulation of cellulose synthesis. It modifies the biosynthetic properties of cellulose synthase complexes and alters the stiffness and thickness of cellulose microfibril bundles in epidermal cell walls.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Agronomy
Abdur Rashid, Brian J. Schutte, April Ulery, Michael K. Deyholos, Soum Sanogo, Erik A. Lehnhoff, Leslie Beck
Summary: Heavy metals and metalloids are environmental pollutants that have adverse effects on crop health and productivity when they accumulate in agricultural soils. Their toxicity depends on various factors including crop type, growth condition, and soil properties. They can disrupt cellular components and metabolic processes in plants, leading to oxidative stress, inhibition of photosynthesis, enzyme/protein inactivation, genetic modifications, hormonal deregulation, and inhibition of soil microbial growth. This review evaluates HM contamination in arable lands, factors affecting HM bioavailability in the soil solution, mechanisms of HM interference in plants, and visual symptoms of toxic HM elements in crops. Suggestions are also provided to minimize crop losses from suspected HM contamination in agricultural soils.
Article
Biochemistry & Molecular Biology
Ningning Wang, Fan Qi, Fu Wang, Yujie Lin, Chunxiao Xiaoyang, Zhanwu Peng, Bi Zhang, Xin Qi, Michael K. Deyholos, Jian Zhang
Summary: Drought stress significantly affects flax plants, causing wilting of leaves and increasing lignin content in fiber flax. The study highlights the rapid responses of flax to drought stress, including morphological, physiological, biochemical, and gene expression changes. These findings provide important evidence for understanding the mechanisms underlying plant response to drought stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)