Article
Biochemistry & Molecular Biology
Lucas Vieira Lima, Alexandre Salino, Michael Kessler, Germinal Rouhan, Weston L. Testo, Caio Suzart Argolo, Thais Elias Almeida
Summary: In this study, we investigated the monophyly of genera in the Gleicheniaceae family using extended sampling and genomic data. The results confirmed the monophyly of most genera, except for Sticherus. We also found that while most Gleicheniaceae genera originated during the Mesozoic, some genera showed diversification in the Neogene and Quaternary periods. Our findings suggest the importance of reticulation and polyploidy in this diversification process, and identify Rouxopteris and Stromatopteris as evolutionary relics.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Review
Plant Sciences
Aniruddha Maity, Amrit Lamichaney, Dinesh Chandra Joshi, Ali Bajwa, Nithya Subramanian, Michael Walsh, Muthukumar Bagavathiannan
Summary: Seed shattering is a natural phenomenon in wild and weedy plant species, controlled by genetics but influenced by environmental conditions and management practices. While undesirable in domesticated crops, it serves as a crucial survival mechanism for weeds, aiding in efficient seed dispersal and soil seedbank development. Weed species have evolved variations in seed shattering as an adaptation to changing management regimes, presenting challenges for agricultural weed management but also opportunities for innovative approaches such as harvest weed seed control.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Cell Biology
Jun-Bin Cheng, Shi-Bao Zhang, Jin-Song Wu, Wei Huang
Summary: In this study, the dynamic changes of flavodiiron proteins (FLVs) and cyclic electron flow (CEF) in non-angiosperms were investigated. It was found that FLVs played a longer functional role in preventing PSI photoinhibition than previously thought, while CEF was mainly involved in energy balancing. When FLVs were inactivated, CEF was re-activated to favor photoprotection and sustain photosynthesis.
Article
Multidisciplinary Sciences
Claudio Casola, Jingjia Li
Summary: This study uses comparative analysis of chloroplast proteins in C-4 and C-3 grass species to reveal higher levels of molecular convergence in C-4 grasses. These findings have important implications for our understanding of the evolution of the C-4 photosynthesis pathway.
Article
Plant Sciences
Conor J. C. Simpson, Pallavi Singh, Deedi E. O. Sogbohossou, M. Eric Schranz, Julian M. Hibberd
Summary: C-4 photosynthesis has evolved multiple times in angiosperms and usually involves changes to the biochemistry, cell biology, and development of leaves. One common modification in C-4 plants is an increase in vein density, which results in a larger proportion of bundle sheath cells in the leaf. This study presents a high-throughput method of quantifying vein density using starch staining, which allows for rapid phenotyping in C-4 species. The method was successfully applied to detect significant variation in vein density in Gynandropsis gynandra, but not in genotypically diverse lines of Zea mays.
PLANT CELL AND ENVIRONMENT
(2023)
Review
Biochemistry & Molecular Biology
Zhenhua Zhang, Xiaoya Ma, Yannan Liu, Lingxiao Yang, Xuan Shi, Hao Wang, Runjie Diao, Bojian Zhong
Summary: This article reviews the knowledge of the origin and evolution of green plants, discussing key morphological innovations and drivers, and highlighting fundamental questions to further understand green plants.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Biology
Pierre Baduel, Vincent Colot
Summary: DNA provides the basic framework for heritability, but heritable trait variation is not completely hard-coded into the DNA sequence. In plants, the epigenetic machinery controls transposable element activity, and DNA methylation underpins most known cases of inherited trait variants independent of DNA sequence changes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Plant Sciences
Jacques W. Bouvier, Steven Kelly
Summary: In this article, the authors respond to criticisms regarding the rubisco kinetic traits and show that these criticisms are unfounded. They demonstrate that phylogenetic constraints have a greater impact on rubisco adaptation than catalytic trade-offs.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Ecology
Isabel Larridon, Daniel Spalink, Pedro Jimenez-Mejias, Jose Ignacio Marquez-Corro, Santiago Martin-Bravo, Muthama Muasya, Marcial Escudero
Summary: Madagascar's sedge family Cyperaceae arrived in the region around 40 million years ago, with about 20 endemic lineages present on the island. These endemic lineages are mainly using the C-3 photosynthetic pathway. The main biogeographical links of Madagascar's sedge flora are to Southern and Tropical Africa.
JOURNAL OF BIOGEOGRAPHY
(2021)
Review
Plant Sciences
Sylvia P. Kinosian, Carol A. Rowe, Paul G. Wolf
Summary: The mechanisms controlling chromosome number and its relationship to genome size in plants are not fully understood. There is a stark difference in chromosome number between homosporous and heterosporous lineages, and understanding the reasons behind this difference is of great importance for evolutionary biology.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Zeping Cai, Zhenyu Xie, Xiaochen Wang, Shuixian Zhang, Qian Wu, Xudong Yu, Yi Guo, Shuyi Gao, Yunge Zhang, Shitao Xu, Honggang Wang, Jiajia Luo
Summary: This study investigates the effects of brassinosteroids (BRs) on the development of fern gametophytes. The results show that high concentrations of brassinolide (BL) inhibit the expression of photosynthetic genes in Adiantum flabellulatum gametophytes. Additionally, the study identifies negative regulation of BR synthase genes by BL in fern gametophytes, indicating the importance of maintaining BR homeostasis in ferns.
Article
Plant Sciences
Jiri Dolezal, Andrea Kucerova, Veronika Jandova, Adam Klimes, Pavel Riha, Lubomir Adamec, Fritz Hans Schweingruber
Summary: Research indicates that plants adjust their internal structures to withstand adverse conditions and evolve similar morphological structures under thermal and hydrological gradients.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Ecology
Mark Davidson Jewell, Graham Bell
Summary: When the environment changes, the entire community of organisms may undergo modifications through physiological processes, evolutionary processes, or shifts in species composition. However, how these sources of change combine to drive community trait dynamics is not well understood.
Article
Multidisciplinary Sciences
Esther M. Sundermann, Martin J. Lercher, David Heckmann
Summary: The regulation of resource allocation in biological systems today is a result of natural selection in ancestral and recent environments. Research suggests that C-4 plants require more nitrogen re-allocation between photosynthetic components to adapt to new environments, indicating that resource distribution patterns still reflect optimality in ancestral environments.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Arjan Banerjee, Sasa Stefanovic
Summary: Most species in Cuscuta subgenus Grammica retain photosynthesis-related plastid genes, but some holoparasitic species in section Subulatae may have lost their plastid genomes entirely.
Review
Plant Sciences
Eftychios Frangedakis, Masaki Shimamura, Juan Carlos Villarreal, Fay-Wei Li, Marta Tomaselli, Manuel Waller, Keiko Sakakibara, Karen S. Renzaglia, Peter Szovenyi
Summary: Hornworts are a critical group in understanding the evolution of key land plant traits as they are the sister group to liverworts and mosses. The emerging hornwort model species, Anthoceros agrestis, provides valuable insights into the molecular biology and genetics of this unique group of land plants, aiding in answering fundamental questions of land plant biology and evolution.
Article
Biochemistry & Molecular Biology
Nasim Rahmatpour, Duncan A. Hauser, Jessica M. Nelson, Pa Yu Chen, A. Juan Carlos Villarreal, Ming-Yang Ho, Fay-Wei Li
Summary: The newly discovered Gloeobacteria member, Anthocerotibacter panamensis, possesses a unique combination of traits and occupies a key position in the evolutionary tree of cyanobacteria. It is capable of oxygenic photosynthesis, providing a new perspective for studying the origin of oxygenic photosynthesis.
Article
Plant Sciences
Jessica M. Nelson, Duncan A. Hauser, Fay-Wei Li
Summary: This study reveals the diverse phylogenetic diversity of symbiotic cyanobacteria in hornworts, which show overlap with soil cyanobacteria, a unique pattern not seen in other plant-cyanobacteria symbioses. Despite differences between cyanobiont communities in hornwort host plants just centimeters apart, no significant effects of sampling time, host species, or distance on cyanobacteria community structure were detected.
AMERICAN JOURNAL OF BOTANY
(2021)
Article
Evolutionary Biology
Hsiao-Pei Yang, Marius Wenzel, Duncan A. Hauser, Jessica M. Nelson, Xia Xu, Marek Elias, Fay-Wei Li
Summary: This study presents high-quality genomes of Monodopsis and Vischeria algae in the order Eustigmatales, revealing differences in biosynthetic pathways and gene splicing compared to Nannochloropsis and Microchloropsis. These findings not only advance research on Eustigmatophyte algae, but also shed new light on their biology and evolution.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
David Wickell, Li-Yaung Kuo, Hsiao-Pei Yang, Amra Dhabalia Ashok, Iker Irisarri, Armin Dadras, Sophie de Vries, Jan de Vries, Yao-Moan Huang, Zheng Li, Michael S. Barker, Nolan T. Hartwick, Todd P. Michael, Fay-Wei Li
Summary: Despite the extensive characterization of crassulacean acid metabolism (CAM) in terrestrial angiosperms, little attention has been given to aquatics and early diverging land plants. Here, the authors assemble the genome of Isoetes taiwanensis and investigate the genetic factors driving CAM in this aquatic lycophyte. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, several key differences are identified, including the recruitment of 'bacterial-type' PEPC and diverged circadian control of key CAM pathway genes in Isoetes.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Anna Neubauer, Stephanie Ruaud, Manuel Waller, Eftychios Frangedakis, Fay-Wei Li, Svenja Noetzold, Susann Wicke, Aurelien Bailly, Peter Szoevenyi
Summary: This study presents a straightforward method to isolate and transform protoplasts of the model hornwort Anthoceros agrestis, which is less laborious than previous approaches. In combination with stable genome transformation technique, this work expands the prospects of functional studies in this model hornwort.
APPLICATIONS IN PLANT SCIENCES
(2022)
Article
Plant Sciences
Tanner Robison, Jessica M. Nelson, Duncan A. Hauser, Louise A. Lewis, Fay-Wei Li
Summary: This study describes a new taxon, Gormaniella terricola, in Chaetopeltidales, and characterizes its organellar genomes. The results show that the chloroplast genome of G. terricola is one of the largest plastid genomes published to date and shares common features with the other sequenced chloroplast genomes in Chaetopeltidales, but is highly rearranged. The mitochondrial genome contains introns that encode homing endonucleases found in fungi, suggesting a possible case of horizontal gene transfer.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Plant Sciences
Alaina R. Petlewski, Duncan A. Hauser, Min Kim, Jeremy Schmutz, Jane Grimwood, Fay-Wei Li
Summary: This study generated a draft genome assembly and conducted DNA sequencing on Dendrolycopodium specimens to determine species relationships and investigate hybridization. The results identified four clades within the genus, confirming hybrid relationships and providing a phylogenetic framework for future taxonomic revision. Further study is needed to ascertain the status of Asian species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Shivesh Kumar, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A. Sciandra, Ning Sui, Rodolfo Zentella, Emily Zahn, Jeffrey Shabanowitz, Donald F. Hunt, Mario J. Borgnia, Alberto Bartesaghi, Tai-ping Sun, Pei Zhou
Summary: Kumar and colleagues have revealed the distinct features of Arabidopsis O-fucosyltransferase SPINDLY (SPY) through cryo-EM structures. They found that SPY has unique active-site features and dynamic conformations that regulate its enzymatic activity. The study also showed that the N-terminal peptide and TPRs in SPY play important roles in inhibiting and regulating its activity.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Gisel Y. de la Cerda, Jacob B. Landis, Evan Eifler, Adriana I. Hernandez, Fay-Wei Li, Jing Zhang, Carrie M. Tribble, Nisa Karimi, Patricia Chan, Thomas Givnish, Susan R. Strickler, Chelsea D. Specht
Summary: This article presents methods used to generate long-read Nanopore sequencing reads for the Liliales and demonstrates how modifications to standard protocols directly impact read length and total output. The goal is to assist those interested in generating long-read sequencing data in determining the necessary steps for optimizing output and results.
APPLICATIONS IN PLANT SCIENCES
(2023)
Editorial Material
Genetics & Heredity
Fay-Wei Li
Summary: Fay-Wei Li recalls a 1966 paper by Klekowski and Baker, where they noted that homosporous pteridophytes had more chromosomes than heterosporous lineages, and proposed hypotheses on the evolutionary impact of polyploidy.
NATURE REVIEWS GENETICS
(2023)
Article
Plant Sciences
Tetsuya Hisanaga, Shuangyang Wu, Peter Schafran, Elin Axelsson, Svetlana Akimcheva, Liam Dolan, Fay-Wei Li, Frederic Berger
Summary: Recent studies have shown variations in the correlation between chromatin modifications and transcription among different eukaryotes. In this study, the chromatin of the hornwort Anthoceros agrestis was investigated to establish similarities across bryophytes and determine the ancestral chromatin organization of land plants. The results suggest that the ancestral genome of bryophytes had a combination of different types of chromatin, including facultative heterochromatin, euchromatin, and constitutive heterochromatin.
Article
Microbiology
Warren Shou Leong Ang, Olivia Burleigh, Sarah Frail, Yago V. S. Santos, Bhavyaa Tyagi, Fay-Wei Li
Summary: Metagenomic analysis of symbiotic cyanobacteria colonies within Gunnera tinctoria stems identified a new strain of Nostoc, and its genome sequence is reported here.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Plant Sciences
David Wickell, Jacob Landis, Elizabeth Zimmer, Fay-Wei Li
Summary: Isoetes appalachiana is a common allopolyploid species, formed from multiple phylogenetic origins. Hybridization is unidirectional, with I. engelmannii consistently being the maternal progenitor. Polyploid lineages are genetically isolated and rarely experience gene flow between geographically distinct populations.
