Article
Plant Sciences
Min Jiang, Jinjing Jian, Chengchuan Zhou, Linfeng Li, Yuguo Wang, Wenju Zhang, Zhiping Song, Ji Yang
Summary: The origin of seeds is a crucial innovation in the evolution of land plants, and it has been a subject of debate whether the integument, the structure surrounding the nucellus within the ovule, arises de novo or evolves from pre-existing structures. By studying the key regulatory genes controlling integument development and their functions, researchers have found homologous genes in seedless plant genomes that play a role in patterning leaf-like lateral organs. This suggests a serial homology between integuments and other lateral organs, indicating that the integument likely evolved from the modification of pre-existing structures.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Sebastian Martinez-Salazar, Elena M. Kramer, Favio Gonzalez, Natalia Pabon-Mora
Summary: In this study, the authors identified a gene, TCP4L, that is involved in the formation of nectar spurs in Tropaeolaceae flowers. They found that TCP4L genes have a role in epidermal development and acquired a new function in spur initiation and elaboration after gene duplication.
Review
Plant Sciences
Facundo Romani, Javier E. Moreno
Summary: Transcription factors play a crucial role in plant evolution, with changes in body plan and physiological responses driving their functional evolution. Some gene regulatory networks are highly conserved, while others emerge in specific lineages. Recent studies offer new insights into the functional evolution of transcription factors.
Article
Biochemistry & Molecular Biology
Cecilia Zumajo-Cardona, Natalia Pabon-Mora, Barbara A. Ambrose
Summary: The study reveals that the euAP2 gene plays a crucial role in vascular plants, initially contributing to spore and sporangium development and later being recruited for ovule, fruit, and floral organ development. The protein sequences of euAP2 are highly conserved, with changes in their function during development likely attributed to alterations in regulatory regions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Nicolas Leurs, Camille Martinand-Mari, Stephanie Venteo, Tatjana Haitina, Melanie Debiais-Thibaud
Summary: The study found that there are three genes (Mgp1, Mgp2, and Bgp) in cartilaginous fishes, instead of the previously reported single Mgp gene. This indicates a dynamic evolutionary scenario for the Mgp/Bgp gene family, including several events of local duplications and translocation events. The research also revealed the expression patterns of Mgp1, Mgp2, and Bgp in cartilaginous fishes, highlighting ancestral and derived features compared to bony vertebrates.
FRONTIERS IN GENETICS
(2021)
Article
Ecology
Alberto Corral-Lopez, Natasha I. Bloch, Wouter van der Bijl, Maria Cortazar-Chinarro, Alexander Szorkovszky, Alexander Kotrschal, Iulia Darolti, Severine D. Buechel, Maksym Romenskyy, Niclas Kolm, Judith E. Mank
Summary: The organization and coordination of fish schools provide insights into the genetic architecture of affiliative behaviors, and the authors of this study used guppies to investigate the genetic basis of sociability phenotypes. They found that experimental evolution of schooling propensity increased the sociability of female guppies swimming with unfamiliar conspecifics, and genes involved in neuron migration and synaptic function played key roles in the evolution of sociability.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Psychology, Multidisciplinary
Laura Nuno de la Rosa, Mihaela Pavlicev, Arantza Etxeberria
Summary: Critiques of the container model and the emergence of new perspectives have led to a reevaluation of the concept of pregnancy as an evolved relational novelty. The idea of historical individuality, as opposed to other views of biological individuality, offers a fresh insight into pregnancy and may help dispel misconceptions.
FRONTIERS IN PSYCHOLOGY
(2021)
Article
Biology
Jason Cheok Kuan Leong, Masahiro Uesaka, Naoki Irie
Summary: The concept of evolutionary conservation is used to explain ancestral features and traits, but it has been misused to evaluate derivedness. Distinguishing these two concepts can help understand phenotypic and organismal evolution. Conservation focuses on common genes or traits, while derivedness covers novel or lost traits and genes to evaluate changes from a common ancestor. Conservation-oriented methods are effective in identifying ancestral features, but may underestimate overall changes. A new method, the transcriptomic derivedness index, uses whole-embryonic transcriptome as a phenotype to estimate phenotypic derivedness.
Article
Biology
James D. Holmes, John R. Paterson, Diego C. Garcia-Bellido
Summary: Analyzing the growth dynamics of trilobites revealed significant changes in post-embryonic axial growth at different developmental stages, which are closely related to sexual maturity in extant euarthropods. The observed body segmentation patterns in trilobites suggest a complex series of changing growth controls, indicating a more complex development than previously thought.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Plant Sciences
Rolf Sattler, Rolf Rutishauser
Summary: Morphological concepts are essential in plant biology, particularly in plant evo-devo. Classical morphology classifies plant organs into three distinct categories, while continuum morphology recognizes a gradual transition between these categories. Process morphology views structures as combinations of processes, with changes occurring during ontogeny and phylogeny. Both continuum and process morphology provide a more comprehensive understanding of plant form compared to classical morphology, and their insights can inspire further research in plant morphology and evo-devo, especially in the field of MorphoEvoDevo.
Review
Plant Sciences
Neha Bhatia, Adam Runions, Miltos Tsiantis
Summary: This article discusses the considerable variation in plant leaf shapes and the genetic control of leaf shape diversity. It emphasizes how live imaging and computational frameworks can help conceptualize regulated cellular growth translating into different leaf shapes. Additionally, it explores the morphogenetic differences between simple and complex leaves, as well as how evolution has shaped leaf diversity in carnivorous plants.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021
(2021)
Article
Anatomy & Morphology
Alexandra A. Vetrova, Tatiana S. Lebedeva, Aleena A. Saidova, Daria M. Kupaeva, Yulia A. Kraus, Stanislav Kremnyov
Summary: Our study focused on the embryonic development of Dynamena pumila, a cnidarian species with apolar gastrulation. We found that morphological polarity in the embryos only appears after gastrulation, while molecular prepatterning already exists during gastrulation. Additionally, we experimentally confirmed that in D. pumila, the oral-aboral axis is robust against perturbations in cWnt activity. Our results suggest that morphogenetic processes are decoupled from molecular axial patterning during gastrulation in D. pumila, which could provide new insights into the relationship between morphological polarization and axial molecular patterning in Metazoa.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Takumi Karasawa, Namiho Saito, Shigeyuki Koshikawa
Summary: The cis-regulatory sequence of the wingless gene in Drosophila guttifera has changed, leading to its expression in new places and the formation of unique wing pigmentation patterns.
Article
Ecology
David A. Salamanca-Diaz, Stephan M. Schulreich, Alison G. Cole, Andreas Wanninger
Summary: This study reports on the gene expression profile of individual cells of the trochophore larva of the invasive freshwater bivalve Dreissena rostriformis as inferred from single cell RNA sequencing. The study identifies seven transcriptionally distinct cell populations and provides insights into the characteristics and functions of these cell populations.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Biology
Tomasz Skawinski, Piotr Kuziak, Janusz Kloskowski, Bartosz Borczyk
Summary: The development of the vertebral column in birds, specifically the ossification patterns in the neck and thoracic vertebrae, remains largely unknown, with ancestral presence of two different ossification sites. While studies on Neoaves are limited, evidence from pigeons and grebes support the ancestral presence of two ossification loci in birds. Despite decades of research, the skeletal development in birds, including the vertebral column, is still not completely understood.
Review
Biochemical Research Methods
Yongjing Liu, Liangyu Fu, Kerstin Kaufmann, Dijun Chen, Ming Chen
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Biochemistry & Molecular Biology
Pawel Mikulski, Mareike L. Hohenstatt, Sara Farrona, Cezary Smaczniak, Yvonne Stahl, Kalyanikrishna, Kerstin Kaufmann, Gerco Angenent, Daniel Schubert
Review
Plant Sciences
Li Chen, Qian-Hao Zhu, Kerstin Kaufmann
Article
Plant Sciences
Tatjana Kleine, Thomas Naegele, H. Ekkehard Neuhaus, Christian Schmitz-Linneweber, Alisdair R. Fernie, Peter Geigenberger, Bernhard Grimm, Kerstin Kaufmann, Edda Klipp, Joerg Meurer, Torsten Moehlmann, Timo Muehlhaus, Belen Naranjo, Joerg Nickelsen, Andreas Richter, Hannes Ruwe, Michael Schroda, Serena Schwenkert, Oliver Trentmann, Felix Willmund, Reimo Zoschke, Dario Leister
Summary: Acclimation is the ability of individuals to adapt to environmental changes throughout their lifetime. Enhanced plant acclimation is seen as a promising strategy to mitigate the impact of global warming on crop yields, given the increasing environmental changes and extremes. Chloroplast plays a central role in acclimation responses at the cellular level, acting as both a sensor of environmental change and a target for cellular acclimation responses.
Review
Plant Sciences
Xiaocai Xu, Cezary Smaczniak, Jose M. Muino, Kerstin Kaufmann
Summary: This review discusses the complexity of cell identities in multicellular organisms and the impact of single-cell technologies on understanding cellular differentiation in plants. Using flower development as a model system, position-based and lineage-based mechanisms of cell identity specification are summarized and compared. The combinatorial action and crosstalk of external and internal signals, often converging on transcription factors, are key to cellular heterogeneity.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Daniele Y. Sunaga-Franze, Jose M. Muino, Caroline Braeuning, Xiaocai Xu, Minglei Zong, Cezary Smaczniak, Wenhao Yan, Cornelius Fischer, Ramon Vidal, Magdalena Kliem, Kerstin Kaufmann, Sascha Sauer
Summary: The researchers have introduced a method for plant nucleus isolation that can be used for single-cell genomics research, demonstrating its applicability in different plant species and tissues. By analyzing the transcriptomes of Arabidopsis thaliana seedlings and developing flowers, the potential of this method in exploring plant development and gene regulation processes was revealed.
Article
Multidisciplinary Sciences
Xuelei Lai, Rosario Vega-Leon, Veronique Hugouvieux, Romain Blanc-Mathieu, Froukje van der Wal, Jeremy Lucas, Catarina S. Silva, Agnes Jourdain, Jose M. Muino, Max H. Nanao, Richard Immink, Kerstin Kaufmann, Francois Parcy, Cezary Smaczniak, Chloe Zubieta
Summary: The MADS transcription factors family is an ancient eukaryotic protein family, divided into two main lineages in plants. The conserved Intervening domain (I domain) is an integral part of the DNA-binding domain of MADS TF, significantly contributing to the functional identity by influencing DNA binding activity and dimerisation specificity.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Suryatapa Ghosh Jha, Alexander T. Borowsky, Benjamin J. Cole, Noah Fahlgren, Andrew Farmer, Shao-Shan Carol Huang, Purva Karia, Marc Libault, Nicholas J. Provart, Selena L. Rice, Maite Saura-Sanchez, Pinky Agarwal, Amir H. Ahkami, Christopher R. Anderton, Steven P. Briggs, Jennifer An Brophy, Peter Denolf, Luigi F. Di Costanzo, Moises Exposito-Alonso, Stefania Giacomello, Fabio Gomez-Cano, Kerstin Kaufmann, Dae Kwani Ko, Sagar Kumar, Andrey Malkovskiy, Naomi Nakayama, Toshihiro Obata, Marisa S. Otegui, Gergo Palfalvi, Elsa H. Quezada-Rodriguez, Rajveer Singh, R. Glen Uhrig, Jamie Waese, Klaas Van Wijk, R. Clay Wright, David W. Ehrhardt, Kenneth D. Birnbaum, Seung Y. Rhee
Summary: With growing populations and urgent environmental issues, the future economy will be increasingly plant-based. Reimagining plant science as a critical component across various fields is crucial. The concept of a Plant Cell Atlas (PCA) is proposed to better understand and engineer plant development, physiology, and environmental responses. A workshop was held to discuss the purpose and utility of this initiative, highlighting current knowledge gaps and technical challenges.
Article
Multidisciplinary Sciences
Manuel Neumann, Xiaocai Xu, Cezary Smaczniak, Julia Schumacher, Wenhao Yan, Nils Bluethgen, Thomas Greb, Henrik Joensson, Jan Traas, Kerstin Kaufmann, Jose M. Muino
Summary: Cellular heterogeneity in growth and differentiation leads to organ patterning. Single-cell transcriptomics allows the study of gene expression heterogeneity in developing organs at an unprecedented resolution, but it loses the original physical location information of cells. This article proposes a method that combines single-nuclei RNA-seq with microscopy-based 3D spatial reconstruction to reconstruct the genome-wide gene expression patterns of individual cells in a 3D flower meristem, and to investigate gene expression differences among meristematic domains giving rise to different tissue and organ types.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Suzanne de Bruijn
News Item
Biochemistry & Molecular Biology
Suzanne de Bruijn
Article
Multidisciplinary Sciences
Liang-Yu Fu, Tao Zhu, Xinkai Zhou, Ranran Yu, Zhaohui He, Peijing Zhang, Zhigui Wu, Ming Chen, Kerstin Kaufmann, Dijun Chen
Summary: ChIP-Hub is an integrated web platform that provides rich resources of plant regulome and epigenome data for visualization and meta-analysis. By manually curating and evaluating the data quality, it allows in-depth investigation of the co-association of different regulators and the dynamic activity of tissue-specific regulatory elements.
NATURE COMMUNICATIONS
(2022)
Review
Plant Sciences
Marcus G. Heisler, Henrik Joensson, Stephan Wenkel, Kerstin Kaufmann
Summary: Plant development is controlled by transcription factors, but the molecular mechanisms behind their diversity and specificity are not well understood. Flower development serves as an ideal context to study these mechanisms, as different floral organs depend on distinct combinations of transcriptional regulators. Recent research also emphasizes the role of leaf polarity regulators in flower development. Understanding how these factors work together will help answer questions about the generation of different shapes and positions of floral organs.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
News Item
Biochemistry & Molecular Biology
Suzanne de Bruijn
Article
Plant Sciences
Hilda van Mourik, Peilin Chen, Cezary Smaczniak, Sjef Boeren, Kerstin Kaufmann, Marian Bemer, Gerco C. Angenent, Jose M. Muino
Summary: This research investigates the regulatory mechanism of the MADS-domain transcription factor FRUITFULL (FUL) in plant tissues and identifies its dual roles in floral transition and pistil development. The study shows that the different in vivo patterns of DNA binding of FUL in these tissues contribute to its distinct regulatory functions. Additionally, the composition of FUL protein complexes varies in a tissue-specific manner, leading to different DNA binding specificity and contributing to its diverse biological functions.
