Article
Plant Sciences
Klara Plackova, Frantisek Zedek, Veit Schubert, Andreas Houben, Petr Bures
Summary: This study reveals a positive relationship between kinetochore and chromosome size in eukaryotes, suggesting that the observed scaling of kinetochore size to genome size may be influenced by the mechanics of cell division. The potential causal link between kinetochore and chromosome size indicates that evolutionary mechanisms, such as centromere drive, could play a role in chromosome and genome size evolution.
Article
Genetics & Heredity
Na Wang, Jianing Liu, William A. Ricci, Jonathan Gent, R. Kelly Dawe
Summary: The research reveals a positive relationship between centromere size and genome size, independent of variations in major centromeric satellite sequences. Additionally, changes in centromere size involve alterations in bound CENH3, but overexpressing CENH3 does not mimic this effect. The study demonstrates that centromere size is among the scalable features affected by multiple limiting factors.
Article
Biochemistry & Molecular Biology
David M. Edwards, Ellen C. Royrvik, Joanna M. Chustecki, Konstantinos Giannakis, Robert C. Glastad, Arunas L. Radzvilavicius, Iain G. Johnston
Summary: A comprehensive genetic model has been constructed to explain how different mechanisms segregate and decrease damage in organelle DNA (oDNA) across eukaryotes. Gene conversion is identified as a powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the advantage of observed oDNA recombination in diverse organisms. This framework provides insights into how eukaryotes avoid Muller's ratchet and explains the puzzling oDNA differences across taxa.
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Konstantinos Giannakis, Samuel J. Arrowsmith, Luke Richards, Sara Gasparini, Joanna M. Chustecki, Ellen C. Royrvik, Iain G. Johnston
Summary: This study utilized over 15,000 oDNA sequences and over 300 whole genome sequences across eukaryotes to identify the properties of genes and mechanisms that determine oDNA retention. The findings suggest that factors such as protein hydrophobicity and binding energy centrality within a protein complex play important roles in oDNA retention.
Article
Biotechnology & Applied Microbiology
James E. E. Titus-McQuillan, Adalena V. V. Nanni, Lauren M. M. McIntyre, Rebekah L. L. Rogers
Summary: By using a set of complexity metrics, the researchers successfully quantified the complexity of the transcriptome and revealed its changes. This study is of great significance for the whole transcriptome analysis in the field of non-model evolutionary genomics, and provides evolutionary inference of complexity changes on deep timescales across the tree of life.
Review
Ecology
Simon A. F. Darroch, Erin E. Saupe, Michelle M. Casey, Maria L. S. P. Jorge
Summary: Geographic ranges are a fundamental unit of biogeography and macroecology. Paleontologists and ecologists are reconstructing geographic ranges of species from fossils to understand long-term processes. Geographic ranges are time-averaged and reflect biotic and abiotic processes. This framework integrates the study of geographic ranges using modern and ancient data, illuminating diversity patterns over various time intervals.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Gemma G. R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin T. Lloyd, Marcelo Gottschalk, Alexander W. (Dan) Tucker, John J. Welch, Lucy A. Weinert
Summary: The study shows that genome reduction is consistently associated with pathogenicity in bacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Paul E. Schavemaker, Sergio A. Munoz-Gomez
Summary: By analyzing the energetic constraints on cell size, the implications of genome architecture, and the presence of endosymbionts, the authors suggest that mitochondria were not necessary for the initial origin of eukaryotes, but played a role in their diversification and expansion.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Soil Science
Leilei Lu, Gen Li, Nianpeng He, Huixin Li, Ting Liu, Xianping Li, Joann K. Whalen, Stefan Geisen, Manqiang Liu
Summary: Drought events are leading to shrinking body size in nematodes, affecting biodiversity and nutrient cycling in soils. This study found that drought stress resulted in a community shift towards smaller-sized species, decreased body size at the population scale, and a decrease in size-at-age of individuals. The reversible plasticity of body size under drought stress was also examined, showing that offspring from parents that experienced severe drought conditions had a relatively smaller reduction in overall body size. The findings highlight the potential far-reaching consequences of drought events on soil nematodes and ecosystems.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Oliver H. E. Philcox, Salvatore Torquato
Summary: The studies of disordered heterogeneous media and galaxy cosmology aim to analyze the distribution of particles or building blocks at microscales and predict the properties of the medium at macroscales. This work applies the theory of disordered heterogeneous media to describe the distribution of galaxies obtained from dark matter simulations. Various techniques are used to characterize the distributions and analyze the correlation functions and percolation properties. The simulations exhibit enhanced large-scale clustering and unique patterns due to early Universe physics, providing new tools for cosmological analyses.
Review
Cell Biology
Marco Massimo, Katherine R. Long
Summary: This review summarizes the key findings on the mechanisms regulating the development of the human neocortex, studied by scientists from various fields at different scales, and explores their interconnections.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Liyan Yang, Betul Akgol Oksuz, Job Dekker, Johan Harmen Gibcus
Summary: Chromosome conformation capture (3C) is a method to detect three-dimensional chromatin interactions. This paper describes an improved Hi-C protocol, Hi-C 3.0, which combines two crosslinkers and two restriction enzymes to increase efficiency. Hi-C 3.0 allows for accurate quantification of genome folding features at different scales. It provides genome-wide information on interaction frequencies between loci.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Review
Biochemistry & Molecular Biology
Philip C. J. Donoghue, Chris Kay, Anja Spang, Gergely Szollosi, Anna Nenarokova, Edmund R. R. Moody, Davide Pisani, Tom A. Williams
Summary: The origin of eukaryotes is a highly debated topic in evolutionary biology, with multiple theories trying to explain the acquisition of eukaryotic characteristics. The main controversy stems from differing views on the defining characteristics of eukaryotes. By defining eukaryotes phylogenetically, we can clarify areas of agreement and test disagreements among hypotheses. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes, while others differ in the order of key evolutionary steps that cannot currently be distinguished phylogenetically.
Review
Cell Biology
Shreyas Sridhar, Tatsuo Fukagawa
Summary: The assembly of functional kinetochore is crucial for accurate chromosome segregation during mitosis. Internal and external structures of kinetochore face multiple challenges, but linker proteins play an important role in force propagation and recruitment of outer kinetochore. Understanding these linkages and regulatory pathways is essential for understanding kinetochore structural diversity and plasticity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Plant Sciences
Pavel Vesely, Petr Smarda, Petr Bures, Charles Stirton, A. Muthama Muasya, Ladislav Mucina, Lucie Horova, Kristyna Vesela, Alexandra Silerova, Jakub Smerda, Ondrej Knapek
Article
Plant Sciences
Frantisek Zedek, Jakub Smerda, Pavel Vesely, Lucie Horova, Jana Kocmanova, Petr Bures
Summary: Previous studies suggested that holocentric chromosomes may provide a selective advantage in high UV-B radiation, aiding in terrestrialization, and the research found that holocentric plants are less stressed by UV-B at higher elevations compared to monocentric plants.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Editorial Material
Biochemical Research Methods
David Galbraith, Joao Loureiro, Ioanna Antoniadi, Jillian Bainard, Petr Bures, Petr Capal, Mariana Castro, Silvia Castro, Martin Certner, Dora Certnerova, Zuzana Chumova, Jaroslav Dolezel, Debora Giorgi, Brian C. Husband, Filip Kolar, Petr Koutecky, Paul Kron, Ilia J. Leitch, Karin Ljung, Sara Lopes, Magdalena Lucanova, Sergio Lucretti, Wen Ma, Susanne Melzer, Istvan Molnar, Ondrej Novak, Nicole Poulton, Vladimir Skalicky, Elwira Sliwinska, Petr Smarda, Tyler W. Smith, Guiling Sun, Pedro Talhinhas, Attila Tarnok, Eva M. Temsch, Pavel Travnicek, Tomas Urfus
Article
Plant Sciences
Marie Kratka, Jakub Smerda, Katerina Lojdova, Petr Bures, Frantisek Zedek
Summary: The centromere drive model explains an evolutionary process caused by centromeric repeats expansion, resulting in preferential segregation of an expanded centromere. The histone protein CenH3 plays a key role in adaptive evolution to counter the detrimental effects of centromere drive. Holocentric chromosomes may prevent centromere drive through their unique kinetochore structure.
FRONTIERS IN PLANT SCIENCE
(2021)
Letter
Plant Sciences
Frantisek Zedek, Pavel Vesely, Lubomir Tichy, Tammy L. Elliott, Emmanuel Garbolino, Patrice de Ruffray, Petr Bures
Review
Biochemical Research Methods
Elwira Sliwinska, Joao Loureiro, Ilia J. Leitch, Petr Smarda, Jillian Bainard, Petr Bures, Zuzana Chumova, Lucie Horova, Petr Koutecky, Magdalena Lucanova, Pavel Travnicek, David W. Galbraith
Summary: Flow cytometry (FCM) is widely used in establishing nuclear DNA content in plants, with a variety of applications in plant science. This paper discusses the advantages and limitations of FCM in determining plant ploidy, genome size, DNA base composition, and provides recommendations on obtaining accurate and reliable results, as well as troubleshooting guidance.
Article
Plant Sciences
Klara Plackova, Frantisek Zedek, Veit Schubert, Andreas Houben, Petr Bures
Summary: This study reveals a positive relationship between kinetochore and chromosome size in eukaryotes, suggesting that the observed scaling of kinetochore size to genome size may be influenced by the mechanics of cell division. The potential causal link between kinetochore and chromosome size indicates that evolutionary mechanisms, such as centromere drive, could play a role in chromosome and genome size evolution.
Article
Biochemistry & Molecular Biology
Yaping Hu, Yun Zhang, Petr Smarda, Petr Bures, Qirong Guo
Summary: Having different number of genome copies affects transcription and metabolite production in plants. This study investigated the effect of haploidy on flavonoid content in ginkgos by measuring the flavonoid content in leaves of haploid and diploid grafted plants and analyzing their transcriptomes and proteomes. Haploids had smaller leaves and lower flavonoid content compared to diploids. The downregulation of key genes involved in flavonoid biosynthesis regulation may contribute to the lower flavonoid content in haploids.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Emanuele Del Guacchio, Petr Bures, Duilio Iamonico, Francesca Carucci, Daniele De Luca, Frantisek Zedek, Paolo Caputo
Summary: Using molecular and morphological evidence, we confirmed the monophyly of Cirsium sect. Eriolepis and proposed to treat it as a separate genus. We also segregated Cirsium italicum into a separate genus based on molecular and morphological data, and published the name of a new hybrid genus. A total of 129 new combinations were proposed.
Article
Plant Sciences
Tammy L. Elliott, Frantisek Zedek, Russell L. Barrett, Jeremy J. Bruhl, Marcial Escudero, Zdenka Hroudova, Simon Joly, Isabel Larridon, Modesto Luceno, Jose Ignacio Marquez-Corro, Santiago Martin-Bravo, A. Muthama Muasya, Petr Smarda, William Wayt Thomas, Karen L. Wilson, Petr Bures
Summary: This study investigates genome and mean chromosome size in the cyperid clade and reveals that cyperids have the smallest mean chromosome size in seed plants, with a large divergence between the smallest and largest values. It is found that cyperid species with smaller chromosomes have larger geographical distributions, and there is a strong inverse association between mean chromosome size and number in this lineage.
Article
Plant Sciences
Petr Smarda, Karel Klem, Ondrej Knapek, Barbora Vesela, Kristyna Vesela, Petr Holub, Vit Kuchar, Alexandra Silerova, Lucie Horova, Petr Bures
Summary: Polyploid plants have enlarged stomata but these do not disadvantage them in low CO2 concentrations and may even contribute to their faster growth. Higher polyploids with large genomes also have increased operational stomatal conductance and lower water-use efficiency.
Article
Plant Sciences
Ester Michalkova, Jakub Smerda, Klara Plackova, Ales Knoll, Petr Bures
Summary: We studied the populations of Cirsium bertolonii in different locations and identified individuals that showed morphological shifts towards co-occurring C. acaulon or C. erisithales. These intermediate individuals were confirmed to be hybrids through various methods. The genetic erosion caused by interspecific hybridization poses a risk to the genetic integrity of C. bertolonii and other narrowly endemic high-mountain Cirsium species in Europe.
PLANT SYSTEMATICS AND EVOLUTION
(2023)