Article
Biochemistry & Molecular Biology
Huan Ma, Wentao Ding, Yiqian Chen, Jingwei Zhou, Wei Chen, Caixia Lan, Hailiang Mao, Qiang Li, Wenhao Yan, Handong Su
Summary: In this study, we investigated the genetics and epigenetics of centromeres in a population of wheat lines. We found that the highly repetitive DNA sequences associated with CENH3 exhibit phylogenetic homogenization across different wheat lines, while the less-associated repeat sequences diverge on their own way in each wheat line. We also observed that CENH3 nucleosome structures show looser wrapping of DNA termini on complex centromeric repeats and that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sheng Zuo, Ramakrishna Yadala, Fen Yang, Paul Talbert, Joerg Fuchs, Veit Schubert, Ulkar Ahmadli, Twan Rutten, Ales Pecinka, Martin A. Lysak, Inna Lermontova
Summary: The evolutionary history of the KNL2 gene in plants has been reconstructed, revealing three ancient duplications and differentiation among different plant groups. The study also suggests that the KNL2 gene is involved in centromere and/or kinetochore assembly for preserving genome stability.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
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)
Article
Plant Sciences
Evgeny A. Elisafenko, Elena V. Evtushenko, Alexander V. Vershinin
Summary: The duplication of CENH3 in cereals led to changes in the exon-intron structure of the beta CENH3 paralog. The general trend towards the expansion of the CENH3 locus reveals the diverse ways different species implement the scenario described in this paper.
Article
Cell Biology
Findley Finseth
Summary: Female meiosis is asymmetric, providing a platform for genetic elements to compete for inclusion in the egg. Centromeres can evolve through 'female meiotic drive', which creates an arms race between selfish centromeres and kinetochore proteins. This study focuses on maize as a model to understand the mechanistic basis of female meiotic drive and monkeyflowers as a model to uncover the dynamics of active selfish centromeres in nature.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2023)
Article
Genetics & Heredity
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
Summary: This study successfully assembled a high-quality and almost complete genome of Arabidopsis thaliana using multiple advanced sequencing technologies. The new genome assembly contains more information compared to the previous reference genome, providing valuable insights into the global pattern of centromeric polymorphisms and the genetic and epigenetic features in plants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Rahman Ebrahimzadegan, Jorg Fuchs, Jianyong Chen, Veit Schubert, Armin Meister, Andreas Houben, Ghader Mirzaghaderi
Summary: The behavior of B chromosomes in Festuca pratensis was studied during meiotic and mitotic stages. The B chromosome exhibited Mendelian segregation behavior during meiosis, but non-Mendelian segregation behavior during the first pollen mitosis, resulting in a drive phenomenon. At least 82% of the B chromosomes showed drive during the first pollen mitosis.
CHROMOSOME RESEARCH
(2023)
Article
Plant Sciences
Yi-Tzu Kuo, Takayoshi Ishii, Joerg Fuchs, Wei-Hsun Hsieh, Andreas Houben, Yann-Rong Lin
Summary: Polyploidization leads to structural changes in genomes, especially allopolyploidization combining genomes of different species. The study compared repeat profiles of diploid and tetraploid Sorghum species, revealing similar repeat frequencies but drastic genome rearrangements in tetraploid species. Both diploid S. bicolor and tetraploid S. halepense exhibit similar centromere compositions, suggesting a potential contribution of S. bicolor in the formation of tetraploid S. halepense.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Patrick Pflughaupt, Aleksandr B. Sahakyan
Summary: Chargaff's second parity rule (PR-2), which states that the complementary base and k-mer contents match within the same strand of a double stranded DNA (dsDNA), has been a subject of many explanations. In this study, we revisited the possibility of mutation rates driving PR-2 compliance and found a set of mutation rate interrelations that allow for PR-2 compliance in most species. Our findings explain PR-2 in genomes that were not previously explained by simpler no-strand-bias constraints based on mutation rate equilibration. We also investigated the time for any genome to reach PR-2, showing that it generally occurs earlier than compositional equilibrium and within the age of life on Earth.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Wenjie Ding, Yuanbin Zhu, Jinlei Han, Hui Zhang, Zhenzhen Xu, Haris Khurshid, Fang Liu, Robert Hasterok, Xinlian Shen, Kai Wang
Summary: Through chromatin immunoprecipitation, researchers identified that the centromeric sequences of Gossypium anomalum only contained retrotransposon-like repeats and lacked long arrays of satellites. These repeats were found in African-Asian and Australian lineage species, suggesting a common ancestor. Interestingly, copy number variations were observed among lineages, indicating that sequence content is not crucial for the adaptive evolution of centromeric repeats, at least for retrotransposon-like repeats.
CHROMOSOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Damian Dudka, Michael A. Lampson
Summary: Centromeres play a crucial role in ensuring the faithful segregation of chromosomes during cell division. The rapid evolution of centromeric DNA and positive selection of centromeric proteins present a paradox to their conserved function. The centromere drive hypothesis suggests that centromeric DNA can act selfishly and lead to non-Mendelian inheritance during asymmetric female meiosis, causing fitness costs and genetic conflicts. This review discusses experimental model systems in yellow monkeyflowers and mice that demonstrate centromere drive, as well as the molecular mechanisms involved. It also explores the role of centromeric proteins in suppressing drive-associated fitness costs and presents outstanding questions for future research.
CHROMOSOME RESEARCH
(2022)
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.
Review
Biochemistry & Molecular Biology
Uma P. Arora, Beth L. Dumont
Summary: This article discusses the existence and impact of meiotic drive in species, and highlights the importance of studying this phenomenon in the model system of house mice to understand the mechanisms and potential consequences of meiotic drive in humans.
CHROMOSOME RESEARCH
(2022)
Article
Ecology
Christina A. Muirhead, Daven C. Presgraves
Summary: Sex chromosomes are susceptible to selfish meiotic drive elements that can lead to evolutionary arms races and genetically suppressed drive systems. In Drosophila species, complex interactions among different classes of selfish DNAs result in the genomic consequences of these evolutionary arms races.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Hongzhong Lu, Eduard J. Kerkhoven, Jens Nielsen
Summary: In this study, draft metabolic models were constructed for 332 yeast species, and the evolutionary trend of metabolism among these species was investigated. The results showed a high level of conservatism in yeast metabolic evolution. Additionally, it was found that the evolutionary distance and genotype to some extent determine model similarity, but not trait similarity.
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
Multidisciplinary Sciences
Klara Plackova, Petr Bures, Frantisek Zedek
Summary: The study found that genome size is a strong predictor of total centromere size in Eukaryotes, regardless of phylogenetic relatedness and centromere type. This implies a common mechanism maintaining stable total centromere size across Eukaryotes.
SCIENTIFIC REPORTS
(2021)
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)