Article
Chemistry, Multidisciplinary
Rafaely N. Lima, Jose A. C. Delgado, Darlon I. Bernardi, Roberto G. S. Berlinck, Nikolaos Kaplaneris, Lutz Ackermann, Marcio W. Paixao
Summary: This new method utilizes visible-light irradiation for selective C-H functionalization of tryptophan and tryptophan-containing peptides, demonstrating a wide substrate scope and excellent tolerance towards sensitive functional groups in the amino acid side chains. The method can also be successfully applied for the synthesis of pharmaco-peptide conjugate scaffolds.
CHEMICAL COMMUNICATIONS
(2021)
Article
Plant Sciences
Francesco Blasio, Pilar Prieto, Monica Pradillo, Tomas Naranjo
Summary: Hybridization and polyploidy are important forces in plant adaptation and speciation. Interspecific gene flow generates adaptive genetic variants and increases yield in crops. The frequency of interspecific hybridization varies among taxa, with an estimated 9% occurrence. Allopolyploidy is more common than homoploid hybrid speciation. Chromosome doubling after hybridization is caused by cellular defects during meiosis. Unreduced gametes, formed at a frequency of 2.52% on average, result from altered spindle organization, disrupted kinetochore functioning, abnormal cytokinesis, or loss of meiotic division. Meiotic changes leading to cytological diploidization in allopolyploids are being understood, particularly in wheat. However, the understanding of homoeologous recombination suppressor genes in other allopolyploids is limited. The merger of two genomes leads to architectural, gene expression, and molecular interaction changes, resulting in phenotypic differences. This article provides an overview of genomic and transcriptomic changes during the early stages of allopolyploid formation.
Article
Plant Sciences
Jiyang Chang, Juan Pablo Marczuk-Rojas, Carrie Waterman, Armando Garcia-Llanos, Shiyu Chen, Xiao Ma, Amanda Hulse-Kemp, Allen Van Deynze, Yves Van de Peer, Lorenzo Carretero-Paulet
Summary: This study sequenced the genome of moringa and found that it did not undergo any additional whole-genome duplication or polyploidy events, but tandem duplications played a prominent role. The results provide valuable guidance for future breeding programs to improve moringa.
Article
Biochemistry & Molecular Biology
Kasper P. Hendriks, Christiane Kiefer, Ihsan A. Al-Shehbaz, C. Donovan Bailey, Alex Hooft van Huysduynen, Lachezar A. Nikolov, Lars Nauheimer, Alexandre R. Zuntini, Dmitry A. German, Andreas Franzke, Marcus A. Koch, Martin A. Lysak, Oscar Toro-Nunez, Baris Ozudogru, Vanessa R. Invernon, Nora Walden, Olivier Maurin, Nikolai M. Hay, Philip Shushkov, Terezie Mandakova, M. Eric Schranz, Mats Thulin, Michael D. Windham, Ivana Resetnik, Stanislav Spaniel, Elfy Ly, J. Chris Pires, Alex Harkess, Barbara Neuffer, Robert Vogt, Christian Brauchler, Heimo Rainer, Steven B. Janssens, Michaela Schmull, Alan Forrest, Alessia Guggisberg, Sue Zmarzty, Brendan J. Lepschi, Neville Scarlett, Fred W. Stauffer, Ines Schonberger, Peter Heenan, William J. Baker, Felix Forest, Klaus Mummenhoff, Frederic Lens
Summary: This study presents the most complete genus-level family phylogenies of the Brassicaceae family to date, based on nuclear and plastome data. The study reveals cytonuclear discordance and evaluates the impact of hybridization on nuclear phylogeny reconstruction. The results support a recently published new family classification and provide an essential tool for biodiversity and plant biology research.
Article
Plant Sciences
Jordan R. Brock, Terezie Mandakova, Michael McKain, Martin A. Lysak, Kenneth M. Olsen
Summary: This study reveals the maternal contributors of polyploid Camelina lineages by sequencing and analyzing chloroplast genomes. The study shows minimal divergence in the genus's chloroplast genomes, with no gene loss or structural variation observed. The researchers also discovered that the tetraploid Camelina evolved through multiple independent hybridization events, and the polyploid lineages closely related to C. sativa emerged around 65 thousand years ago. Chromosome counts confirmed the variation in ploidy and cytotypes within C. microcarpa. Overall, this study provides insights into the hybridization and polyploidization history of Camelina.
HORTICULTURE RESEARCH
(2022)
Article
Geography
Hans Westlund, Pia Nilsson
Summary: The purpose of this paper is to study the role of the agricultural sector in complete urbanization and the post urban world, using the Stockholm region as a case study to analyze spatial and temporal changes in land-use and agricultural activities. The results are important for a deeper understanding of agriculture's function in metropolitan regions and its transformation in a world where traditional urban-rural relations are changing.
JOURNAL OF RURAL STUDIES
(2022)
Article
Plant Sciences
Mert Dogan, Milan Pouch, Terezie Mandakova, Petra Hlouskova, Xinyi Guo, Pieter Winter, Zuzana Chumova, Adriaan Van Niekerk, Klaus Mummenhoff, Ihsan A. Al-Shehbaz, Ladislav Mucina, Martin A. Lysak
Summary: The unigeneric tribe Heliophileae, which includes more than 100 Heliophila species, is morphologically diverse and endemic to southern Africa. Their evolution involves whole-genome duplication, diploidization, species radiations, and different ecological life histories. Despite the shared phylogenetic relationship between Chamira and Heliophila, they do not share tandem repeat sequences.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Meng Lu, Zhi Li, Zi-Yu Zhu, Fang Peng, Yang Wang, Xi-Yin Li, Zhong-Wei Wang, Xiao-Juan Zhang, Li Zhou, Jian-Fang Gui
Summary: This study investigates the reproductive characteristics and genomic changes in unisexual and sexual reproduction transitions in polyploid Carassius fish species. The findings provide comprehensive evidence of how changes in ploidy drive reproductive transitions and prevent genomic decay.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Maria Fernanda Moreno-Aguilar, Luis A. Inda, Aminael Sanchez-Rodriguez, Itziar Arnelas, Pilar Catalan
Summary: The repeatome in Loliinae grasses, a subtribe of cold seasonal grasses, is composed of diverse families of repetitive DNA. These repetitive elements show variations in abundance and composition across different species and lineages. The study reveals a correlation between repeatome changes and genome size variations in Loliinae species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Yong Hu, Qing Li, Zexi Chen, Zhanwu Xu, Hongyu Li, Congfa Wen, Liu Duan, Hong Yang, Li Liu
Summary: In this study, we developed an axenic cultivation system to propagate and multiply Vesicularia montagnei, a robust moss with varying environmental conditions. Through artificial induction of diploidization, we generated diploid V. montagnei lines with an enhanced rhizoid system. Transcriptomic analysis showed that genes responsible for jasmonic acid (JA) biosynthesis and signaling had significantly higher expression levels in the diploid lines compared to the wild type. Our findings provide useful information for studying other Vesicularia species and suggest the potential of diploid V. montagnei lines for greenery applications. Additionally, the study sheds light on the biosynthesis and functions of JA in early land plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Federico Marangelli, Vera Pavese, Giuseppe Vaia, Michela Lupo, Muhammad Ajmal Bashir, Valerio Cristofori, Cristian Silvestri
Summary: Polyploid induction is important for the development of new varieties in horticultural plants. In this study, a protocol for in vitro polyploid induction of highbush blueberry leaf tissues was studied. Different concentrations of colchicine and oryzalin were used, and it was found that colchicine can induce polyploidization. The resulting polyploids showed morphological differences compared to diploids.
Article
Biochemistry & Molecular Biology
Jesus A. Ballesteros, Emily V. W. Setton, Carlos E. Santibanez-Lopez, Claudia P. Arango, Georg Brenneis, Saskia Brix, Kevin F. Corbett, Esperanza Cano-Sanchez, Merai Dandouch, Geoffrey F. Dilly, Marc P. Eleaume, Guilherme Gainett, Cyril Gallut, Sean McAtee, Lauren McIntyre, Amy L. Moran, Randy Moran, Pablo J. Lopez-Gonzalez, Gerhard Scholtz, Clay Williamson, H. Arthur Woods, Jakob T. Zehms, Ward C. Wheeler, Prashant P. Sharma
Summary: This study utilized multiple molecular data categories to resolve the phylogenetic relationships of sea spiders, revealing their basal topology and including families that were not fully sampled before. In addition, molecular divergence time estimation confirmed the Ordovician origin of crown group sea spiders, showing that in the evolutionary process sea spiders exhibit greater resilience to mass extinction episodes compared to mollusk and echinoderm lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Qinghua Shi, Xianrui Guo, Handong Su, Yingxin Zhang, Zanmin Hu, Jing Zhang, Fangpu Han
Summary: In this study, researchers found that the induced tetraploid Th. elongatum and the natural tetraploid Th. elongatum are morphologically similar, except for slower development and lower seed setting in the induced tetraploid. Using various molecular probes, the researchers identified differences between two chromosome sets of the natural tetraploid Th. elongatum, but not the induced one. Analysis of hybrid individuals and meiosis in the induced tetraploid revealed that chromosome pairing was successful, indicating rapid diploidization in the induced tetraploid.
Article
Business, Finance
Yerzhan Tokbolat, Hang Le
Summary: This paper investigates the influence of corporate diversification on stock returns during and after the market crash caused by Covid-19. Through regression and survival analyses, we discover that diversified firms perform worse in terms of returns and stock price recovery compared to focused firms. However, diversified firms with a diversification premium exhibit better returns and faster recovery compared to those trading at a discount.
FINANCE RESEARCH LETTERS
(2022)
Article
Business, Finance
Jang Ho Kim
Summary: The cryptocurrency market offers diversification opportunities for asset allocation, but its high volatility limits its benefits for risk-based optimized portfolios.
FINANCE RESEARCH LETTERS
(2022)
Article
Plant Sciences
Yalu Ru, Terezie M. Mandakova, Martin A. Lysak, Marcus A. Koch
Summary: A dodecaploid Eurasian deciduous woodland species, Cardamine bulbifera, has an evolutionary history dating back to the early Pleistocene and shows past gene flow with its hexaploid sister species, C. quinquefolia, likely occurring during the last glacial maximum.
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
Terezie Mandakova, Martin A. Lysak
Summary: This study presents the progress in understanding the genome of camelina, revealing the molecular evolutionary history of the polyploid complex. By studying the tetraploid camelina genome in detail, researchers have identified a high collinearity with two maternally inherited subgenomes of the hexaploid camelina.
Article
Plant Sciences
Ihsan A. Al-Shehbaz, Terezie Mandakova, Klaus Mummenhoff, Martin Lysak
Summary: The new species Heliophila verna is described and its distinguishing characters from the related glabrous annuals, especially H. namaquana, are discussed. The chromosome number (2n = 18) of this species is reported here.
Article
Plant Sciences
Martin A. Lysak, Mark Edginton, Sheng Zuo, Xinyi Guo, Terezie Mandakova, Ihsan A. Al-Shehbaz
Summary: The taxonomic limits of Arabidella, Cuphonotus, and Lemphoria (Brassicaceae, Microlepidieae) have been revised based on a critical evaluation of morphology considering recent cytogenomic and molecular phylogenetic findings. As a result, Lemphoria has been reinstated to include species previously classified under Cuphonotus and Arabidella. A new species, Lemphoria queenslandica, has been described, and new combinations such as L. andraeana, L. eremigena, L. humistrata, and L. procumbens have been proposed. Keys to differentiate Arabidella and Lemphoria species, as well as an expanded generic description of Lemphoria, are provided.
Correction
Plant Sciences
Mert Dogan, Milan Pouch, Terezie Mandakova, Petra Hlouskova, Xinyi Guo, Pieter Winter, Zuzana Chumova, Adriaan Van Niekerk, Klaus Mummenhoff, Ihsan A. Al-Shehbaz, Ladislav Mucina, Martin A. Lysak
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kristyna Hlavata, Jana Leong-Skornickova, Eliska Zaveska, Otakar Sida, Mark Newman, Terezie Mandakova, Martin A. Lysak, Karol Marhold, Tomas Fer
Summary: This study used a targeted enrichment NGS approach to construct the phylogeny of Amomum Roxb. It compared the phylogenies based on different genetic markers and found four groups in the genus. It also observed an increasing trend in genome size (GS) during evolution and found a weak connection between phylogeny, GS, and geography in Amomum.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Cell Biology
Ricardo S. Randall, Claire Jourdain, Anna Nowicka, Kateina Kaduchova, Michaela Kubova, Mohammad A. Ayoub, Veit Schubert, Christophe Tatout, Isabelle Colas, Kalyanikrishna, Sophie Desset, Sarah Mermet, Aurelia Boulaflous-Stevens, Ivona Kubalova, Terezie Mandakova, Stefan Heckmann, Martin A. Lysak, Martina Panatta, Raffaella Santoro, Daniel Schubert, Ales Pecinka, Devin Routh, Celia Baroux
Summary: This article provides a compendium of strategies for analyzing the spatial distribution of nuclear and chromosomal signals from three-dimensional image stacks obtained through fluorescence microscopy imaging. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and better explore the discovery potential of their images.
Article
Multidisciplinary Sciences
Piotr Wlodzimierz, Fernando A. Rabanal, Robin Burns, Matthew Naish, Elias Primetis, Alison Scott, Terezie Mandakova, Nicola Gorringe, Andrew J. Tock, Daniel Holland, Katrin Fritschi, Anette Habring, Christa Lanz, Christie Patel, Theresa Schlegel, Maximilian Collenberg, Miriam Mielke, Magnus Nordborg, Fabrice Roux, Gautam Shirsekar, Carlos Alonso-Blanco, Martin A. Lysak, Polina Y. Novikova, Alexandros Bousios, Detlef Weigel, Ian R. Henderson
Summary: Centromeres play a critical role in cell division by loading specific histone variant nucleosomes, forming kinetochores, and allowing chromosome segregation. Despite their conserved function, there is diversity in centromere size and structure among different species. By analyzing centromeres from Arabidopsis thaliana and Arabidopsis lyrata accessions, we found a high degree of intra- and inter-species diversity. Our findings suggest that centromere evolution is driven by cycles of transposon invasion and purging through satellite homogenization, which contribute to species diversification.
Article
Plant Sciences
Perla Farhat, Terezie Mandakova, Jan Divisek, Hiroshi Kudoh, Dmitry A. German, Martin A. Lysak
Summary: The establishment of Arabidopsis as the most important plant model has led to increased focus on other crucifer species for comparative research. In this study, the unispecific genus Catolobus, a close relative of Capsella, was analyzed for chromosome number, genome structure, genetic variation, and habitat suitability. The findings revealed that Catolobus underwent whole-genome duplication and subsequent diploidization, with a reduction in chromosome number. The hypotetraploid Catolobus genome provides a unique model for comparative studies of tetraploid genomes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Dmitry A. German, Kasper P. Hendriks, Marcus A. Koch, Frederic Lens, Martin A. Lysak, C. Donovan Bailey, Klaus Mummenhoff, Ihsan A. Al-Shehbaz
Summary: Based on recent phylogenetic studies, a new classification system for Brassicaceae is proposed, with improvements at the subfamilial and supertribal levels. The family is now divided into two subfamilies, Aethionemoideae and Brassicoideae. The Brassicoideae is further divided into five supertribes, including Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additionally, several newly recognized tribes are described, and clarifications are provided for 17 other tribes.
Article
Plant Sciences
Nikolai M. Hay, Michael D. Windham, Terezie Mandakova, Martin A. Lysak, Kasper P. Hendriks, Klaus Mummenhoff, Frederic Lens, Kathleen M. Pryer, C. Donovan Bailey
Summary: This study successfully resolved the phylogeny of the Boechera tribe using sequence data from target enrichment approaches. The results provide a foundation for a new taxonomy and further research on Boechera as a model system.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Yile Huang, Xinyi Guo, Kang Zhang, Terezie Mandakova, Feng Cheng, Martin A. Lysak
Summary: The high diversity of the South African Cape flora is not associated with polyploidy. However, the genome assembly of the cruciferous species Heliophila variabilis reveals an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome likely originated through hybridization between two allotetraploids formed by distant hybridization, and its rediploidization was marked by extensive reorganization of subgenomes and genome downsizing.
Article
Multidisciplinary Sciences
Fei Shen, Shixiao Xu, Qi Shen, Changwei Bi, Martin A. A. Lysak
Summary: Polyploidization provides genetic variation for adaptive evolution and speciation, but understanding subgenome evolution and its consequences remains challenging. This study sequenced the telomere-to-telomere reference genome of allotetraploid horseradish and found significant differences in the (epi)genomic architecture and chromatin structure of the subgenomes. The study also revealed the role of polyploidization and subgenome differentiation in shaping key traits such as the biosynthesis of glucosinolates and horseradish peroxidases.
NATURE COMMUNICATIONS
(2023)
Letter
Plant Sciences
Ladislav Mucina, Klaus Mummenhoff, Pieter Winter, Adriaan van Niekerk, Terezie Mandakova, Martin A. Lysak
