Article
Biochemistry & Molecular Biology
Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Frederic Guerin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch
Summary: Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages, but the maintenance of WGD-derived paralogs is still debated. The analysis of 13 Paramecium species revealed that gene retention biases and strong selective pressures against post-WGD gene loss play a major role in maintaining duplicate genes. Paramecium is an exceptional model organism in evolutionary cell biology, and this dataset of 13 species sharing an ancestral WGD will be useful for future studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Nissanka P. De Silva, Christopher Lee, Paul Battlay, A. Fournier-Level, Joslin L. Moore, Kathryn A. Hodgins
Summary: This study presents the genome assembly and annotation of Bothriochloa decipiens, an Australian grass species with a complex history of hybridization and polyploidy. Comparative analysis reveals a recent whole-genome duplication event and differences in repeat activity and gene retention between subgenomes. Bothriochloa decipiens has ecological importance and potential for climate change-resilient restoration of Australian grasslands. The reference genome provides a valuable resource for future population genomic research on Australian grasses.
Article
Biochemistry & Molecular Biology
Daniel Evans-Yamamoto, Alexandre K. Dube, Gourav Saha, Samuel Plante, David Bradley, Isabelle Gagnon-Arsenault, Christian R. Landry
Summary: This study investigates the repeated maintenance and functional complementation of the HRR25 gene in yeast species. The results show that most duplicated copies of the HRR25 gene in different species are unable to complement each other, indicating a process of nonfunctionalization or neofunctionalization.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Sarah Farhat, Maria Vittoria Modica, Nicolas Puillandre
Summary: The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Zijiang Yang, Shanshan Chen, Shufen Wang, Ying Hu, Guanghui Zhang, Yang Dong, Shengchao Yang, Jianhua Miao, Wei Chen, Jun Sheng
Summary: A high-quality genome assembly of Siberian ginseng was reported, revealing a high proportion of transposable elements and a large number of predicted protein-coding genes. Comparative analysis with other plant genomes showed that whole-genome duplication events and a burst expansion of chromoviral elements may have contributed to adaptation in the Araliaceae family.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Agriculture, Multidisciplinary
Huang Yi-le, Zhang Ling-kui, Zhang Kang, Chen Shu-min, Hu Jian-bin, Cheng Feng
Summary: Whole genome duplication (WGD) and tandem duplication (TD) are important mechanisms in plant genome evolution. This study found that Vitis vinifera, which did not undergo a whole genome triplication event, retained more tandem duplicated gene (TDG) clusters compared to Solanaceae species that experienced the event. There was also a bias in the functional categories of genes retained through WGD and TD, with WGD retaining dose-sensitive genes and TD retaining stress resistance genes. The study also provided evidence of gene fusion events in TDG clusters, which contribute to functional innovation.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Plant Sciences
Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
Summary: In this study, we assembled the largest nuclear dataset for ferns and investigated the fern phylogeny, whole genome duplications (WGDs), and gene retention patterns following WGDs. Our results revealed high levels of gene tree-species tree conflict in the fern phylogeny and identified multiple WGDs events. We also found that functions of retained genes following WGDs were largely convergent.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Rui-Min Yu, Ning Zhang, Bo-Wen Zhang, Yu Liang, Xiao-Xu Pang, Lei Cao, Yi-Dan Chen, Wei-Ping Zhang, Yang Yang, Da-Yong Zhang, Er-Li Pang, Wei-Ning Bai
Summary: Background: Autopolyploidy is a valuable model for studying whole-genome duplication without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after duplication. In this study, we investigated these changes in Cyclocarya paliurus, a natural diploid-autotetraploid species. Results: The autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and most of these homologous chromosomes showed similar characteristics. The genomic regions of synteny, structural variation, and nonalignment to the diploid genome accounted for different proportions of the autotetraploid genome. Moreover, we found that genes with allelic loss were often located near structural variations and transposable elements, and these genes showed reduced interaction with other genes. Furthermore, we identified genes with more than four copies in the autotetraploid genome, and these genes exhibited higher expression levels than their diploid counterparts. These genes were involved in stress response and plant defense, suggesting their role in the evolutionary success of autotetraploids. Population genomic analyses revealed a single origin of autotetraploids and recent divergence from diploids. Conclusions: Our findings indicate the potential for genomic and functional reorganization in autotetraploid C. paliurus, which may contribute to their evolutionary success.
Article
Biochemistry & Molecular Biology
Chi-Fa Huang, Wen-Yu Liu, Mei-Yeh Jade Lu, Yi-Hua Chen, Maurice S. B. Ku, Wen-Hsiung Li
Summary: Through studying leaf-development transcriptomes, it was found that whole-genome duplication (WGD) facilitated four aspects of C-4 photosynthesis evolution in G. gynandra, including the retention of duplicated genes related to nitrogen recycling and vein development, the evolution of C-4 enzyme genes, and upregulation of genes encoding photosystem I proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Julian C. B. Ponsford, Charley J. Hubbard, Joshua G. Harrison, Lois Maignien, C. Alex Buerkle, Cynthia Weinig
Summary: The composition of microbial communities associated with plants is influenced by the genetic background and ploidy level of the host. This study investigated the effects of genome duplication on rhizosphere bacterial communities in Arabidopsis thaliana and found that both the host genetic background and ploidy level affected the composition of the microbial communities. Additionally, the microbial communities derived from specific genetic backgrounds and ploidy levels had negative effects on plant growth. These findings suggest an interaction between host genetic background, ploidy level, and bacterial community assembly.
Article
Biochemistry & Molecular Biology
Shaohua Xu, Zixiao Guo, Xiao Feng, Shao Shao, Yuchen Yang, Jianfang Li, Cairong Zhong, Ziwen He, Suhua Shi
Summary: Whole-genome duplication (WGD) increases the chance of adaptation to new and unstable environments, such as the interface between land and sea. WGD duplicates in mangrove plants have acquired derived differential expression in response to changes in salt gradient treatment, suggesting their collaborative function in coping with different salinity levels.
Article
Agriculture, Multidisciplinary
Niels Agerbirk, David Pattison, Terezie Mandakova, Martin A. Lysak, Sabine Montaut, Dan Staerk
Summary: The GSL profiles of four Limnanthaceae species, including the oil crop Limnanthes alba, were investigated using ultrahigh-performance liquid chromatographyquadrupole time-of-flight tandem mass spectrometry (UHPLC-QToF-MS/MS) analysis. The study provided an overview of biosynthetic capabilities in the genera Floerkea and Limnanthes and proposed potential biosynthetic schemes and gene families relevant for tailoring GSL profiles in Limnanthes crops.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Plant Sciences
Christian Parisod, Sebastien Lavergne, Hang Sun, Joachim W. Kadereit
Summary: This special issue of Alpine Botany brings together studies and syntheses on plant evolution in major mountain ranges worldwide, providing insight into the factors determining plant variation and distribution in topographically complex areas.
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
Plant Sciences
Luka N. Olsen, Marie K. Brandrud, Terezie Mandakova, Martin A. Lysak, Charlotte S. Bjora, Eduardo Cires, Inger Nordal, Anne K. Brysting
Summary: Considerable chromosome variation has occurred in northern European Cochlearia plants without corresponding morphological differentiation, resulting in a complex species group. This study investigates the situation in Iceland, discussing the distribution, genetic structure, taxonomy, and origin of the two cytotypes present. The findings suggest geographically structured genetic variation along the Icelandic coast and environmentally structured genetic differentiation between coastal and alpine populations.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Plant Sciences
Laszlo Bartha, Terezie Mandakova, Ales Kovarik, Paul-Adrian Bulzu, Nathalie Rodde, Vaclav Mahelka, Martin A. Lysak, Margaux-Alison Fustier, Jan Safar, Petr Capal, Lujza Keresztes, Horia L. Banciu
Summary: This study provides evidence supporting the integration hypothesis of alien ribosomal DNA (rDNA) from eudicots into the genome of the monocot genus Erythronium. The transferred eudicot-type rDNA is still active in the monocot host, adding a new example of nuclear-to-nuclear DNA transfer between eudicots and monocots.
Article
Plant Sciences
Christoph Rosche, Annett Baasch, Karen Runge, Philipp Brade, Sabrina Trager, Christian Parisod, Isabell Hensen
Summary: This study used historical DNA to investigate local extinctions in the Biscutella laevigata subsp. gracilis populations in Central Germany. The results showed that gene flow was affected by spatial distance and floristic composition, and highlighted the potential of floristic composition as a predictor of functional connectivity. The study also found a negative relationship between sampling year and heterozygosity and germination.
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
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
Zoology
Dorothy Maushe, Vera Ogi, Keerthi Divakaran, Arletys Maria Verdecia Mogena, Paul Anton Himmighofen, Ricardo A. R. Machado, Benjamin Daniel Towbin, Ralf-Udo Ehlers, Carlos Molina, Christian Parisod, Christelle Aurelie Maud Robert
Summary: This review provides a comprehensive overview of the response of entomopathogenic nematodes (EPNs) to various stresses, including starvation, temperature, desiccation, osmotic stress, hypoxia, and ultra-violet light. It also discusses EPN defense strategies against biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing these strategies to the nematode model Caenorhabditis elegans, new avenues and targets for selecting and engineering precision nematodes adapted to specific field conditions are proposed.
JOURNAL OF INVERTEBRATE PATHOLOGY
(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