Article
Plant Sciences
Zhong-Shuai Zhang, Qing-Yin Zeng, Yan-Jing Liu
Summary: The variation of chromosome number and genome size within the Salicaceae family demonstrates frequent ploidy changes and widespread sharing of the salicoid whole genome duplication event among relatives of Populus and Salix. Genome size reduction after whole genome duplication suggests substantial loss of genomic components. The phylogenetic asymmetry in the clade of Populus, Salix, and their close relatives indicates a delayed subsequent radiation post the salicoid whole genome duplication event.
Article
Biochemistry & Molecular Biology
Xinyi Guo, Terezie Mandakova, Karolina Trachtova, Baris Ozudogru, Jianquan Liu, Martin A. Lysak
Summary: This study reveals the complex genomic history of the mustard family tribe Biscutelleae, showing contentious relationships within this plant family. Genome evolution in Biscutelleae was influenced by pervasive hybridizations and subsequent genome duplications, leading to a complex pattern of relationships among the genera.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Gulru Yucel, Alexander Betekhtin, Evren Cabi, Metin Tuna, Robert Hasterok, Bozena Kolano
Summary: This study investigates the evolution of chromosome number and rDNA loci in Onobrychis species. It found that diploid species showed a high level of polymorphism in rDNA loci number and localisation, while polyploid species exhibited similar rDNA loci patterns. Phylogenetic analysis revealed that x = 8 was the ancestral chromosome number and dysploidy and polyploidisation were the major mechanisms driving chromosome number evolution. Additionally, the study reconstructed the ancestral state of rRNA gene loci in Onobrychis, with one locus of 5S rDNA and one locus of 35S rDNA in an interstitial chromosomal position.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Natalia Borowska-Zuchowska, Magdalena Senderowicz, Dana Trunova, Bozena Kolano
Summary: Cytogenetics is a branch of genetics focused on cellular components, especially chromosomes, and their relationship to heredity, genome structure, function, and evolution. Modern cytogenetic approaches allow for the visualization of different sequences in the plant genome and contribute to understanding its evolutionary history.
Article
Virology
Reimar Johne, Katja Schilling-Loeffler, Rainer G. Ulrich, Simon H. Tausch
Summary: Rotaviruses, known for causing diarrhea in humans and animals, have been classified into species A to J, with potential new species K and L recently identified. Through genome analysis, strain KS14/0241 has been classified as a prototype strain of the novel rotavirus species L, showing only 47% identity to reference strains. Phylogenetic analyses show that species L clusters separately from known rotavirus species, with a close relationship to RVH and RVJ.
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
Jie Huang, Weibin Xu, Junwen Zhai, Yi Hu, Jing Guo, Caifei Zhang, Yiyong Zhao, Lin Zhang, Christopher Martine, Hong Ma, Chien-Hsun Huang
Summary: This study generated transcriptomes/genomes for 180 Solanaceae species and constructed a highly resolved phylogenetic tree. The study revealed a specific whole-genome triplication event in the evolutionary history of Solanaceae, which may have contributed to the development of fleshy fruits.
PLANT COMMUNICATIONS
(2023)
Article
Plant Sciences
Ana Paula Moraes, Thaissa Brogliato Junqueira Engel, Eliana R. Forni-Martins, Fabio de Barros, Leonardo P. Felix, Juliano Sarmento Cabral
Summary: The study on Maxillariinae reveals that genome size and chromosome number are partially correlated with ecological data in the evolutionary process, suggesting the significance of these genomic traits in the ecological niche.
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
Plant Sciences
Xiu-Jiang Su, Wen-Qun Fei, Ding Zhao, Ying Liu, Qin-Er Yang
Summary: Sinosenecio minshanicus, a new species of Asteraceae, Senecioneae, is discovered in south-eastern Gansu and northern Sichuan, China. It is similar to S. rotundifolius in appearance, but differs in the presence of stolons, thinner rhizomes, sparsely fulvous arachnoid or glabrescent stems, and inconspicuous main veins on adaxial surface of leaves. The chromosome number of the new species is reported to be 2n = 60. The article provides color photographs and a distribution map of the new species, as well as correcting the geographical distribution of S. rotundifolius.
Article
Plant Sciences
Julia E. Steier, Terezie Mandakova, Martin F. Wojciechowski, Kelly P. Steele
Summary: The genus Medicago contains about 90 species, including important forage crop and genomic model species. Some Medicago species lack information on chromosome number and genome size, particularly those from Medicago section Buceras. Research suggests that there are distinct entities within currently recognized species, with differences in chromosome number and genome size, indicating the role of polyploidy and chromosomal abnormalities in genome evolution. This data provides a foundation for whole-genome sequencing projects and further research on paraphyletic lineages.
Review
Evolutionary Biology
Itay Mayrose, Martin A. Lysak
Summary: Chromosome numbers are a fundamental genomic attribute, providing strong phylogenetic signals, but vary widely among eukaryotes. Changes in chromosome numbers, often indicating major genomic events, can be inferred through mechanistic processes, experimental procedures, and computational methodologies. These tools allow for valuable predictions about historical events that have influenced chromosome numbers and genome structures.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Qiong Zhang, Lei Zhao, Ryan A. Folk, Jian-Li Zhao, Nelson A. Zamora, Shi-Xiong Yang, Douglas E. Soltis, Pamela S. Soltis, Lian-Ming Gao, Hua Peng, Xiang-Qin Yu
Summary: This study used transcriptomes or low-depth whole-genome sequencing data from 57 species of Theaceae, along with additional plastome sequence data, to investigate phylogenetic relationships at both tribal and generic levels. The study also inferred possible whole-genome duplication events and identified potential hybridization events among species within the family. The results of the study improved our understanding of phylogenetic relationships within Theaceae and highlighted the importance of low-copy nuclear genes in phylogenetic analyses.
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)
News Item
Ecology
Hannes Becher
Correction
Multidisciplinary Sciences
Grit Winterfeld, Hannes Becher, Stephanie Voshell, Khidir Hilu, Martin Roser
Article
Plant Sciences
Wencai Wang, Tao Wan, Hannes Becher, Alena Kuderova, Ilia J. Leitch, Sonia Garcia, Andrew R. Leitch, Ales Kovarik
Article
Biochemistry & Molecular Biology
Hannes Becher, Benjamin C. Jackson, Brian Charlesworth
Article
Biochemistry & Molecular Biology
Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Summary: Current methods for inferring population history assume neutrality, but neglect the effects of direct and background selection. The study shows that background selection can lead to mis-inferences of population growth, especially with increasing strength of purifying selection and density of directly selected sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Hannes Becher, Robyn F. Powell, Max R. Brown, Chris Metherell, Jaume Pellicer, Ilia J. Leitch, Alex D. Twyford
Summary: The study investigated genome size variation within and between species of British eyebrights and found significant intraspecific genome size variation. It demonstrated the utility of treating genome size as the outcome of polygenic variation, which may be influenced by ongoing hybridization and population subdivision.
Article
Genetics & Heredity
Surabhi Ranavat, Hannes Becher, Mark F. Newman, Vinita Gowda, Alex D. Twyford
Summary: Angiosperms have various reproductive strategies, including flexistyly, a floral strategy characterized by two morphs with different timing of stylar movement. A study investigated the genetic basis of flexistyly by sequencing the genome of Alpinia nigra and using Pool-seq to identify candidate regions. The results suggest that flexistyly may be governed by a small genomic region that is hard to detect with Pool-seq, or a complex genomic region that is difficult to assemble.
Article
Plant Sciences
Phen Garrett, Hannes Becher, Galina Gussarova, Claude W. dePamphilis, Rob W. Ness, Shyam Gopalakrishnan, Alex D. Twyford
Summary: This study conducted a phylogenomic analysis of Euphrasia species and found extensive phylogenetic discordance at deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hannes Becher, Jacob Sampson, Alex D. Twyford
Summary: Genome size variation within plant taxa is caused by presence/absence variation, which affects low-copy sequences or genomic repeats of different frequency classes. In this study, a novel approach based on k-mers is used to analyze genome size variation in diploid eyebrights. The results show that the sequences underlying genome size variation are mainly rDNA sequences, a genomic satellite, and a repeat associated with an Angela transposable element. This study also emphasizes the importance of studying non-repetitive sequences to fully understand genome size variation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Max R. Brown, Hannes Becher, Sebastian Williams, Alex D. Twyford
Summary: The study investigated the potential cross-ploidy hybridization in British eyebrights and found that recent cross-ploidy hybridization is rare or absent in the study area. However, the results suggest that cross-ploidy introgression may still occur over evolutionary timescales.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Hannes Becher, Richard A. Nichols
Summary: This article introduces two statistical methods to estimate the abundance of nuclear inserts even without a nuclear genome assembly. The first method only requires low-coverage sequencing data commonly generated for population studies. The second method additionally requires individuals carrying extranuclear DNA with diverged genotypes. The study demonstrates the utility of low-coverage high-throughput sequencing data for quantifying nuclear vagrant DNAs.
MOLECULAR ECOLOGY RESOURCES
(2023)
Meeting Abstract
Dermatology
Eleri Jones, Supatra Marsh, Ryan O'Shaughnessy, Monique Aumailley, John McGrath, Edel O'Toole, Matthew Caley
BRITISH JOURNAL OF DERMATOLOGY
(2023)
Meeting Abstract
Dermatology
Luke Johnston, Mona Etorban, Hannes Becher, Martina Elias, Sara Brown
BRITISH JOURNAL OF DERMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hannes Becher, Max R. Brown, Gavin Powell, Chris Metherell, Nick J. Riddiford, Alex D. Twyford
PLANT COMMUNICATIONS
(2020)