Review
Plant Sciences
Martina Bednarova, Miroslava Karafiatova, Eva Hribova, Jan Bartos
Summary: B chromosomes, supernumerary genomic elements found in thousands of eukaryotic species, have been the subject of numerous studies seeking to understand their origin, composition, and effects on carriers. Despite advancements in molecular methods, such as next-generation sequencing, there is still limited knowledge about the processes that led to the emergence of Bs and their transmission mechanisms. The genus Sorghum, which has been on the outskirts of scientific interest, is now being explored for the occurrence and characteristics of Bs, shedding light on possible maintenance and elimination mechanisms and hypotheses for their origin.
Article
Biochemistry & Molecular Biology
Matthew A. Conte, Frances E. Clark, Reade B. Roberts, Luohao Xu, Wenjing Tao, Qi Zhou, Deshou Wang, Thomas D. Kocher
Summary: This study investigates the evolution of a giant sex chromosome in cichlid fish, finding that it consists of three distinct regions and contains unprecedented amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Comparative analysis across 69 teleost genomes supports the hypothesis that the giant sex chromosome originated from the fusion of a B chromosome.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Aleksander Salomon-Perzynski, Joanna Barankiewicz, Marcin Machnicki, Irena Misiewicz-Krzeminska, Michal Pawlak, Sylwia Radomska, Agnieszka Krzywdzinska, Aleksandra Bluszcz, Piotr Stawinski, Malgorzata Rydzanicz, Natalia Jakacka, Iwona Solarska, Katarzyna Borg, Zofia Spyra-Gorny, Tomasz Szpila, Bartosz Pula, Sebastian Grosicki, Tomasz Stoklosa, Rafal Ploski, Ewa Lech-Maranda, Jana Jakubikova, Krzysztof Jamroziak
Summary: Tracking genetic changes during multiple myeloma progression reveals different patterns of mutation evolution, with mutation loss pathway associated with better treatment response. Many druggable genes are mutated, even in heavily pre-treated patients. Redefining R-ISS at relapse is clinically valuable.
Article
Virology
Vladimir Loukachov, Karel A. van Dort, Louis Jansen, Henk W. Reesink, Neeltje A. Kootstra
Summary: A novel Hepatitis B Virus (HBV) encoded miRNA, HBV-miR-6, was identified and validated in liver tissue from chronic hepatitis B (CHB) patients. Its expression was correlated with hepatic HBV-DNA and plasma HBsAg levels, suggesting a potential role in viral excretion or particle formation.
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Daiyan Li, Alevtina Ruban, Joerg Fuchs, Houyang Kang, Andreas Houben
Summary: Some eukaryotes exhibit significant differences in genome size between cells of different organs due to the programmed elimination of chromosomes. Aegilops speltoides, a diploid species from the Poaceae family, has both standard A chromosomes and additional B chromosomes. The B chromosomes in this species are precisely eliminated in the roots during early embryo development, while the number of Bs remains stable in aerial parts of the plant. Through X-ray mutagenesis, restructured B chromosomes were identified, and variations in the elimination process were observed in the roots.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Hematology
Madhavi Maddali, Arvind Venkatraman, Uday Prakash Kulkarni, Sathya Mani, Santhosh Raj, Elanthenral Sigamani, Anu Korula, N. A. Fouzia, Sharon Anbumalar Lionel, Sushil Selvarajan, Marie Therese Manipadam, Aby Abraham, Biju George, Vikram Mathews, Poonkuzhali Balasubramanian
Summary: This study demonstrates the utility of targeted NGS in improving the characterization of triple-negative myeloproliferative neoplasms (TN-MPN) by establishing clonality and detecting noncanonical mutations in driver genes, thereby aiding in clinical decision-making.
ANNALS OF HEMATOLOGY
(2022)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Review
Medicine, General & Internal
Andrew D. King, Hany Deirawan, Paytra A. Klein, Bahar Dasgeb, Catherine I. Dumur, Darius R. Mehregan
Summary: Over the past decade, Next-Generation Sequencing (NGS) has greatly contributed to the diagnosis and management of various dermatological conditions, including genetic diseases of the skin, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma.
FRONTIERS IN MEDICINE
(2023)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Article
Plant Sciences
Martin Mau, Terezie M. Mandakova, Xingliang Ma, Jana Ebersbach, Lifang Zou, Martin A. Lysak, Timothy F. Sharbel
Summary: This study investigates the molecular evolution, gene regulation, and chromosomal location of a male apomeiosis factor (UPG2) in Boechera, revealing its origin in the apomixis genome and demonstrating selective pressure to maintain its function for unreduced pollen formation in apomicts.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Ekaterina D. Badaeva, Fedor A. Konovalov, Helmut Knupfer, Agostino Fricano, Alevtina S. Ruban, Zakaria Kehel, Svyatoslav A. Zoshchuk, Sergei A. Surzhikov, Kerstin Neumann, Andreas Graner, Karl Hammer, Anna Filatenko, Amy Bogaard, Glynis Jones, Hakan Ozkan, Benjamin Kilian
Summary: This study provides a comprehensive survey of the cytogenetic and genomic diversity of the GGA(t)A(t) genepool of wheat, highlighting its potential for wheat improvement. The survey revealed three distinct lineages within the extant GGA(t)A(t) genepool, with chromosomal rearrangements playing a significant role in intraspecific diversity. The findings shed new light on the evolutionary history and domestication of the GGA(t)A(t) wheat genepool, paving the way for its increased utilization in wheat improvement.
THEORETICAL AND APPLIED GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Jianyong Chen, James A. Birchler, Andreas Houben
Summary: B chromosomes, also known as supernumerary chromosomes, are dispensable elements in the genome of many plants, animals, and fungi. This study summarizes the findings of the drive process of plant B chromosomes, focusing on maize and rye.
CHROMOSOME RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Alevtina Ruban, Andreas Houben
Summary: The ability to generate (di)haploid plants has significantly accelerated the crop-breeding process, with each doubled haploid representing a pure line for further evaluation of agronomically important traits. While haploids can be induced through in vitro or in vivo methods, many crop species still lack efficient haploid technology.
Article
Plant Sciences
Daniel Arend, Dennis Psaroudakis, Junaid Altaf Memon, Elena Rey-Mazon, Danuta Schueler, Jedrzej Jakub Szymanski, Uwe Scholz, Astrid Junker, Matthias Lange
Summary: The research data life cycle is an integral part of current research, but its complexity often exceeds the expertise and infrastructure available to scientists. This article explores how data stewards can address the challenges in data-driven research, using concrete use cases and best practices from plant phenotyping. By enhancing the necessary digital transformation, data stewards can improve the quality of progressive research.
Article
Biochemistry & Molecular Biology
Anastassia Boudichevskaia, Anne Fiebig, Katrin Kumke, Axel Himmelbach, Andreas Houben
Summary: The B chromosome has a significant impact on the transcriptome of the standard A chromosomes, affecting processes such as gene silencing, DNA methylation, chromatin silencing, gene expression regulation, epigenetics, post-embryonic development, and chromosome organization. Genes responsive to B chromosomes in rye and wheat have similar biological functions. The number of B chromosomes is positively correlated with the presence of B-specific transcripts.
CHROMOSOME RESEARCH
(2022)
Article
Plant Sciences
Dmitri Demidov, Inna Lermontova, Michael Moebes, Andriy Kochevenko, Joerg Fuchs, Oda Weiss, Twan Rutten, Eberhard Sorge, Erika Zuljan, Ricardo Fabiano Hettwer Giehl, Martin Mascher, Saravanakumar Somasundaram, Udo Conrad, Andreas Houben
Summary: Targeted degradation of CENH3 protein can be used to generate haploids in Arabidopsis thaliana. By using a recombinant anti-GFP nanobody fused to ligase proteins, EYFP-tagged CENH3 can be recognized and degraded through the ubiquitin-proteasome pathway. This strategy achieves a haploid frequency of up to 7.6%.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Mathematical & Computational Biology
Manuel Feser, Patrick Koenig, Anne Fiebig, Daniel Arend, Matthias Lange, Uwe Scholz
Summary: In recent years, advancements in data collection in life science have increased the demand and opportunities for advanced bioinformatics. Good research data management strategies are crucial for the use and re-use of genotypic data. The development of reusable and maintainable tools and ecosystems is essential for sustainable software. Using established file formats improves tool reusability and overall interoperability. Building strong communities for tool maintenance is also important.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2022)
Article
Plant Sciences
Tanja Zahn, Zihao Zhu, Niklas Ritoff, Jonathan Krapf, Astrid Junker, Thomas Altmann, Thomas Schmutzer, Christian Tueting, Panagiotis L. Kastritis, Steve Babben, Marcel Quint, Klaus Pillen, Andreas Maurer
Summary: Novel exotic ELF3 alleles have been discovered and shown to be associated with agronomic traits in barley. These findings suggest a central role for ELF3 in barley adaptation.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Multidisciplinary Sciences
Pavel Neumann, Ludmila Oliveira, Tae-Soo Jang, Petr Novak, Andrea Koblizkova, Veit Schubert, Andreas Houben, Jiri Macas
Summary: The transition from monocentric to holocentric organization in Cuscuta was associated with loss or truncation of kinetochore-related genes, disruption of centromeric localization of kinetochore proteins, and degeneration of the spindle assembly checkpoint. This indicates that holocentric Cuscuta species lack a standard kinetochore and do not employ the SAC to control microtubule attachment to chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Lamonier Chaves Ramos, Mariana Baez, Joerg Fuchs, Andreas Houben, Reginaldo Carvalho, Andrea Pedrosa-Harand
Summary: The genus Agave has a bimodal karyotype, which is believed to be a result of allopolyploidy in the ancestral form of Agavoideae. However, the accumulation of repetitive DNA may also play a significant role.
Article
Plant Sciences
Andrew R. Leitch, Lu Ma, Steven Dodsworth, Joerg Fuchs, Andreas Houben, Ilia J. Leitch
Summary: Angiosperm genomes consist of genes and their regulatory regions, repeats, semi-degraded repeats, and "dark matter". This study compares the histone modifications associated with chromatin packaging of these different genomic components in two species with significantly different genome sizes. The results reveal distinct associations between certain histone marks and different genomic features, providing insights into epigenetic profiles and chromatin organization.
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
Biology
Patrick Koenig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Summary: DivBrowse is a web application that allows interactive visualization and exploratory analysis of genomic diversity data stored in VCF files. It combines BLAST as an entry point with features like principal component analysis, providing a unique set of capabilities for studying genomic biodiversity datasets. The application also supports data interoperability and integration with existing web applications.
Review
Plant Sciences
Holger Puchta, Andreas Houben
Summary: Spontaneous chromosomal rearrangements (CRs) play a vital role in speciation, genome evolution and crop domestication. Chromosome engineering, through methods such as chromosomal translocations, inversion reversions, and construction of minichromosomes, has the potential to modify genetic linkage groups, change the number of chromosomes, and establish genetic isolation, thus aiding breeding and plant biotechnology.
Article
Plant Sciences
Michelle Roenspies, Carla Schmidt, Patrick Schindele, Michal Lieberman-Lazarovich, Andreas Houben, Holger Puchta
Summary: This study demonstrates the suppression of meiotic recombination through chromosome restructuring, inducing a heritable inversion and discovering that genetic exchange mainly occurs at telomeric ends.