Article
Biotechnology & Applied Microbiology
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: The study developed a tool called Montage to enhance the accuracy of detecting mosaic copy number variants, identified numerous mosaic CNVs associated with phenotypes, and presented a novel algorithm for efficient detection of mosaic CNVs.
Article
Biochemistry & Molecular Biology
Luzia Stalder, Ursula Oggenfuss, Norfarhan Mohd-Assaad, Daniel Croll
Summary: This study analyzes how a fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. The research shows that gene duplications and deletions are major sources of adaptive genetic variation, with most gene duplications resulting from segmental chromosomal duplications. The pathogen utilizes these adaptive genetic variations to exploit the host and resist fungicides.
Article
Biochemical Research Methods
Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
Summary: The recent advance of single-cell copy number variation (CNV) analysis is important in addressing intratumor heterogeneity and restoring tumor-evolving trajectories. However, existing tools lack real-time interaction and are hard to reproduce. We present an online platform for real-time interactive visualization of single-cell genomics data to accelerate the understanding of cancer clonal evolution.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Robin Nicole Bosman, Jessica Anne-Marie Vervalle, Danielle Lisa November, Phyllis Burger, Justin Graham Lashbrooke
Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Gregg W. C. Thomas, Richard J. Wang, Jelena Nguyen, R. Alan Harris, Muthuswamy Raveendran, Jeffrey Rogers, Matthew W. Hahn
Summary: The study analyzed patterns of CNV mutations in rhesus macaque individuals, finding a low rate of CNV mutations per generation and no correlation between parental age and the number of CNVs passed on to offspring. Rhesus macaques and humans differ in the proportion of segregating deletions, with both species having more segregating deletions than duplications.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Ondrej Pos, Jan Radvanszky, Gergely Buglyo, Zuzana Pos, Diana Rusnakova, Balint Nagy, Tomas Szemes
Summary: Copy number variants are common features of the human genome, playing roles in evolution, population diversity, disease development, and host-microbiome interactions. They have potential applications in molecular diagnosis and prenatal care, with expected significant impact on screening, diagnosis, prognosis, and monitoring of disorders such as cancer and cardiovascular disease.
BIOMEDICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: In this study, we introduce SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. We demonstrate that SCONCE2 outperforms existing methods in copy number calling and phylogeny estimation. The method enables the inference of tumor phylogenies, providing deeper insights into tumor evolution.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
DeElegant Robinson, Michael Place, James Hose, Adam Jochem, Audrey P. Gasch
Summary: This study found that individual differences in yeast strains dominate the fitness costs of gene overexpression, with global differences in the consequences of gene overexpression independent of the amplified gene, as well as gene-specific effects dependent on the genetic background. Natural variation in response to gene overexpression could be explained by several models, including strain-specific physiological differences, resource limitations, and regulatory sensitivities.
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Review
Oncology
Christopher D. Steele, Nischalan Pillay, Ludmil B. Alexandrov
Summary: The genome of each cell is constantly damaged by various processes, resulting in DNA damage and mutations. The mutational signatures of small mutational events have been extensively studied, and the focus has shifted to understanding the mutational signatures of copy number alterations (CNAs). The study of these mutational signatures has practical implications in basic science, cancer treatment, and cancer prevention.
JOURNAL OF PATHOLOGY
(2022)
Article
Microbiology
Sean A. Bergin, Fang Zhao, Adam P. Ryan, Carolin A. Muller, Conrad A. Nieduszynski, Bing Zhai, Thierry Rolling, Tobias M. Hohl, Florent Morio, Jillian Scully, Kenneth H. Wolfe, Geraldine Butler
Summary: We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We found that the increased copy number of the RTA3 gene is associated with resistance to the drug miltefosine. Additionally, we discovered that mutations in flippase genes can also contribute to resistance.
Review
Genetics & Heredity
Ivan Pokrovac, Zeljka Pezer
Summary: The field of population genomics has experienced a substantial growth in the study of genomic structural variation over the past two decades. These studies have revealed that structural variation is widely found in different taxa and is a major contributor to genetic diversity within species. With recent advancements in technology, specifically the development of long-read sequencing platforms, previously inaccessible regions of the genome have been explored for structural variants, uncovering a greater extent of structural variation that contributes to evolution. However, the functional consequences of the majority of structural variants are still unknown, and there is a lack of evidence on the phenotypic effects of the structural variants that are suggested to have adaptive potential. It is suggested that more research on non-human genomes is necessary to accurately assess the contribution of structural variants to evolution.
FRONTIERS IN GENETICS
(2022)
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Genetics & Heredity
Simone Fouche, Ursula Oggenfuss, Emilie Chanclud, Daniel Croll
Summary: Transposable elements play a major role in genome expansions through self-copying mechanisms. Plant pathogens finely control the expression of virulence factors through epigenetic regulation targeted at nearby transposable elements. However, the derepression of transposable elements during stress and infection processes may lead to long-term evolutionary conflicts and genome size expansions, posing a devil's bargain for pathogens.
TRENDS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Sandra Gonzalez-Sayer, Ursula Oggenfuss, Ibonne Garcia, Fabio Aristizabal, Daniel Croll, Diego M. Riano-Pachon
Summary: In this study, we successfully assembled and annotated the genome of Pseudocercospora ulei, the causal agent of South American Leaf Blight (SALB) in rubber trees. The assembled genome is of high quality, making it the largest among Mycosphaerellaceae and containing a high proportion of retrotransposons. This research provides essential genomic resources for future studies on P. ulei and related species.
GENETICS AND MOLECULAR BIOLOGY
(2022)
Article
Plant Sciences
Jean-Sebastien Reynard, Justine Brodard, Nathalie Dubuis, Isabelle Kellenberger, Anne-Sophie Spilmont, David Roquis, Varvara Maliogka, Cecile Marchal, Sandrine Dedet, Ophelie Gning, Daniel Croll, Katia Gindro, Olivier Schumpp, Jean-Laurent Spring, Thierry Lacombe
Summary: The study found that only a few grapevine accessions from the United States were infected with GRBV in European repositories. The virome of the Swiss grapevine collection mainly consisted of RNA viruses, with little to no presence of DNA viruses. This suggests that the abundance of DNA viruses infecting grapevines in Switzerland is minimal or non-existent.
JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sabina Moser Tralamazza, Leen Nanchira Abraham, Claudia Sarai Reyes-Avila, Benedito Correa, Daniel Croll
Summary: The study reveals that highly conserved genes marked by H3K27me3 are more likely to be dispensable during host infection, while conserved genes exposed to repressive H3K27me3 marks across distantly related fungi are associated with transcriptional perturbation on a microevolutionary scale.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lea Stauber, Daniel Croll, Simone Prospero
Summary: This study investigated the genetic diversity of the chestnut blight pathogen C. parasitica in the presence of its hyperparasite CHV1. The results showed that both pathogen population structure and CHV1 prevalence remained stable over time, suggesting recent bottlenecks influenced the population structure. The virus infection rates remained stable and had no significant impact on fungal population diversity.
Article
Biochemistry & Molecular Biology
Luzia Stalder, Ursula Oggenfuss, Norfarhan Mohd-Assaad, Daniel Croll
Summary: This study analyzes how a fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. The research shows that gene duplications and deletions are major sources of adaptive genetic variation, with most gene duplications resulting from segmental chromosomal duplications. The pathogen utilizes these adaptive genetic variations to exploit the host and resist fungicides.
Article
Multidisciplinary Sciences
Hadjer Bellah, Gwilherm Gazeau, Sandrine Gelisse, Reda Amezrou, Thierry C. Marcel, Daniel Croll
Summary: To predict future risks of crop pathogens, monitoring tools are needed to identify genetic changes in pathogen populations. This study developed a microfluidics-based gene sequencing method that can simultaneously detect 798 loci targeting virulence and fungicide resistance genes, as well as randomly selected genome-wide markers. The method showed stable and high success rates in different samples, both pure genomic DNA and material extracted from infected wheat leaves. The study also demonstrated the potential of the method to recover the pathogen population structure across French wheat fields.
Article
Plant Sciences
Sepideh Hatami Rad, Leila Ebrahimi, Daniel Croll
Summary: Managing pathogen damage in wheat production is crucial. This study analyzed the evolution of the AvrStb6 effector in Iranian isolates of Z. tritici. It found a high genetic diversity and global diversity patterns of AvrStb6, highlighting its importance for Z. tritici virulence.
Article
Multidisciplinary Sciences
Alice Feurtey, Cecile Lorrain, Megan C. McDonald, Andrew Milgate, Peter S. Solomon, Rachael Warren, Guido Puccetti, Gabriel Scalliet, Stefano F. F. Torriani, Lilian Gout, Thierry C. Marcel, Frederic Suffert, Julien Alassimone, Anna Lipzen, Yuko Yoshinaga, Christopher Daum, Kerrie Barry, Igor V. Grigoriev, Stephen B. Goodwin, Anne Genissel, Michael F. Seidl, Eva H. Stukenbrock, Marc-Henri Lebrun, Gert H. J. Kema, Bruce A. McDonald, Daniel Croll
Summary: Human activity affects the evolution of many species. Global trade of agricultural goods contributes to the spread of pathogens and alters their genetic makeup. Understanding how pathogens adapt and cope with new climates is crucial for predicting their impact on crop diseases.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Sergio Latorre, Vincent Were, Andrew Foster, Thorsten Langner, Angus Malmgren, Adeline Harant, Soichiro Asuke, Sarai Reyes-Avila, Dipali Rani Gupta, Cassandra Jensen, Weibin M. Ma, Nur Uddin Mahmud, Md. Shabab Mehebub, Rabson Mulenga, Abu Naim Md. Muzahid, Sanjoy Kumar Paul, S. M. Fajle Rabby, Abdullah Al Mahbub Rahat, Lauren M. Ryder, Ram-Krishna Shrestha, Suwilanji R. Sichilima, Darren Soanes, Pawan Kumar Singh, Alison Bentley, Diane G. O. H. Saunders, Yukio Tosa, Daniel Croll, Kurt Lamour, Tofazzal J. Islam, Batiseba Tembo, Joe Win, Nicholas Talbot, Hernan A. Burbano, Sophien Kamoun
Summary: Wheat, a vital food crop, is being threatened by a pandemic of the blast disease. Research reveals that a clonal lineage of the wheat blast fungus has spread to Asia and Africa from South America. The lineage can be controlled by a disease resistance gene and fungicides, but there is a potential for the clone to evolve resistance to fungicides and sexually recombine with African lineages. Genomic surveillance is urgently needed to track and mitigate the spread of wheat blast and guide breeding for resistant varieties.
Article
Microbiology
Ursula Oggenfuss, Daniel Croll
Summary: Transposable elements (TEs) are engines of evolution and have important impacts on pathogen evolution. We analyzed numerous high-quality genomes of a fungal wheat pathogen species and found that the reactivation and activity of TEs were primarily driven by specific factors such as proximity to genes.
Article
Microbiology
Reda Amezrou, Colette Audeon, Jerome Compain, Sandrine Gelisse, Aurelie Ducasse, Cyrille Saintenac, Nicolas C. Lapalu, Clementine Louet, Simon H. Orford, Daniel Croll, Joelle H. Amselem, Sabine Fillinger, Thierry H. Marcel
Summary: This study identified a specific protein AvrStb9 in the fungal pathogen Zymoseptoria tritici, which causes a major disease in wheat. AvrStb9 interacts with the wheat resistance gene Stb9, triggering an immune response. The AvrStb9 protein is highly conserved in the Ascomycota class and may be a core effector. Multiple amino acid substitutions in AvrStb9 are conserved in global Z. tritici populations, suggesting strong positive diversifying selection for escaping host recognition. These findings contribute to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.
Article
Microbiology
Hadjer Bellah, Nicolas F. F. Seiler, Daniel Croll
Summary: Plant diseases can be aggravated by co-infections of multiple pathogens. The outcome of mixed infections by different genotypes of the same pathogen species is poorly understood. In this study, we investigated the interactions among 14 genetically diverse strains of the wheat pathogen Zymoseptoria tritici. We found that co-cultured strains and co-infected plant leaves showed complex competitive outcomes, indicating that strain competition dynamics are influenced by the host immune system.
MICROBIOLOGY SPECTRUM
(2023)
Review
Genetics & Heredity
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, Jose A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklos Balint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Hoglund
Summary: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts. Reference genomes play a key role in facilitating biodiversity research and conservation. Integrating the use of reference genomes as a best practice in conservation genomics is essential.
TRENDS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Artemis D. Treindl, Jessica Stapley, Daniel Croll, Adrian Leuchtmann
Summary: Antagonistic selection between pathogens and hosts drives evolutionary change and leaves molecular footprints in genomes. This study provides insights into complex adaptive processes in natural plant pathogen systems.