Kirov, Ilya Dudnikov, Maxim Merkulov, Pavel Shingaliev, Andrey Omarov, Murad Kolganova, Elizaveta Sigaeva, Alexandra Karlov, Gennady Soloviev, Alexander
Published in
Plants (Basel, Switzerland)
The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered "junk", DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RN...
Höijer, Ida Johansson, Josefin Gudmundsson, Sanna Chin, Chen-Shan Bunikis, Ignas Häggqvist, Susana Emmanouilidou, Anastasia Wilbe, Maria den Hoed, Marcel Bondeson, Marie-Louise
...
Published in
Genome Biology
BackgroundOne ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMRT-OTS and Nano-OTS, two novel, amplification-free, long-read sequencing protocols for detection of gRNA-driven...
Dhorne-Pollet, Sophie Barrey, Eric Pollet, Nicolas
Published in
BMC Genomics
BackgroundMitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonucleas...
Hennion, Magali Arbona, Jean-Michel Lacroix, Laurent Cruaud, Corinne Theulot, Bertrand Tallec, Benoît Le Proux, Florence Wu, Xia Novikova, Elizaveta Engelen, Stefan
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Published in
Genome Biology
Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,...
Xie, Yichun Zhong, Yiyi Chang, Jinhui Kwan, Hoi Shan
Published in
Fungal genetics and biology : FG & B
The homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks. The mutations in mating type factors A and B result in the special feature of clamp formation and fr...
Rugbjerg, Peter Dyerberg, Anne Sofie Brask Quainoo, Scott Munck, Christian Sommer, Morten Otto Alexander
Published in
Metabolic engineering
Reprogramming organisms for large-scale bioproduction counters their evolutionary objectives of fast growth and often leads to mutational collapse of the engineered production pathways during cultivation. Yet, the mutational susceptibility of academic and industrial Escherichia coli bioproduction host strains are poorly understood. In this study, w...
Vereecke, Nick Bokma, Jade Haesebrouck, Freddy Nauwynck, Hans Boyen, Filip Pardon, Bart Theuns, Sebastiaan
Published in
BMC Bioinformatics
BackgroundImplementation of Third-Generation Sequencing approaches for Whole Genome Sequencing (WGS) all-in-one diagnostics in human and veterinary medicine, requires the rapid and accurate generation of consensus genomes. Over the last years, Oxford Nanopore Technologies (ONT) released various new devices (e.g. the Flongle R9.4.1 flow cell) and bi...
Lipworth, Samuel Pickford, Hayleah Sanderson, Nicholas Chau, Kevin K. Kavanagh, James Barker, Leanne Vaughan, Alison Swann, Jeremy Andersson, Monique Jeffery, Katie
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Published in
Microbial Genomics
Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The widespread application of this technique is curren...
Henrich, Birgit Hammerlage, Stephanie Scharf, Sebastian Haberhausen, Diana Fürnkranz, Ursula Köhrer, Karl Peitzmann, Lena Fiori, Pier Luigi Spergser, Joachim Pfeffer, Klaus
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Published in
Mobile DNA
BackgroundMobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a minimal set of genes, seem to accumulate mobile genetic elements. In Mycoplasma hominis, a facultative pathogen of the human urogen...
Ip, Jonathan Daniel Kok, Kin-Hang Chan, Wan-Mui Chu, Allen Wing-Ho Wu, Wai-Lan Yip, Cyril Chik-Yan To, Wing-Kin Tsang, Owen Tak-Yin Leung, Wai-Shing Chik, Thomas Shiu-Hong
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Published in
Clinical Microbiology and Infection
Objectives SARS-CoV-2 has evolved rapidly into several genetic clusters. However, data on mutations during the course of infection are scarce. This study aims to determine viral genome diversity in serial samples of COVID-19 patients. Methods Targeted deep sequencing of the spike gene was performed on serial respiratory specimens from COVID-19 pati...
