A5086184788- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Computational Geometry and Mesh Generation
- Protist diversity and phylogeny
- Plant Virus Research Studies
- Advanced Graph Theory Research
- Multimedia Communication and Technology
- Advanced Numerical Analysis Techniques
- Telecommunications and Broadcasting Technologies
- Image and Video Quality Assessment
- RNA and protein synthesis mechanisms
- Digital Image Processing Techniques
- Genetic diversity and population structure
- Marine and coastal ecosystems
- Microbial Natural Products and Biosynthesis
- Wastewater Treatment and Nitrogen Removal
- Glycosylation and Glycoproteins Research
- Algorithms and Data Compression
- Plant Pathogens and Fungal Diseases
- 3D Shape Modeling and Analysis
- 3D Modeling in Geospatial Applications
- Chromosomal and Genetic Variations
- Fungal Biology and Applications
- Aquatic Ecosystems and Phytoplankton Dynamics
University of Groningen
2021-2025
Massachusetts Institute of Technology
2016-2024
Alvernia University
2022
Wellesley College
2022
University of Washington
2022
University of Würzburg
2012-2021
Max Planck Institute for Medical Research
2016-2021
Vassar College
2018
Institute of Software
2004-2016
Graz University of Technology
2005-2015
Today, the base code of DNA is mostly determined through sequencing by synthesis as provided Illumina sequencers. Although highly accurate, resulting reads are short, making their analyses challenging. Recently, a new technology, single molecule real-time (SMRT) sequencing, was developed that could address these challenges, it generates several thousand bases. But, broad application has been hampered high error rate. Therefore, hybrid approaches use high-quality short to correct erroneous...
Recent advances in understanding the ecology of marine systems have been greatly facilitated by growing availability metagenomic data, which provide information on identity, diversity and functional potential microbial community a particular place time. Here we present dataset comprising over 5 terabases data from 610 samples spanning diverse regions Atlantic Pacific Oceans. One set metagenomes, collected GEOTRACES cruises, captures large geographic transects at multiple depths per station....
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that no longer functional considered to be "genomic fossils." Genomic surveys EVEs, however, strongly biased toward animals plants, whereas protists, represent the majority eukaryotic diversity, remain poorly represented. Here, we show protist harbor tens thousands diverse, ~14 40 kbp long dsDNA viruses. These composed virophages, Polinton-like viruses, related...
Marine sponges are ancient metazoans that populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read PacBio long-read sequencing followed un-targeted metagenomic binning. We identified a total 37 high-quality bins representing 11 bacterial phyla two candidate phyla. Statistical comparison symbiont genomes with selected reference revealed...
Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with diverse microbial community that coexists them. Comparative genomics cultivated isolates has helped address questions regarding patterns evolution diversity among microbes, but can be is miniscule compared to wild. To further probe these groups extend utility reference sequence databases, we report data set single...
Most plants grow and develop by taking up nutrients from the soil while continuously under threat foraging animals. Carnivorous have turned tables capturing consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand evolution of botanical carnivory, we compared draft genome Venus flytrap (Dionaea muscipula) with that its aquatic sister, waterwheel plant Aldrovanda vesiculosa, sundew Drosera spatulata. We identified an early whole-genome...
Significance Phosphonates are a class of phosphorus metabolites characterized by highly stable C-P bond. accumulate to high concentrations in seawater, fuel large fraction marine methane production, and serve as source microbes inhabiting nutrient-limited regions the oligotrophic ocean. Here, we show that 15% all bacterioplankton surface ocean have genes phosphonate synthesis most belong abundant groups Prochlorococcus SAR11. Genomic chemical evidence suggests phosphonates incorporated into...
Virophages are small dsDNA viruses that hijack the machinery of giant during co-infection a protist (i.e., microeukaryotic) host and represent an exceptional case “hyperparasitism” in viral world. While only handful virophages have been isolated, vast diversity virophage-like sequences uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection replication strategy, ability to integrate into virus genomes potential role antiviral defense made topic broad...
Abstract Background Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild isolate that identified as Anthostomella pinea . The fungus belongs complex polyphyletic genus family Xylariaceae , which is known comprise endophytic pathogenic produce plethora interesting secondary metabolites. Despite that, largely...
Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent fossils, whereas others still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes lytic giant CroV. We hypothesized endogenous virophages may act as an antiviral defense system protists, but no protective effect of wild host populations has been shown so far. Here, we tested...
Whole genome alignments and comparative analysis are key methods in the quest of unraveling dynamics evolution. Interactive visualization exploration generated alignments, annotations, phylogenetic data important steps interpretation initial results. Limitations existing software inspired us to develop our new tool AliTV, which provides interactive whole alignments. AliTV reads multiple or automatically generates from provided data. Optional feature annotations phylo- genetic information...
Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into nuclear genome of marine flagellate Cafeteria burkhardae reactivates upon superinfection with CroV. In natural systems, however, prevalence diversity host-virophage associations has not been systematically explored. Here, we report dozens integrated virophages four globally sampled C. strains that...
Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in oceans. Gene content variation among picocyanobacterial populations separate ocean basins often mirrors selective pressures imposed by region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across global ocean, we show that capacity for siderophore-mediated iron uptake is widespread low-light adapted deep chlorophyll maximum layers of iron-depleted regions...
ABSTRACT Endogenous viral elements (EVEs) are fragments of genomic material embedded within the host genome. Retroviruses contribute to majority EVEs because their integration during life cycle; however, latter can also arise from non‐retroviral RNA or DNA viruses, then collectively known as (nr) EVEs. Detecting nrEVEs poses challenges sequence and structural diversity, contributing scarcity specific tools designed for detection. Here, we introduce detectEVE , a user‐friendly open‐source...
Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, agents, phage satellites). The information enclosed these structures represents a substantial portion HGT potential available planktonic ecosystems, but whether some genes might be preferentially transported one type nanoparticle versus another unknown. Here we use...
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable sequence, it confined this to low-level phylogenetics only. However, combination of sequence and its highly conserved secondary structure improves resolution(1) allows inference at multiple taxonomic ranks, including species delimitation(2-8). Database(9) presents an exhaustive dataset sequences from NCBI GenBank(11) accurately...
Abstract Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are most abundant photosynthetic organisms on earth, spanning vast regions oceans contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology evolution. Although many cyanophage genomes have been sequenced, insight into functional role genes is limited by lack a genetic engineering system. Here, we describe simple, generalizable method for...
The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface exposed to oxygen. Concrete biodeterioration and steel corrosion have been linked growth of iron- manganese-oxidizing biofilms areas saline water seepage. Surprisingly, previous 16S rRNA gene surveys biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed identify genomes metabolic potential for novel...
Abstract Long-read sequencing technologies hold big promises for the genomic analysis of complex samples such as microbial communities. Yet, despite improving accuracy, basic gene prediction on long-read data is still often impaired by frameshifts resulting from small indels. Consensus polishing using either complementary short reads or to a lesser extent long themselves can mitigate this effect but requires universally high depth, which difficult achieve in where majority community members...
Marine picocyanobacteria Prochlorococcus and Synechococcus, the most abundant photosynthetic cells in oceans, are generally thought to have a primarily single-celled free-living lifestyle. However, while studying ability of supplement carbon fixation with use exogenous organic carbon, we found widespread occurrence genes for breaking down chitin, an source that exists as particles. We show encode chitin degradation pathway display activity, attach particles, enhanced growth under low light...