A5007863793- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Insect symbiosis and bacterial influences
- Plant and animal studies
- RNA and protein synthesis mechanisms
- Marine and coastal ecosystems
- Health Sciences Research and Education
- Academic Writing and Publishing
University of British Columbia
2016-2022
Canadian Institute for Advanced Research
2016
Abstract Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken nonfunctional gene fragments can quickly accumulate form a substantial fraction of the genome. Identification these genes, called pseudogenes, is critical step for understanding evolutionary forces acting upon, potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an...
Ciliates comprise a diverse and ecologically important phylum of unicellular protists. One the most specious best-defined genera is Euplotes, which constitutes more than 70 morphospecies, many have never been molecularly tested. The increasing number described Euplotes taxa emphasizes importance for detailed characterizations new ones, requiring standardized morphological observations, sequencing molecular markers careful comparison with previous literature. Here we describe curdsi sp. nov.,...
High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort manually screen available small subunit (SSU) rRNA gene sequences and produce public, high-quality informative framework of phylogeny-based taxonomic annotations. In context EukRef, we present database for monophyletic phylum Ciliophora, one complex,...
Abstract Environmental sequences have become a major source of information. High‐throughput sequencing ( HTS ) surveys been used to infer biogeographic patterns and distribution broad taxa protists. This approach is, however, more questionable for addressing low‐rank (less inclusive) such as species genera, because the increased chance errors in identification due blurry taxonomic boundaries, low sequence divergence, or errors. The specious ciliate genus Euplotes partially escapes these...
Abstract Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts extreme population bottlenecks (such those experienced by symbionts pathogens), pseudogenes can quickly accumulate form a substantial fraction the genome. Identification is, thus, critical step for understanding evolutionary forces acting upon, functional potential encoded within,...