A5016440829- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Mitochondrial Function and Pathology
- Fungal and yeast genetics research
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- Plant Pathogens and Fungal Diseases
- Marine Ecology and Invasive Species
- RNA modifications and cancer
- Marine Biology and Ecology Research
- Plant-Microbe Interactions and Immunity
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- RNA Research and Splicing
- Algal biology and biofuel production
- Marine Invertebrate Physiology and Ecology
- Genetics, Bioinformatics, and Biomedical Research
- Mass Spectrometry Techniques and Applications
- Bacterial Genetics and Biotechnology
- Identification and Quantification in Food
- Trypanosoma species research and implications
- Fungal Biology and Applications
Université de Montréal
2016-2025
Leiden University
2023
Jean Mayer Human Nutrition Research Center on Aging
2018
University of Miami
2018
Taylor's University
2018
Tufts University
2018
Département de Chimie Moléculaire
2013
Institut thématique Génétique, génomique et bioinformatique
2010-2013
Czech Academy of Sciences, Biology Centre
2010
Czech Academy of Sciences, Institute of Molecular Genetics
2010
Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with overall mortality rate that exceeds 50%. As a representative paraphyletic basal group fungal kingdom called "zygomycetes," R. also used as model to study evolution. Here we report genome sequence strain 99-880, isolated from fatal case mucormycosis. The highly repetitive 45.3 Mb assembly contains abundant transposable elements (TEs), comprising...
The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to evolution algae and plants. We analyzed draft genome transcriptome data from basally diverging alga Cyanophora paradoxa provide evidence for a single eukaryote supergroup Plantae. C. retains ancestral features starch biosynthesis, fermentation, protein translocation common plants but lacks typical eukaryotic light-harvesting complex proteins. Traces an ancient link parasites such as Chlamydiae...
The most bacteria-like mitochondrial genome known is that of the jakobid flagellate Reclinomonas americana NZ. This also encodes largest gene set among DNAs (mtDNAs), including RNA subunit RNase P (transfer processing), a reduced form transfer–messenger (translational control), and four-subunit polymerase, which in other eukaryotes substituted by nucleus-encoded, single-subunit, phage-like enzyme. Further, protein-coding genes are preceded potential Shine–Dalgarno translation initiation...
Abstract Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span diversity of eukaryotic tree life. However, genetic tractability has been limited to a few species, which do not represent or environmentally relevant taxa. Here, we report on development tools range protists primarily from marine environments. We present evidence for foreign DNA delivery and expression 13 species never before transformed advancement eight other as...
Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes their structure can be challenging time-consuming. Even automated tools genome annotation often require manual analysis curation by skilled experts. The most difficult steps (i) the structural modelling of intron-containing genes; (ii) identification delineation Group I II introns; (iii) moderately conserved, non-coding RNA (ncRNA) specifying 5S...
The evolution of multicellular animals (Metazoa) from their unicellular ancestors was a key transition that accompanied by the emergence and diversification gene families associated with multicellularity. To clarify timing order specific events in this transition, we conducted expressed sequence tag surveys on 4 putative protistan relatives Metazoa including choanoflagellate Monosiga ovata, ichthyosporeans Sphaeroforma arctica Amoebidium parasiticum, amoeba Capsaspora owczarzaki, 2 members...
According to the chromalveolate hypothesis (Cavalier-Smith T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, sporozoan plastid origins eukaryote family tree. J Eukaryot Microbiol 46:347–366), four eukaryotic groups with chlorophyll c–containing plastids originate from a single photosynthetic ancestor, which acquired its by endosymbiosis red alga. So far, molecular phylogenies have failed either support or disprove this view. Here, we...
Animal mtDNAs are typically small (≈16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes also present in the closest unicellular relatives of animals, i.e., choanoflagellate and ichthyosporean protists. We find gene content architecture Monosiga brevicollis , Amoebidium parasiticum Metazoa radically different from one another. The mtDNA with its long intergenic regions is four times as large...
Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches a given against one or more databases, arduous for large datasets. Results We present AutoFACT, fully automated and customizable annotation tool that assigns biologically informative functions sequence. Key features this are it (1) analyzes nucleotide protein data; (2) determines the most functional description by combining...
5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene easily identified in archaeal, bacterial nuclear genome sequences. However, organelle homologs (rrn5) appear to be absent from most mitochondrial several chloroplast genomes. Here, we re-examine distribution rrn5 by building mitochondrion- plastid-specific covariance models (CMs) with which screened We not only recover all genes annotated GenBank records, but also identify more than 50 previously...
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset 200 single-copy conserved genes employed strategies reduce compositional Such include using novel dataset-specific profile mixture models recoding schemes, removing sites, taxa that are compositionally biased. We show the Rickettsiales Holosporales (both groups intracellular...
The mitochondrial DNA (mtDNA) of Porphyra purpurea, a circular-mapping genome 36,753 bp, has been completely sequenced. A total 57 densely packed genes identified, including the basic set typically found in animals and fungi, as well seven characteristic protist plant mtDNAs specifying ribosomal proteins subunits succinate:ubiquinone oxido-reductase. large subunit rRNA gene contains two group II introns that are extraordinarily similar to those cyanobacterium Calothrix sp, suggesting recent...