A5026480633- Protist diversity and phylogeny
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Parasitic Infections and Diagnostics
- Marine Sponges and Natural Products
- Environmental DNA in Biodiversity Studies
- Parasite Biology and Host Interactions
- Insect symbiosis and bacterial influences
- Marine and coastal plant biology
- Insect and Arachnid Ecology and Behavior
- Plant and animal studies
- Marine Ecology and Invasive Species
- Aquaculture disease management and microbiota
- Legume Nitrogen Fixing Symbiosis
- Amoebic Infections and Treatments
- Microbial infections and disease research
- Evolution and Paleontology Studies
- Botanical Research and Applications
- Bacteriophages and microbial interactions
- Genetic diversity and population structure
- SARS-CoV-2 detection and testing
- Geomagnetism and Paleomagnetism Studies
- Myxozoan Parasites in Aquatic Species
- Microbial Fuel Cells and Bioremediation
- Cancer Research and Treatments
University of South Bohemia in České Budějovice
2020-2025
Czech Academy of Sciences, Biology Centre
2017-2025
Institute of Parasitology
2017-2025
Czech Academy of Sciences
2018-2024
Biomedical Research Center of the Slovak Academy of Sciences
2024
University of British Columbia
2014-2023
Dalhousie University
2007-2018
Canadian Institute for Advanced Research
2009-2016
Charles University
2005
Abstract This revision of the classification eukaryotes follows that Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved resolution many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling intervening years has massively increased genetic information at hand. Consequently, discovered novel clades, exciting new genera uncovered a massive species level...
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites humans and animals with immense socio-economic health impacts. We sequenced nuclear genomes Chromera velia Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways the endomembrane trafficking systems associated a lifestyle have been progressively non-randomly lost during adaptation parasitism. ancestor contained...
Apicomplexans are a major lineage of parasites, including causative agents malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which have complex metabolic dependency. Here, we examine the origin apicomplexan parasitism by resolving evolutionary distribution several key characteristics in their closest relatives, photosynthetic chromerids predatory colpodellids....
the origin of echolocation and flight in bats. Nature 403:188– 192. van Rheede, T., T. Bastiaans, D. N. Boone, S. B. Hedges, W. de Jong, O. Madsen. 2006. The platypus its place: nuclear genes indels confirm sister group relation monotremes therians. Mol. Biol. Evol. 23:587–597. Waddell, P. J., H. Kishino, R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141– 154. Okada, M. Hasegawa. 1999. Towards resolving interordinal relationships placental...
Blastocystis is the most prevalent eukaryotic microbe colonizing human gut, infecting approximately 1 billion individuals worldwide. Although has been linked to intestinal disorders, its pathogenicity remains controversial because carriers are asymptomatic. Here, genome sequence of subtype (ST) presented and compared previously published sequences for ST4 ST7. Despite a conserved core genes, there unexpected diversity between these STs in terms their sizes, guanine-cytosine (GC) content,...
Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages their distribution. However, the value these data is critically dependent on quality reference databases used to assign an identity environmental sequences. Existing contain errors struggle keep pace with rapidly changing eukaryotic taxonomy, influx novel diversity, computational challenges related assembling high-quality alignments trees needed for...
Phylogenomic analyses of hundreds protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are publicly available high-quality curated databases designed deep (>100 million years) in the tree eukaryotes. To address these issues, we developed an easy-to-use package,...
Abstract Apicomplexans and related lineages comprise many obligate symbionts of animals; some which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here, we sought reconstruct the evolution cryptic plastids in apicomplexans, chrompodellids, squirmids (ACS clade) by generating five new single-cell transcriptomes understudied gregarine...
Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution these two eukaryotic assemblages have yet be fully elucidated, P. may a key lineage in tracing those groups' evolution. In present study, we analyzed 'phylogenomic' alignment 157 genes clarify phylogeny. 157-gene phylogeny, was found basal clade cryptophytes,...
Blastocystis sp. is a common intestinal protist colonising the human intestine prevalence of which varies across non-industrialized and industrialized countries. Its role in gut ecosystem remains unclear due to persisting gaps knowledge epidemiology factors affecting colonization. Here, we aimed expand gut-healthy humans one European countries, including distribution its subtypes, correlation between occurrence several such as lifestyle, contact with animals, age sex. A total 288 stool...
Discoveries of diverse microbial eukaryotes and their inclusion in comprehensive phylogenomic analyses have crucially re-shaped the eukaryotic tree life 21st century.1Burki F. Roger A.J. Brown M.W. Simpson A.G.B. The New Tree Eukaryotes.Trends Ecol. Evol. 2020; 35: 43-55Abstract Full Text PDF PubMed Scopus (216) Google Scholar At deepest level, diversity comprises 9–10 "supergroups." One these supergroups, Metamonada, is particularly important to our understanding evolutionary dynamics...
Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including devastating human pathogens Plasmodium falciparum Cryptosporidium hominis. In contrast, data on invertebrate-infecting gregarines remains sparse their evolutionary relationship to other apicomplexans obscure. Most retain highly modified plastid, while mitochondria remain metabolically conserved. spp. inhabit an anaerobic host-gut...
Abstract PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets consist protein sequences from eukaryotic organisms. Unlike many existing pipelines, comes with manually curated database 240 protein‐coding genes, subset previous phylogenetic dataset sampled 304 taxa. The also utilize user‐created proteins, which may more appropriate shallow evolutionary questions. equipped set utilities to aid...
While we know much about the evolutionary patterns of endosymbiotic organelle origins, less how actual process unfolded within each system. This is partly due to massive changes endosymbiosis appears trigger, and because most organelles evolved in distant past. The dinotoms are dinoflagellates with diatom endosymbionts, they represent a relatively recent but nevertheless obligate association. We have carried out deep sequencing both host endosymbiont transcriptomes from two dinotoms,...