PRF

Written by Marek Kincl on 17 March 2023. Posted in PRF.

Deciphering complex reticulation in aquatic plants: what is the relationship among climate oscillations, hybridization and polyploidization?

Principle investigator: Zdeněk Kaplan (BÚ AVČR, Průhonice)
Co-investigator from the department: Petr Koutecký
Funding provider: the Grant Agency of the Czech Republic
Grant No.: 22-10464S
Duration: 2022- 2024

Aquatic plants show specific biological characteristics fundamentally affecting their genetic variation and evolution. In spite of this, they are largely ignored by evolutionary biology. The project aims at disentangling the pathways of reticulate evolution in Ranunculus sect. Batrachium (Water Crowfoots) as a model group of aquatic plants that is distinguished by enormous levels of polyploidy and hybridization. Using a holistic approach integrating cytogenetic methods, up-to-date DNA sequencing approaches and cutting-edge bioinformatics tools we will unravel the evolutionary history of this
group and reconstruct the genomic constitutions of allopolyploids. We will identify main evolutionary drivers that shaped this diversity as well as the role of the Quaternary climatic oscillations for triggering speciation processes in aquatics. Conclusions will supplement existing knowledge conducted on terrestrial plants and thus shed a new perspective on evolution of plants in general.

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Written by Marek Kincl on 17 March 2023. Posted in PRF.

Applications of species composition analysis of diatom (Bacillariophyceae) communities in forensic practice

Principle investigator: Jan Kaštovský
Funding provider: Ministry of the Interior - OPSEC
Grant No.: OPSEC VK01010069
Duration: 2023- 2025

Diatoms are widespread microscopic algae with specific frustules. Inhalation of water with diatoms causes them to pass into the bloodstream and deposit their frustules in the internal organs. Their presence reveals the fact of drowning in natural water, and the analysis of the species composition can also help to reveal the exact place where the drowning occurred. Similar analysis can be carried out on the clothing and skin of drowned persons. Diatom analysis (and analysis of other algae) is used in the Czech Republic and abroad in forensic practice, but only to a limited extent and does not exploit the full potential of these organisms. The main goal of the project is to design, test and implement new methods of sample treatment and species analysis of diatom communities ( or also communities of other algae).

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Written by Marek Kincl on 17 March 2023. Posted in PRF.

Consolidating cyanobacterial systematics through harmonization of polyphasic and genomic taxonomy

Principle investigator: Jan Mareš (HBÚ BC)
Co-investigator from the department: Jeffrey R. Johansen
Funding provider: the Grant Agency of the Czech Republic
Grant No.: 22-06374S
Duration: 2022- 2024

Since 2000, criteria for recognition of cyanobacterial taxa utilizing the polyphasic approach have
been developed. Due to the slow pace of phylum-wide revision, genome taxonomy approaches
have been introduced to avoid a taxonomic bottleneck in metagenomic studies. Genome
taxonomy has not been integrated into the existing taxonomy, which has caused substantial
confusion between the fields. We will compare these approaches by collecting complementary
data within the model group, Synechococcales, the best studied group in terms of both
genomes assembled and recent polyphasic taxonomic effort. Direct comparison will allow us to
integrate both approaches, evaluate taxonomic boundaries, and derive taxonomic concepts for
cyanobacteria that will satisfy and be workable for all researchers.
Aims of the project:
1) To assemble a set of strains characterized by polyphasic data and whole genome sequence
2) To assess taxonomic boundaries among species, genera, families, and orders by both
approaches
3) To propose a unified concept, based in phylogenomics but compatible with existing
taxonomy and nomenclature

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Written by Marek Kincl on 14 March 2023. Posted in PRF.