Reticulate or divergent evolution? Resolving processes behind the high species richness and endemism in Brassicaceae genera
APVV-21-0044, 2022-2026, principal investigator: Karol Marhold
Reticulate evolution is a challenging research topic, which has gained increased attention in recent years, stimulated by the progress made in genomic research and developments of new scientific techniques and approaches. It is now widely recognized that introgression and hybridization significantly affect plant evolution, but there is still much to discover and understand about these processes and their impact on diversification and speciation. The project focuses on reticulate evolution in four genera of the Brassicaceae family (Alyssum, Cardamine, Erysimum, and Odontarrhena). Here we aim to explore in detail how reticulation events have shaped the evolution of the studied genera, to test whether the high endemism rate reflects multiple independent polyploidization events or increased diversification of polyploid lineages. We will also examine how historical and recent range shifts have stimulated introgression and allopolyploid speciation, and track the mode and rate of allopolyploid genome evolution. We will take an integrative approach that will combine methods of phylogenomics (RADseq and HybSeq techniques of next generation sequencing, complemented by microsatellite markers), cytogenomics, flow cytometry, morphometrics and ecological niche modeling. Bringing together data from diverse sources provides complementary views and different perspectives on the patterns and processes studied. Our studies, focusing on several unrelated species groups, will also include a comparative aspect, go beyond species- or genus-specific patterns, and attempt to infer common and general mechanisms of reticulate evolution in plants.
Integrative Bioinformatics Analysis of Next Generation Sequencing Data for Advanced Plant Research
Recovery and Resilience Plan for Slovakia, Fellowships for excellent researchers R2-R4
09I03-03-V04-00494, 2024-2026,to: Marek Šlenker
The rapid progress in botany, particularly in the area of plant phylogeny and the investigation of the origin of polyploid species, can undoubtedly be attributed to the widespread application of new generation sequencing methods (NGS) in recent years and concurrent development of bioinformatics tools designed to process such data. While these methods are generally universal and broadly applicable, there is an increasing recognition of the need for customized approaches that consider the unique characteristics of the plant species under study. This project’s primary objective is to provide innovative, custom tailored bioinformatics solutions for the analysis of NGS data, obtaining answers to specific scientific questions. The developed scripts and tools will be made openly available, facilitating their use by other researchers in their studies and allowing for potential modifications to ensure further development.
Uncovering cryptic diversity and evolution in polyploid species complexes
Recovery and Resilience Plan for Slovakia, Fellowships for excellent researchers R2-R4
09I03-03-V04-00489, 2024-2026,to: Judita Zozomová
It is well known that the world’s biodiversity is greatly underestimated, and, surprisingly, this is also true for the flora of Europe. Many species with wide ranges in ecologically heterogeneous environments rarely represent a single species, but form complexes of cryptic or just understudied species. The present project focuses on uncovering and understanding evolutionary processes in such plant species complexes with expected cryptic diversity, particularly those with a high incidence of polyploids and suspected reticulate events both in the past and in recent times. The project takes an integrative, multi-method and interdisciplinary approach, which combines different theories and methods, employs state-of-the-art phylogenomic and cytogenomic techniques, and bioinformatic algorithms and tools. The project will significantly enhance and expand the scientific work, scope, and topics addressed by the researcher, enable the establishment of a new research team, and through international collaboration also promote, advance and diversify the research directions of the host organization.
Beyond the visible: Uncovering hidden diversity and recent speciation with phylogenomics
VEGA 2/0010/25, 2025-2028, principal investigator: Judita Zozomová
The project aims at exploring the evolution of recently diverged and species-rich plant groups, which are characterized by extensive but poorly structured variation, ambiguous species delimitation, complicated reticulate and polyploid evolutionary history, and may also include cryptic diversity. We will take a phylogenomic approach and apply two efficient next-generation sequencing methods that allow us to generate and process data from hundreds to thousands of loci in the genome of a large number of individuals. Two cruciferous genera, Odontarrhena and Erysimum, will be used as model objects to uncover common evolutionary drivers characteristic of such groups, as well as unique and rare processes that may contribute to the broad range of factors shaping the diversity and evolution of recently diverged genera. The project has the potential to improve our assessment of true species diversity in Europe and contribute significantly to a better understanding of evolutionary processes in plants.
Tracing the effects of whole-genome multiplication on clonal reproduction in plants: from genes to distributional patterns
GAČR 24-12318S, 2024-2026, principal investigator: Patrik Mráz (Department of Botany, Charles University, Prague), participant from CBRB SAS: Barbora Šingliarová
Our principal objective is to determine the consequences of whole genome multiplication on multiple phenotypic, phytohormonal and genomic traits that alter the reproduction strategies of autopolyploids and determine their evolutionary success.
Neopolyploids originating via whole genome multiplication within one species – autopolyploids – suffer from reduced fitness compared to diploid ancestors due to disturbed meiosis and the negative effect of majority-minority cytotype interaction. Enhanced clonal reproduction might promote the successful establishment of neopolyploids. However, it is unknown if the increased clonal growth is directly caused by polyploidization, what are its underlying genetic and physiological factors, and finally what is the ecological impact of such reproduction shift between closely related cytotypes. We will investigate these questions in the diploidautopolyploid Pilosella rhodopea model by combining observational, experimental, anatomical, biochemical phytohormones) and molecular (microsatellites, transcriptomics) approaches. Our results will provide an integrative insight into the role of autopolyploidization in the formation of new reproductive traits which determine the evolution of neopolyploids.