Věda, výzkum, biologie

Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored.

Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events.

Praktický kurz fylogenomických metod se zaměřením na NGS metodu Hyb-Seq. Metoda Hyb-Seq kombinuje cílené obohacení a tzv. mělké sekvenování genomu. V rámci kurzu budou probrány základy i nejnovějších poznatky v oblasti Hyb-Seq (návrh sond, laboratorní postup, analýza dat). Součástí kurzu je i práce s daty a jejich praktické analýzy různými přístupy, od primárních dat po konstrukci evolučních stromů koalescenčními a dalšími metodami. V laboratorní části kurzu budou připravovány a obohacovány NGS knihovny s využitím sonikátoru.

Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges.

Although whole-genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.

Praktický kurz fylogenomických metod se zaměřením na NGS metodu Hyb-Seq. Metoda Hyb-Seq kombinuje cílené obohacení a tzv. mělké sekvenování genomu. V rámci kurzu budou probrány základy i nejnovějších poznatky v oblasti Hyb-Seq (návrh sond, laboratorní postup, analýza dat). Součástí kurzu je i práce s daty a jejich praktické analýzy různými přístupy, od primárních dat po konstrukci evolučních stromů koalescenčními a dalšími metodami. V laboratorní části kurzu budou připravovány a obohacovány NGS knihovny s využitím sonikátoru.

On the basis of new gatherings at the type locality, Taraxacum primigenium was evaluated taxonomically. Its achenes differ substantially from the protologue description that is based on achenes of T. assemanii. Taraxacum primigenium, also on the basis of an nrDNA analysis, is close to T. sect. Piesis, and represents a narrow endemic confined to the Lalezar Mts., SE Iran. Taraxacum assemanii, newly typified, is known from mountains of SE Anatolia and Lebanon, and from the Zagros in SW Iran.

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome.

Taraxacum mirabile Wagenitz (Asteraceae, Cichorieae, Crepidinae), a remarkable but taxonomically unexplored endemic species of Central Anatolia, is examined in detail. It is shown to be a sexually reproducing diploid (2n=16) species. It used to be included in Taraxacum sect. Orientalia in the literature. However, the nrDNA analysis revealed that T. mirabile is remote from that section.

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.