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Bioinformatics

By vojta , 5 August 2024

Deciphering Pteronia's evolution in the Cape Floristic Region: A comprehensive study disputes polyploid deficiency and affirms diploid radiation

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
HybSeq
Faculty of Science, Charles University
Science, research, biology
By vojta , 13 May 2024

Target enrichment in taxonomy, HybSeq course 2024

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 17 October 2023

Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates

The first species-level phylogeny of the Sabulina verna group is presented. Genetic clusters are congruent with geography and mostly supported by morphological traits. Metalliferous and serpentine soils were colonized multiple times independently.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
Population genetics
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 4 August 2023

Ancient hybridization in Curcuma (Zingiberaceae)—Accelerator or brake in lineage diversifications?

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.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
HybSeq
Faculty of Science, Charles University
Science, research, biology
By vojta , 21 June 2023

Phylogenetic challenges in a recently diversified and polyploid-rich Alyssum (Brassicaceae) lineage: low divergence, reticulation, and parallel polyploid speciation

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.

Články
Arabidopsis and Brassicaceae
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
HybSeq
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 29 May 2023

Target enrichment in taxonomy, HybSeq course 2023

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 12 October 2022

The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae)

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.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
HybSeq
Science, research, biology
By vojta , 12 October 2022

The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution

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.

Články
Arabidopsis and Brassicaceae
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeography
Population genetics
Faculty of Science, Charles University
Science, research, biology
By vojta , 3 June 2022

Target enrichment for plant systematics - HybSeq course 2022

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 11 January 2022

Virtual machine for my courses

For my courses ofwork in Linux command line not only for MetaCentrum and with molecular data in R I provide VirtualBox image, which allows to run complete desktop Linux (in this case openSUSE Leap) with all preinstalled applications needed for both courses. It's easy way how to get fully working Linux to play with. It requires at least bit powerful notebook, e.g. at least quad-core with at least 8 GB RAM, but more is better.

Články
Bioinformatics
Linux (and another software)
openSUSE
Faculty of Science, Charles University
Teaching

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KDE - K Desktop Environment

openSUSE GNU/Linux

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