HybSeq

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.

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.

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.

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.

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.

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.

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.

Intensive 4-days (5^th day is not compulsory, but is open for any discussion, if there would be interest) course to learn all theory about HybSeq and practically learn how to analyze HybSeq data, how to solve all problems, and how to evaluate differences among gene trees. Important part is enough time to discuss everything, including practical problems and projects of individual participants.

Poster presented at Botany 2018 conference of the Botanical Society of America titled Hunting the treasure of Cape Oxalis diversity (Zeisek, Oberlander, Dreyer, Schmickl, Schneeweiss):