Premise: Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited... Show morePremise: Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae.Methods: To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae‐specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low‐copy nuclear genes using both supermatrix and species coalescence methods.Results: Our analyses resulted in a well‐resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes.Conclusions: This study presents the first broadly sampled, well‐resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system. Show less
PREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate... Show morePREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort.METHODS AND RESULTS: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24–31%) and Brassicaceae (35–59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%).CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole. Show less
Summary of the Thesis: Vegetables have always been considered as healthy food. So also Brassica vegetables are well known all over the world as a common food due to the presence of health affecting... Show moreSummary of the Thesis: Vegetables have always been considered as healthy food. So also Brassica vegetables are well known all over the world as a common food due to the presence of health affecting compounds (Chapter 2). A vast amount of data is available for health promoting compounds in Brassicaceae vegetables. These health promoting affects are due to a range of phytochemicals including primary (carbohydrates, amino acids and organic acid) and secondary metabolites (phenolics and glucosinolates), along with vitamins and minerals. These metabolites are interconnected through different biosynthetic pathways and are affected by different external stimuli. Plant metabolic responses are specific for different kinds of stress, but use in part similar metabolic pathways (Chapter 3). Certain internal or external factors play an important role for the metabolite profile of vegetables, thus changing the nutritional value for human (Chapter 4). These factors are related to the plant response to external stress factors and helping the plant to survive. These factors includes bacteria (Chapter 5), metals ions ( Chapter 6) and post harvest storage conditions (Chapter 7). The aim of this thesis was to study the Brassica phytochemicals and their response to stress factors by using a holistic analytical approach. Show less
