Application of RAD-seq in Evolutionary Genomics of Non-Model Organisms

Next generation sequencing (NGS) technologies are revolutionizing how we study genetics and evolution in the modern world. Data is generated at such a fast pace that scientists are struggling to keep up with the innovations in methodology and analytical tools. Genomes are being sequenced at an unprecedented rate, and scientists in fields that until recently found no use in learning molecular techniques are venturing into the world of high-throughput sequencing. Almost 10 years ago, a research group developed Restriction-site Associated DNA Sequencing (RAD-seq), a method that targets polymorphisms in close proximity to restriction cut sites in hundreds of samples simultaneously. The beauty of RAD-seq lies in that it is highly customizable and it does not require a reference genome, or intimate prior knowledge of the genetics of the study organism one would like to use. The most exciting part about new RAD-seq methods being developed is that their accessibility has opened the door to many non-model organisms to be used in new areas of research. The overarching theme of my dissertation is the application of RAD-seq data to answer questions in evolutionary, quantitative, or population genetics and genomics using non-model species. A secondary goal is the development of genomic resources for non-model organisms. In Chapter 1, I studied the genetics of a recent shift from self-incompatibility to self-compatibility in an insular lineage of Tolpis, with an aim to identify putative genomic regions responsible for this shift in mating system. To do that, I assembled a draft genome, annotated it, and used RAD-seq data from a mapping population to discover variants. In my second chapter, I focus on a pyralid moth and the genetic basis of male song characters that are attractive to females. For that purpose, I again used RAD-seq data from hundreds of individuals, and, additionally, I assembled and annotated a genome for this non-model organism. In my last chapter, I focused on the bioinformatic challenges associated with RAD-seq data. I explored the question of whether or not using a genome sequence helps in the construction of loci from RAD-seq reads. The evaluation of the last question is on a fairly basic level but it opens up future avenues that I am excited to explore

Role of salicylic acid in acclimation to low temperature

Low temperature is one of the most important limiting factors for plant growth throughout the world. Exposure to low temperature may cause various phenotypic and physiological symptoms, and may result in oxidative stress, leading to loss of membrane integrity and to the impairment of photosynthesis and general metabolic processes. Salicylic acid (SA),phenolic compound produced by a wide range of plant species, a may participate in many physiological and metabolic reactions in plants. It has been shown that exogenous SA may provide protection against low temperature injury in various plant species, while various stress factors may also modify the synthesis and metabolism of SA. In the present review, recent results on the effects of SA and related compounds in processes leading to acclimation to low temperatures will be discussed

Interaction of Temperature and Light in the Development of Freezing Tolerance in Plants

Abstract Freezing tolerance is the result of a wide range of physical and biochemical processes, such as the induction of antifreeze proteins, changes in membrane composition, the accumulation of osmoprotectants, and changes in the redox status, which allow plants to function at low temperatures. Even in frost-tolerant species, a certain period of growth at low but nonfreezing temperatures, known as frost or cold hardening, is required for the development of a high level of frost hardiness. It has long been known that frost hardening at low temperature under low light intensity is much less effective than under normal light conditions; it has also been shown that elevated light intensity at normal temperatures may partly replace the cold-hardening period. Earlier results indicated that cold acclimation reflects a response to a chloroplastic redox signal while the effects of excitation pressure extend beyond photosynthetic acclimation, influencing plant morphology and the expression of certain nuclear genes involved in cold acclimation. Recent results have shown that not only are parameters closely linked to the photosynthetic electron transport processes affected by light during hardening at low temperature, but light may also have an influence on the expression level of several other cold-related genes; several cold-acclimation processes can function efficiently only in the presence of light. The present review provides an overview of mechanisms that may explain how light improves the freezing tolerance of plants during the cold-hardening period

Staff Adaptation in Selected Company

The main aim of the master's thesis is to evaluate the staff adaptation management system in the company Personal Partner s. r. o. Various techniques for data collection have been used in the preparation of the thesis. The theoretical part of the work represents a review, based on topic-specific and professional literature, which covers the necessary terminology and the specifics of human resources management and employee adaptation. The analytical part of the thesis makes use of descriptive analysis for the purposes of company characterisation. It further focuses on staff fluctuation in the company in the years 2012 - 2015. The analytical part aims at evaluating the current state of the staff adaptation management system and has been carried out on the basis of a questionnaire survey and an interview with a human resources employee. The questionnaire survey presented the opportunity to assess the situation from the staff's viewpoint, while the interview with the human resources specialist helped describe the system's operation from the employer's perspective. The final chapter of the thesis consists of recommendations for improvement of the stability of the company's human resources

Differentially methylated region-representational difference analysis (DMR-RDA): a powerful method to identify DMRs in uncharacterized genomes

Over the last years, it has become increasingly clear that environmental influences can affect the epigenomic landscape and that some epigenetic variants can have heritable, phenotypic effects. While there are a variety of methods to perform genome-wide analyses of DNA methylation in model organisms, this is still a challenging task for non-model organisms without a reference genome. Differentially methylated region-representational difference analysis (DMR-RDA) is a sensitive and powerful PCR-based technique that isolates DNA fragments that are differentially methylated between two otherwise identical genomes. The technique does not require special equipment and is independent of prior knowledge about the genome. It is even applicable to genomes that have high complexity and a large size, being the method of choice for the analysis of plant non-model systems