TY - GEN A1 - Tort, Jose F. A1 - Mitreva, Makedonka A1 - Brehm, Klaus R. A1 - Rinaldi, Gabriel T1 - Editorial: Novel Frontiers in Helminth Genomics T2 - Frontiers in Genetics N2 - No abstract available. KW - flatworm KW - nematodes KW - genomics KW - helminths KW - neglected diseases Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-210209 SN - 1664-8021 VL - 11 IS - 791 ER - TY - THES A1 - Terhoeven, Niklas T1 - Genomics of carnivorous Droseraceae and Transcriptomics of Tobacco pollination as case studies for neofunctionalisation of plant defence mechanisms T1 - Genomik karnivorer Droseraceae und Transkriptomik der Befruchtung von Tabak als Fallstudien zur Umfunktionierung pflanzlicher Verteidigungsmechanismen N2 - Plants have evolved many mechanisms to defend against herbivores and pathogens. In many cases, these mechanisms took other duties. One example of such a neofunction- alisation would be carnivory. Carnivory evolved from the defence against herbivores. Instead of repelling the predator with a bitter taste, the plant kills it and absorbs its nutrients. A second example can be found in the pollination process. Many of the genes involved here were originally part of defence mechanisms against pathogens. In this thesis, I study these two examples on a genomic and transcriptomic level. The first project, Genomics of carnivorous Droseraceae, aims at obtaining annotated genome sequences of three carnivorous plants. I assembled the genome of Aldrovanda vesiculosa, annotated those of A. vesiculosa, Drosera spatulata and Dionaea muscipula and com- pared their genomic contents. Because of the high repetitiveness of the D. muscipula genome, I also developed reper, an assembly free method for detection, classification and quantification of repeats. With that method, we were able to study the repeats without the need of incorporating them into a genome assembly. The second large project investigates the role of DEFL (defensin-like) genes in pollen tube guidance in tobacco flowers. We sequenced the transcriptome of the SR1 strain in different stages of the pollination process. I assembled and annotated the transcriptome and searched for differentially expressed genes. We also used a method based on Hidden- Markov-Models (HMM) to find DEFLs, which I then analysed regarding their expression during the different stages of fertilisation. In total, this thesis results in annotated genome assemblies of three carnivorous Droser- aceae, which are used as a foundation for various analyses investigating the roots of car- nivory, insights into the role of DEFLs on a transcriptomic level in tobacco pollination and a new method for repeat identification in complex genomes. N2 - Im Laufe der Evolution haben Pflanzen viele Methoden entwickelt, um sich gegen Fress- feinde und Pathogene zu verteidgen. Viele dieser Methoden wurden im Laufe der Zeit umfunktioniert. Ein Beispiel hierfür ist die Karnivorie, welche aus der Verteidigung ge- gen Fressfeinde entstanden ist. Anstelle einen Angreifer durch bitteren Geschmack zu vertreiben, tötet die Pflanze das Tier und nimmt seine Nährstoffe auf. Ein weiteres Bei- spiel ist der Bestäubungs- und Befruchtungsprozess. Viele der Gene, die hier involviert sind, stammen ursprünglich aus Mechanismen zur Verteidigung gegen Pathogene. In dieser Arbeit untersuche ich diese beiden Beispiele auf genomischer und transkrip- tomischer Ebene. Die Zielsetzung des ersten Projekts, Genomik von karnivoren Dro- seraceaen, ist es, assemblierte und annotierte Genome von drei karnivoren Pflanzen zu generieren. Ich habe dazu das Genom von Aldrovanda vesiculosa assembliert und dieses, sowie die Genome von Drosera spatulata und Dionaea muscipula annotiert und mit- einander verglichen. Aufgrund des hohen Anteils repetitiver Elemente im D. muscipula Genom habe ich reper, eine Methode zum Detektieren, Klassifizieren und Quantifizieren von Repeats, entwickelt. Mit dieser Methode ist es nun möglich, repetitive Elemente zu untersuchen, ohne diese in einem Genomassembly integrieren zu müssen. Das zweite große Projekt untersucht die Rolle von DEFL (defensin-like) Genen im Pollenschlauchwachstum in Tabakblüten. Dazu haben wir das Transkriptom der SR1 Variante zu verschiedenen Zeitpunkten im Befruchtungsprozess sequenziert. Ich habe dieses Transkriptom assembliert und annotiert und darin nach differentiell exprimierten Genen gesucht. Zudem haben wir mit einer auf Hidden Markov Modellen (HMM) ba- sierten Methode nach DEFL Genen gesucht und ich habe die Expression dieser in den verschiedenen Stadien untersucht. Zusammenfassend beinhalten die Ergebnisse dieser Thesis annotierte Genomassemb- lies von drei karnivoren Droseraceaen, Erkenntnisse über die Rolle von DEFL Genen bei der Befruchtung auf einer transkriptomischen Ebene und eine neue Software zur Analyse von repetitiven Elementen in komplexen Genomen. KW - Droseraceae KW - Genom KW - Nicotiana tabacum KW - Transkriptomanalyse KW - Repeats KW - genomics KW - carnivorous plants KW - next generation sequencing Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189712 ER - TY - JOUR A1 - Esken, Jens A1 - Goris, Tobias A1 - Gadkari, Jennifer A1 - Bischler, Thorsten A1 - Förstner, Konrad U. A1 - Sharma, Cynthia M. A1 - Diekert, Gabriele A1 - Schubert, Torsten T1 - Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two‐component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies JF - MicrobiologyOpen N2 - Energy conservation via organohalide respiration (OHR) in dehalogenating Sulfurospirillum species is an inducible process. However, the gene products involved in tetrachloroethene (PCE) sensing and signal transduction have not been unambiguously identified. Here, genome sequencing of Sulfurospirillum strains defective in PCE respiration and comparative genomics, which included the PCE‐respiring representatives of the genus, uncovered the genetic inactivation of a two‐component system (TCS) in the OHR gene region of the natural mutants. The assumption that the TCS gene products serve as a PCE sensor that initiates gene transcription was supported by the constitutive low‐level expression of the TCS operon in fumarate‐adapted cells of Sulfurospirillum multivorans. Via RNA sequencing, eight transcriptional units were identified in the OHR gene region, which includes the TCS operon, the PCE reductive dehalogenase operon, the gene cluster for norcobamide biosynthesis, and putative accessory genes with unknown functions. The OmpR‐family response regulator (RR) encoded in the TCS operon was functionally characterized by promoter‐binding assays. The RR bound a cis‐regulatory element that contained a consensus sequence of a direct repeat (CTATW) separated by 17 bp. Its location either overlapping the −35 box or 50 bp further upstream indicated different regulatory mechanisms. Sequence variations in the regulator binding sites identified in the OHR gene region were in accordance with differences in the transcript levels of the respective gene clusters forming the PCE regulon. The results indicate the presence of a fine‐tuned regulatory network controlling PCE metabolism in dehalogenating Sulfurospirillum species, a group of metabolically versatile organohalide‐respiring bacteria. KW - genomics KW - organohalide respiration KW - RNA sequencing KW - tetrachloroethene KW - transcriptomics KW - two‐component system Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-225754 VL - 9 IS - 12 ER -