@phdthesis{Terhoeven2020,
  author    = {Terhoeven, Niklas},
  title     = {Genomics of carnivorous Droseraceae and Transcriptomics of Tobacco pollination as case studies for neofunctionalisation of plant defence mechanisms},
  doi       = {10.25972/OPUS-18971},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189712},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {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.},
  subject      = {Droseraceae},
  language  = {en}
}
@misc{TortMitrevaBrehmetal.2020,
  author    = {Tort, Jose F. and Mitreva, Makedonka and Brehm, Klaus R. and Rinaldi, Gabriel},
  title     = {Editorial: Novel Frontiers in Helminth Genomics},
  series = {Frontiers in Genetics},
  volume    = {11},
  journal   = {Frontiers in Genetics},
  number    = {791},
  issn      = {1664-8021},
  doi       = {10.3389/fgene.2020.00791},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210209},
  year      = {2020},
  abstract  = {No abstract available.},
  language  = {en}
}
@article{EskenGorisGadkarietal.2020,
  author    = {Esken, Jens and Goris, Tobias and Gadkari, Jennifer and Bischler, Thorsten and F{\"o}rstner, Konrad U. and Sharma, Cynthia M. and Diekert, Gabriele and Schubert, Torsten},
  title     = {Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies},
  series = {MicrobiologyOpen},
  volume    = {9},
  journal   = {MicrobiologyOpen},
  number    = {12},
  doi       = {10.1002/mbo3.1138},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-225754},
  year      = {2020},
  abstract  = {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.},
  language  = {en}
}