Niklas Terhoeven

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Terhoeven

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Niklas

ORCID

0000-0002-8669-0000

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Publications 1 - 7 of 7

The bilaterian roots of cordon-bleu
Schultz, Jörg; Terhoeven, Niklas (2013)
BMC Research Notes
Background The actin cytoskeleton is essential for many physiological processes of eukaryotic cells. The emergence of new actin fibers is initiated by actin nucleators. Whereas most of them are evolutionary old, the cordon-bleu actin nucleator is classified as vertebrate specific. Findings Using sensitive methods for sequence similarity detection, we identified homologs of cordon-bleu not only in non-vertebrate chordates but also in arthropods, molluscs, annelids and platyhelminthes. These genes contain only a single WH2 domain and therefore resemble more the vertebrate cordon-bleu related 1 protein than the three WH2 domain containing cordon-bleu. Furthermore, we identified a homolog of the N-terminal, ubiquitin like, cobl domain of cordon-bleu in the cnidarian Nematostella vectensis. Conclusion Our results suggest that the ur-form of the cordon-bleu protein family evolved already with the emergence of the bilateria by the combination of existing cobl and WH2 domains. Following a vertebrate specific gene-duplication, one copy gained two additional WH2 domains leading to the actin nucleating cordon-bleu. The function of the ur-form of the cordon-bleu protein family is so far unknown. The identification of a homolog in the model organism Drosophila melanogaster could facilitate its experimental characterization.
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
Ankenbrand, Markus J.; Terhoeven, Niklas; Hohlfeld, Sonja; et al. (2017)
F1000Research
The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component.
Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory
Palfalvi, Gergo; Hackl, Thomas; Terhoeven, Niklas; et al. (2020)
Current Biology
Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.
Continuation of embryo development during diapause in the roe deer (Capreolus capreolus)
Rüegg, Anna B.; Terhoeven, Niklas; van der Weijden, Vera; et al. (2022)
Conference Handbook BSDB/BSCB Spring Meeting
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
Terhoeven, Niklas; Schultz, Jörg; Hackl, Thomas (2018)
Journal of Open Source Software
chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data
Ankenbrand, Markus J.; Pfaff, Simon; Terhoeven, Niklas; et al. (2018)
Journal of Open Source Software
A systematic comparison of chloroplast genome assembly tools
Freudenthal, Jan A; Pfaff, Simon; Terhoeven, Niklas; et al. (2020)
Genome Biology
Background Chloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information. Plastid genomes accommodate essential genes and are regularly utilized in biotechnology or phylogenetics. Different assemblers that are able to assess the plastid genome have been developed. These assemblers often use data of whole genome sequencing experiments, which usually contain reads from the complete chloroplast genome. Results The performance of different assembly tools has never been systematically compared. Here, we present a benchmark of seven chloroplast assembly tools, capable of succeeding in more than 60% of known real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements. The examination of 105 data sets from species with unknown plastid genomes leads to the assembly of 20 novel chloroplast genomes. Conclusions We create docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow the analysis and screening of data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts within genomic sequencing data is feasible.

Publications 1 - 7 of 7

Niklas Terhoeven

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