TY  - JOUR
A1  - Bemm, Felix
A1  - Becker, Dirk
A1  - Larisch, Christina
A1  - Kreuzer, Ines
A1  - Escalante-Perez, Maria
A1  - Schulze, Waltraud X.
A1  - Ankenbrand, Markus
A1  - Van de Weyer, Anna-Lena
A1  - Krol, Elzbieta
A1  - Al-Rasheid, Khaled A.
A1  - Mithöfer, Axel
A1  - Weber, Andreas P.
A1  - Schultz, Jörg
A1  - Hedrich, Rainer
T1  - Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
JF  - Genome Research
N2  - Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.
KW  - Dionaea-muscipula ellis
KW  - Plant utricularia-gibba
KW  - Programmed cell-death
KW  - Genomics data sets
KW  - RNA-SEQ data
KW  - Arabidopsis-thaliana
KW  - Jasmonate perception
KW  - Action potentials
KW  - Stress responses
KW  - Wonderful plants
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188799
VL  - 26
IS  - 6
ER  - 
TY  - JOUR
A1  - Schwarz, Roland F.
A1  - Tamuri, Asif U.
A1  - Kultys, Marek
A1  - King, James
A1  - Godwin, James
A1  - Florescu, Ana M.
A1  - Schultz, Jörg
A1  - Goldman, Nick
T1  - ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
JF  - Nucleic Acids Research
N2  - Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).
KW  - visualization
KW  - multiple sequence alignments
KW  - phylogenetic trees
KW  - Alvis
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166374
VL  - 44
IS  - 8
ER  -