Research   Theses  CV  Publications  Presentations  help    to staff list 

Research Interests:

• Analysis and annotation of ESTs
• Next-generation sequencing technologies
• De novo transcriptome assembly
• Mapping of Illumina reads
• Phylogenetic analysis


Current Research (PhD Thesis):

Most of the Chrysomelina species are highly specialized in their feeding habit, and host plant shifts of larvae play a crucial role in the evolution of leaf beetle’s chemical defense. The defensive chemistry of those chrysomelid larvae is still not known in detail. Therefore, in my research I focus on the annotation of putative proteins involved in the transport mechanisms of plant glycosides.
Several cDNA libraries have been created: 454 sequences of Phaedon cochleariae, Illumina sequences of P. cochleariae (cDNA pool, glandular cDNA, cDNA of antennae), and Illumina sequences of Chrysomela populi (cDNA pool, cDNA of gut, hemolymph, glands and malpighian tubules). The (paired-end) sequences have been de novo assembled by applying various assembler tools.The assembled transcripts have been annotated using several methods, such as BLAST against Tribolium castaneum, the red flour beetle, and PfamScan, and Blast2GO.
Furthermore, the short tissue specific Illumina reads have been mapped onto the corresponding transcriptome by applying Bowtie. Thereafter, the differential expression as well as abundancy of transcripts is identified by using DESeq (Bioconductor package, R statistics).
To get deeper insights, the sugar transporter transcripts of P. cochleariae (containing sugar_tr domain), especially those highly abundant in glandular tissue, have been chosen to study substrate specificity, phylogeny, and RNAi experiments.
last updated on 2013-04-05