Nils Koppers
A genomic perspective on the evolution of C4 photosynthesis in Brassicaceae
C4 photosynthesis is a carbon fixation pathway developed independently by more than 60 different angiosperm lineages. C4 plants are able to fix carbon more efficiently in hot and dry environments in comparison to plants with the more common C3 photosynthesis. Climatic change and a decrease in atmospheric CO2 level were postulated to be the initiators for the convergent evolution from C3 to C4 photosynthesis. That most likely did not occur in one single step. The current model of C4 evolution hypothesizes several intermediate C3-C4 states on the way from a C3 to a C4 plant.
Previous computational approaches studied the evolution of C4 photosynthesis primarily on the level of gene expression, missing possible changes on the genomic level. De novo whole-genome assemblies of plants with large genomes and high amount of repetitive genome content based on short read sequencing data result in heavily fragmented assemblies with a considerable amount of gaps. The recently developed ‘single molecule real time sequencing technologies’ produce significantly longer reads, thus making it possible to assemble highly contiguous and accurate genomes.
We want to study the evolution of C4 photosynthesis in this project, by assembly and annotation of different genomes of C3 and C3-C4 Brassicaceae species as well as a C3/C3-C4 crossbreed. Once, a final genome assembly for all species is available, a comparative genomics approach will elucidate, whether positive selection of genomic traits and and changes in the genomic structure were required to evolve the C3-C4 pathway.
Starting date: 02.02.2016 / PhD student
Thesis committee members: Andreas Weber,
Mini Academic CV:
- 2016: Master of Science in Molecular Biology, specialization Bioinformatics, Westphalian University of Applied Sciences, Recklinghausen
- Thesis: "De Novo genome assembly of Azolla filiculosis"
- 2013: Bachelor of Science in Molecular Biology, Westphalian University of Applied Sciences, Recklinghausen
- Thesis: “Computational search for variations in the transcriptome"