Are you interested in putting genomes together and discovering what they do?
Next-generation sequencing has enabled the rapid expansion of genome sequencing for thousands of ecologically and economically important organisms. Our group has recently sequenced the genome of four plant-pathogenic Botryosphaeria spp. using next generation sequencing (NGS). NGS methods, generally, do not remove mitochondria from the cells before sequencing; therefore, contained within the reads is the DNA sequence of both the nuclear and mitochondrial genomes. It is believed that mitochondria originated after endosymbiosis of a bacterial ancestor with early eukaryotes. Since that time the evolution of mitochondrial genomes is marked by extensive gene loss and translocation of genes to the nuclear genome. Most importantly however, mitochondrial genomes still carry genes encoding for both the large and small ribosomal subunits and genes for the respiratory chain complexes. Mitochondria are essential for energy production in all eukaryotic cells.
The aims of this project are to use bioinformatics tools to separate the mitochondrial and nuclear sequence reads, assemble and fully annotate the mitochondrial genome of four closely related plant pathogenic species. This project will involve a wide range of bioinformatics tools, including genome assembly, annotation and graphical representation. Students should expect no wet-lab work but instead heavy exposure to quality control of NGS data, de novo assembly tools and ab initio genome annotation.