Please use this identifier to cite or link to this item: http://hdl.handle.net/1946/4630
Draft genome assembly of lichenized Nostoc from Peltigera membranacea
Lichens are a combination of a fungus and a photosynthetic partner in a symbosis. In the case of Peltigera membranacea the photosynthetic partner is a cyanobacterium.
This thesis is about an approach to assemble the Nostoc genome of the lichen species Peltigera membranacea based on parallel sequencing (454, Solexa and etc.) of an uncultured sample.
A contig is a continuous sequence of nucleotides bases A,C,G,T assembled from overlapping DNA fragments. If the contigs are sorted in a descending size order and we sum up to the half of the total length of the contigs, the length of the last contig at half of the total length is the N-50 contig size.
We had disappointing results with the initial assembly using all the 454-data with the proprietary assembly program Newbler. The number of contigs was high and the N-50 contig size was low, compared to the amount of sequencing.
The solution we found was to sort the 454-reads and Newbler contigs using Blast with known Nostoc genomes, then assemble the sorted reads using Mira. This is a novel method since we are assembling multiple genomes without separating individual species before sequencing.