You have shotgun sequenced four related termite gut samples and obtained a total of 40 Gbp of sequence data (10 Gbp per sample). You perform a de novo assembly of the data and wish to extract (bin) individual population genomes from the metagenome.
(a) Describe TWO (2) binning approaches that you could apply to the data to obtain population genomes including any known limitations of the approaches. (6 MARKS)
(b) A member of candidate phylum ZB3 is present in the termite gut community at an estimated relative abundance of 0.5%. Assuming that its genome size is 2 Mbp, calculate its expected genome coverage in the metagenomic assembly (show your working). Is this coverage likely to yield a good or poor assembly of the ZB3 population genome (assuming no strain heterogeneity)?
You have shotgun sequenced four related termite gut samples and obtained a total of 40 Gbp of sequence data (10 Gbp per sample). You perform a de novo assembly of the data and wish to extract (bin) individual population genomes from the metagenome.
(a) Describe TWO (2) binning approaches that you could apply to the data to obtain population genomes including any known limitations of the approaches. (6 MARKS)
(b) A member of candidate phylum ZB3 is present in the termite gut community at an estimated relative abundance of 0.5%. Assuming that its genome size is 2 Mbp, calculate its expected genome coverage in the metagenomic assembly (show your working). Is this coverage likely to yield a good or poor assembly of the ZB3 population genome (assuming no strain heterogeneity)?
