When whole genome sequencing is done for eukaryotes, how is the DNA from bacteria that must inevitably be mixed with the whole DNA extract accounted for? Is it possible to remove the bacterial DNA before the whole genome sequencing is done, or is it removed bioinformatically, after the sequencing is done? Some details would be much appreciated. Thanks.
It's typically done bioinformatically afterwards. Most folks use a reference genome and reads that don't map aren't included in the final assembly. You can also parse them bioinformatically by abundance and GC content.
Hi,
I am afraid that selective isolation of unknown bacterial total DNA from a sample that contain 99.99% of plant DNA is impossible even in theory. You can try to cultivate your endophytes on variety of different media before the DNA extraction, or amplify a number of conservative regions of bacterial genome, but, do remember that chloroplast and mitochondrial DNA of plants are highly similar to genomes of endophytes or obligate parasites of plants..
Article Extraction of DNA from plant and fungus tissues in situ
It might be done with a number of bioinformatic techniques. The problem is that none of them guarantee the total purification. Good start is a clustering with K-means of triplet dictionaries of contigs: bacteral ones clearly seen in separate cluster. Again, the problem is that this cluster a) also contain some "host" contigs, and b) some bacterial contigs still deteriorate the "host" body. GC-content is less reliable approach.
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