Does whole genome sequencing capture plasmids?

Question

[robjohn70000]

Hi,

Just a question about a confusing concept. Does whole genome sequencing of bacteria mean sequencing the entire genome content i.e., chromosome and the plasmids (if present)?

Thanks

[Zev.Kronenberg]

Welcome to biostars. I modified the question title to be slightly more specific.

[robjohn70000]

Thanks Zev

Answer 1

[iraun]

I would say that yes, the reads obtained after the whole genome sequencing of a given bacteria, will include sequences derived from all the DNA present in the sequenced sample, including chromosome(s) and plasmids. Doing downstream analysis like an assembly of the reads... etc, you could be able to distinguish genomic DNA from plasmid DNA somehow.

[robjohn70000]

Thanks airan. How can one distinguish between the two molecules in the sequence assembly reads?

[iraun]

Well, it's not easy. You can read this thread to have some ideas: Distinguishing Bacterial And Plasmid Genomes. They mention cBar program, I've never use it so I can tell you nothing else :).

[robjohn70000]

Many thanks airan. Just wondering if blasting the contigs against the NCBI plasmid (ftp://ftp.ncbi.nih.gov/genomes/Plasmids/), then locate the plasmids and remove their sequences from contigs might be logical.

Answer 2

[Zev.Kronenberg]

Yes. Unless you specifically capture or degrade certain molecules all DNA is sequenced.

In Eukaryotes, whole genome sequencing includes the mitochondria.

[robjohn70000]

Thanks Zev. Mitochondria is another thing that I always wondered if its included in the Eukaryotic genome sequence.

Answer 3

[Prasad]

Yes, whole genome sequencing includes the plasmid and mitochondria. plasmidSPAdes assembles plasmids from whole genome sequences.