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Old 06-19-2013, 02:41 AM   #1
Inma
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Default :confused: Integrated plasmid

Hi all,

We think that a genome we sequenced recently has a integrated plasmid. We have found plasmid related proteins within the annotation, and related species have one or more of this elements. However, experimental assays show that there aren't extrachromosomal elements so we think it could be integrated.
How can we know if there are an integrated plasmid? There are any bioinformatic procedure to elucidate that or give some clues?

Thank you very much!!!

Inma
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Old 07-15-2013, 03:47 AM   #2
Inma
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Hi all,

I am going to explain my question in another way. How do you know if there are an integrated plasmid within the sequenced genome?
We have found tra genes and others related to plasmid conjugation, however, the assembly doesn't reveal extrachromosomal plasmid presence.

Thank you in advance!!

Inma
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Old 07-15-2013, 05:04 AM   #3
rhinoceros
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1. Integrated plasmids are very common
2. If it's in the middle of your scaffold/contig, would it not mean that it's integrated?
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Old 07-15-2013, 06:25 AM   #4
Inma
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Hello Rhinoceros,

Yes. It will probably be integrated, but the question is how I can find it within the genome.

Thanks!

Inma
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Old 07-15-2013, 09:37 AM   #5
swbarnes2
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I think in order to prove that its integrated, you will have to find either paired ends where one read is in the plasmid, and the other is in genomic, or read that cross the junction, so are half plasmid, and half host genome.

For the first, the .bam entry for each read will helpfully tell you where its mate aligned, so look for entries where one end aligns to plasmid and the other aligns to genome.

For the second, it might be best to figure out exactly what the plasmid sequence flanking the junction should look like, and the search your fastq for reads which have that sequence, and then you can see what host sequences follow it.
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Old 07-15-2013, 10:46 AM   #6
dpryan
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You could also just run a Southern blot, particularly if you don't particularly care about the exact integration location.
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