Hi,
I am running PlasmidFinder on fasta files containing assembled contigs. The results seem to indicate the presence of two replicons in the same contig even if I am not completely sure of how to interpret the results.I attached a screenshot. In my opinion, the first and the third hit could be different replicons on the same contig (so same plasmid??)..Is it possible to have multiple replicons on the same plasmid in Gram negative bacteria?However the two hits refer to two different plasmids, IncFII(K) and IncFIB(K). I am a little bit confused..If the replicons are on the same plasmid, shouldn't I find the same plasmid for the two hits?
Thank you very much,
Silvia
Dear Silvia,
Some plasmids have more than one replicon. This is common in plasmids of the incompatibility group F (IncF). In your file the FII and FIB replicons are in the same contig (NODE 11), so the most likely is that your strain has two plasmids, one multireplicon plasmid (FII-FIB) and another IncQ plasmid. Submit your data to the pMLST of incF plasmids in CGE, so you will have the FAB formula of this plasmid.
Kind regards,
Marcos
Thank you for your answer.I was also wondering if It is possible PlasmidFinder does not identify some plasmids. For example, I expect the presence of another resistance plasmid in my strain but I can't find it with Plasmid Finder..To what could this be due?Could this also be due to some parts missing in the sequence of the contig?
Thanks again
Hi Silvia - The other thing to be aware of is that if there are any regions on the two plasmids that have sequence identity, ie they both carry the same resistance gene or the same IS element, and if that region of identify is longer than your sequence reads, the contig assignment may not be correct (or there might have been recombination between the regions).
Dear Silvia Caprari ,
Your research is rather interesting. I kindly invite you to cooperation and send your articles by e-mail [email protected] to our “Biotechnologia Acta” journal. Our site is www.biotechnology.kiev.ua . Publication in our journal is free of charge and it is indexed in 16 data bases of 9 countries.
I look forward to hearing from you.
Sincerely yours
Alyona Vinogradova,
executive editor of Biotechnologia Acta.
- Badges
- Science topic