I have all my agrobacterium tumefaciens strains sequenced using nanopore-sequencing technology. And use canu and nanopolish to assemble my genomes. However, when I try to orientate genome make it start with either dnaA (circlular chromosome) or repA (plasmids) by blast against dnaA and repA download from NCBI, I noticed it is very often to have more than one ori on plasmids.
Can any one have any explanation for this?
Great appreciate in advance.
Hi Limin,
Yes, plasmids can have multiple origins! Usually the ones we use in the lab only have one because it makes it easier to handle (smaller plasmids = easier). But natural plasmids can have multiple origins that can increase host range/copy number/change regulation. See below for two papers on it (the one by pagotto et al. has some good references for other papers too):
Initiation of DNA replication in ColE1 plasmids containing multiple potential origins of replication. Martin-Parras et al. 1992. J. Biol. Chem.
Multiple Origins and Replication Proteins Influence Biological Properties of β-Lactamase-Producing Plasmids from Neisseria gonorrhoeae. Pagotto et al. 2001. J. Bacteriol.
Hope this helps!
Andrew
If your strain is recombination proficient, many plasmids might exist in dimer, trimer, tetramer forms etc. Or this could be an artifact of your genome assembly software as well.
Thank you so much for both of you, Dr. Andrew and Dr. Michael. both your answers are so helpful.
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