Dear all,

I assembled MiSeq reads using SPAdes. The sample is an endosymbiont bacteria.

I found a long contig, almost 100 Kb, good coverage. At first, I thought it was part of my target bacteria chromosome. However, when I make PCR primers connecting the contig at each ends, it generate a single band in gel electrophoresis. I sequenced the band, and it does connect the two ends. It seems it is a circular plasmid.

So,

the problem is, when I annotated the contig in RAST, the result shows me that all of the ORFs are hypothetical protein. I could not find any repA (I annotated 5 other plasmids, and all of them have it) or any predicted gene in the contig.

Now I am in doubt. It is a plasmid, or anything else? circular DNA from temperate phage?

Any suggestion will be very helpful. Thank you.