Plasmids part of core genome

[Mona]

Hi,

I am trying to compare the core genome of 7 different species bacteria. One of them also contains plasmid sequences. Should I keep the plasmid sequence also in the analysis or not?

[westerman]

One way of looking at this is that 6 of your 7 species do not have plasmid information so how could you do the comparison even if you wanted to do so? In general I would consider the term "core genome" to not include non-chromosomal elements such as plasmids.

[Mona]

One way of looking at this is that 6 of your 7 species do not have plasmid information so how could you do the comparison even if you wanted to do so? In general I would consider the term "core genome" to not include non-chromosomal elements such as plasmids.

Thanks westerman,
Thats quite logical But isn't it possible that plasmids having chromosal genes?