I am surprised to see this query, as I have the similar doubt for a short while! But, I suggest you to read more reviews where we can try ourself to find a difference. Good luck!

We can exchange reviews we have. I send tomorrow the most relevant I have read.

Srinivasan, you have an expert on the topic just close to you: David Ussery - Technical University of Denmark. I will not doubt to contact him and have a short conversation if possible.

Here are some reviews:

Comparative genomics: the bacterial pan-genome_Tettelin 2008

Ten years of pan-genome analyses: Tettelin_2015

The microbial pan-genome: Medini_2005

Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt_Ozer_2014.

Let me know if that helps.

 Loubna and  Srinivasan,

You have asked (realized) a very important question! 

First, we need to define the concept of “genome”.  Genome is not just about the DNA sequences.

Then we need to realize that there is no “fixed genome” for most species with asexual reproduction, as the sexual reproduction serves as a “filter” to purify and maintain the core genome.

Please find two pieces from our group that address this issue.

The genome-centric concept: resynthesis of evolutionary theory.

Heng HH.  Bioessays. 2009 May;31(5):512-25.

Decoding the genome beyond sequencing: the new phase of genomic research.

Heng HH, Liu G, Stevens JB, Bremer SW, Ye KJ, Abdallah BY, Horne SD, Ye CJ.

Genomics. 2011 Oct;98(4):242-52.

Let me know your thoughts.

Thanks.