how to define open-pangenome?

Question

[Kumar]

I have done pan-genome analysis using roary pipeline and I determined that my bacterial genome datasets posses open-pangenome based on roary pipeline generated pan-genome progress plot (No. of genes in the pan−genome plot). Is it enough evidence to conform the open pan-genome or do we need to do any calculation for conforming the open-pangenome? Please guide me in this regard.

Thanks in advance.

Answer 1

[Nelly]

Hello Kumar

To decide that a set has an open pangenome the alpha parameter of the Heap law should be less or equal to one. It is important to remark that this curve adjustment is not absolute, tha pangenome cang change when you add more genomes. You can find this definition here -> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418249/