This is one of the most recent papers about constructing a minimal genome. It goes in depth on how minimal genomes are created (see figure attached), and it also brings up important problems associated with this project. One problem that I thought was interesting was that although they are creating the minimal genome for Mycoplasmas,the genes associated with this cell are not necessarily universally essential.
Yes, the Mycoplasma minimal genome might not reveal a universal minimal genome, and will likely uncover genes that are essential for Mycoplasma but not other organisms. I'm sure though that important pieces of information will still be discovered. As the article also points out, there may be no such entity as a universal minimal genome anyway.
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