How complete do microbial genomes have to be for metabolic predictions (to be useful)?
In this day an age of rapid shotgun sequencing of genomes, many people are moving away from finishing the genomes. As some may know, I was a co-author many years ago on a paper arguing for the need to finish (rather than just shotgun sequence) microbial genomes for many scientific questions. But as sequencing costs continued to plummet, the relative cost of shotgun sequencing genomes kept going down while the cost of finishing genomes did not change much. So. two years ago I posted to my blog a question regarding this: "Wanted:Feedback on Importance of Finishing (Microbial) Genomes" and got a lot of useful feedback. And eventually, I came around to the argument that finishing was unnecessary for many purposes (and even got some props for admitting I was wrong).
Well, I am back. Now I am arguing to some colleagues that if we want to make metabolic pathway predictions and metabolic models for genomes, we probably don't need finished genomes. But alas, I have no evidence to back that up. And in fact, I am not really sure anyway. So I am asking everyone and anyone out there ... does anyone have data/evidence/opinions about whether there will be much difference in metabolic predictions one would make for an organism based upon a complete genome vs. a shotgun assembly of a genome generated by Illumina sequencing?
Storification of some comments: