Re: ? the average % of genes that plants share with animals?

How similar are the genes of plants and animals?

This is a tough question to answer, because when we ask "how many genes are conserved between animals and plants?", we have to also specify "how well conserved?". Plants and animals have lots of genes coding for proteins with similar functions – cytochromes that carry electrons in the mitochondria, DNA polymerases (as you suggest), etc. To compare the whole genomes, though, it's necessary to use some process of computer alignment and comparison of similar sequences.

The National Center for Biotechnology Information has a lot of resources for searching known genes for similarities (and lots of other resources too -- you should be using it if you're not already). One of its tools is called homologene. It's specifically designed to compare whole proteomes (that is, all the proteins made by an organism). In it you'll find a feature called taxplot, where you can choose one organism and then look for similarities to its proteins in the proteomes of two other organisms. One way to get an answer to your question would be to compare the proteome of Homo sapiens to itself and to the proteome of a plant (the only one available in taxplot is Arabidopsis thaliana, a member of the same family as broccoli that is used a lot in research).

If we do that comparison, the taxplot output looks like this:

Distribution of Homo sapiens (human) homologs

20407 query proteins produced 15809 hits.

The scale on each side is the matching score, an index of similarity between proteins. Higher scores mean more similarity. The most obvious thing here is that human proteins are a lot more similar to themselves than to Arabidopsis proteins, no big surprise. However, you'll note that of 20407 proteins, 15809 had scores high enough to pass the cutoff (10) and be plotted here. So, at that level of matching, you could say about 77% of proteins (and no doubt the genes that code for them) are conserved between human and Arabidopsis. That's a pretty low cutoff value, though. I prefer to use a score around 250; proteins that match at that level in this case have about a 10 to -20th probability of being chance similarities rather than real ones, which is about the cutoff I would usually pick for claiming two genes are really similar. You can choose the cutoff score on the homologene page and run it yourself -- it winds up giving 6057 out of 20407 that match with scores 250 or higher. That's about 30% of proteins (and genes) that I would be very confident in saying show significant similarity between Arabidopsis and humans.

A caution, though; you can't rule out the possibility that some of the similarity you see here is necessary for the function of the proteins without being actually due to common ancestry -- that is, it could be due to analogy rather than homology. Comparisons of individual proteins, though, suggest there is a good bit more similarity between, for instance, cytochrome C, in plants and animals than is necessary to provide the common function. Thus a lot of the similarity here is probably homology.

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