"Transgenic" is the NPOV term we use to describe genetically engineered crops that have genes from other species. Bt (Bacillus thuringiensis) crops with a bacterial gene for an insect-killing toxin are a well-known example. If you worry about whether such crops are "natural", then the latest example of natural gene transfer among species -- fungus to aphid, in this case -- might be of interest. The paper was published in Science, by Nancy Moran and Tyler Jarvik. Ed Yong has a clear explanation.
My book will argue that we should look to nature for ideas and information to improve agriculture, but not in a simple-minded, "nature-is-perfect" way. If aphids have been transgenic for many generations, that shows that transgenes don't necessarily have severe negative long-term effects on the recipient species. And what about the hypothesis that humans got a key brain-development gene from Neanderthals, as claimed in a 2008 paper in Trends in Genetics (vol.24, p.19)? (I read about this in Microscosm, Carl Zimmer's interesting book on E. coli.) But a few positive examples don't disprove the possibility of negative effects in other cases.