And this is in the set of "Instructions for Authors", Plant Physiology journal:
Nomenclature. In the abstract, at first mention in the text, and in "Materials and Methods," include complete botanical names (genus, species, and, when appropriate, cultivar) for all experimental plants. Do NOT use the genus name alone, unless that is the accepted common name. Identify algae and microorganisms by a collection number or that of a comparable listing. Following first mentions, generic names should be abbreviated to the initial, except when confusion could arise by reference to genera with the same initial. Common names can be used after first mention. When the genus name is the accepted common name, the name should be in lowercase, roman type. Arabidopsis (no italics) is an accepted common name for A. thaliana.
@tj: you can definitely argue your point but in the end, you better just follow your reviewer"s suggestion....make your life easier...
-casandra-
thanks guys, I knew in the end I would have to change it to the style the examiner indicated, I just wanted to prove to myself that I wasn't completely wrong 
-toejam-
