The present invention relates to methods of designing nucleic acid molecules for improved expression of the encoded polypeptides in plants. In such methods, codon usage frequencies are biased towards codon usage frequencies of a plant virus, group of plant viruses, or a subset of nucleic acid molecules therefrom. In preferred embodiments, the encoded polypeptide affects the phenotype of the plant. The invention also pertains to nucleic acid molecules encoding insecticidal polypeptides wherein the nucleic acid molecules have been designed to have plant virus codon-biased. The invention also pertains to transgenic plants and progeny thereof with increased expression of insecticidal polypeptides for improved resistance to insects and other pests that are detrimental to plants of agricultural value.