Not a matter of preference: The polyketide borrelidin contains both a trans and a cis double bond. The corresponding dehydratases in the polyketide synthase are found to have identical preferences for thioester substrates in vitro and to generate trans double bonds, undermining the idea that cis double bonds arise from dehydration of 3S rather than 3R alcohols.
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Vergnolle et al. (2011) studied this question.
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