Analysis of Fatty Acid (FA) Biosynthesis Homologs

To identify genes related to pathways that govern FA biosynthesis in shea, the lipid metabolic pathway was downloaded from the A. thaliana acyl-lipid metabolism database² and full-length protein sequences of the implicated lipid metabolic genes were downloaded from the TAIR database³. Additional relevant protein sequences from A. thaliana and Theobroma cacao (cocoa tree) were downloaded from PLAZA⁴. FA biosynthesis homologs in shea and T. cacao were identified via BLASTP searches against the protein sequences of fetched A. thaliana lipid metabolic genes. Candidate FA biosynthesis genes in A. thaliana, T. cacao, and V. paradoxa were aligned using MAFFT (Katoh and Standley, 2013) and concatenated for phylogenetic analysis. Maximum likelihood gene trees based on protein sequences were constructed using IQ-TREE with the GTR + G model and 1,000 bootstrap replicates (Nguyen et al., 2015). Finally, microsynteny plots were generated using MCScan-Jcvi (Tang et al., 2008) as a means of probing the origins of those FA biosynthesis genes exhibiting relatively high copy number in shea.