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The overall performance of using SV and differential expression to predict associated genes is shown ( Methods ). Triangles marked with different colors represent the SVs that existed in C. colocynthis and/or C. amarus listed in Supplementary Table 1 . The gray squares on the left represent the agronomic traits and selective sweeps. Agronomic-traits-related genes were previously reported, while predicted genes from selective sweeps are newly identified by homologous comparison. The tissues used for expression profiling are indicated at the bottom of each column.

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