*4.5. Synteny Analysis and Detection of Tandemly/Segmentally Duplicated TPSs*

To identify the synteny of TPS family genes among species, we performed all-to-all BLASTP between the genome of *P. persica* and other four species *(P. mira*, *M. domestica*, *F. vesca*, *R. chinensis*). The collinearity analysis was also performed between *F. vesca* and *R. chinensis.* For the three representative species (*F. vesca*, *M. domestica*, *P. persica*), we also performed self-blast by comparing protein-coding genes against their genome using BLASTP with an E-value cut-off of 0.00001. All BLASTP hits were used as input for software MCScanX (Multiple Collinearity Scan toolkit) [36] to identify possible collinear blocks within and between genomes of different species. Based on the self-blast results, we detected the tandemly/segmentally duplicated TPSs for each species. In addition to the tandem duplication that was determined by MCScanX, paralogues that were either adjacent or separated by ≤5 genes along a chromosome were also assigned as tandem duplicates. If paralogues were within known genomic duplication blocks, they were considered to be duplicated through segmental duplication. All intra/inter-genomic synteny relationships were visualized with TBtools [33].
