Fig. 4

Analysis of gene families involved in black pepper piperine metabolism. a Expansion of genes involved in the phenylpropanoid pathway, lysine metabolism and acyltransferase family in black pepper. b Tissue-specific upregulated expression of genes involved in the phenylpropanoid pathway, lysine metabolism and acyltransferases in different tissues. The heatmap on the right shows the piperine content in the freeze-dried fresh tissues. MAP: months after pollination. c–h Selection analysis of HCT, LDC and BAHD-AT gene expansion events. Red points indicate positive selection. Green points indicate episodic selection. Purple points indicate episodic positive selection. Blue bars show sequencing depth. A significance threshold of α = 0.1 was used for both SLAC and MEME. c Normalised dN-dS (SLAC) values across a multispecies alignment of 94 HCT sequences with 195 sites. Points indicate statistically significant evidence for codons under selection. One site shows positive selection across the entire tree (SLAC); eight sites show episodic selection (MEME). d Comparison of episodic selection on particular codons across black pepper HCT genes (n = 69). e Normalised dN-dS (SLAC) values across a multispecies alignment of 72 LDC sequences with 80 sites. Two sites show positive selection across the entire tree (SLAC); five sites show episodic selection (MEME). f Comparison of episodic selection on particular codons across black pepper LDC genes (n = 57). g Normalised dN-dS (SLAC) values across a multispecies alignment of 87 BAHD-AT sequences with 375 sites. One site shows positive selection across the entire tree (SLAC); nine sites show episodic selection (MEME). h Comparison of episodic selection on particular codons across black pepper BAHD-AT genes (n = 6). i Schematic representation of the phenylpropanoid pathway and lysine metabolism branch with the reactions associated with piperine biosynthesis genes. The solid lines indicate genes catalysing major reactions that were characterised in our study. The dotted lines indicate genes catalysing reduction reactions in lysine metabolism and approximate derivative reactions in the phenylpropanoid pathway that were not characterised in our study. The source data underlying Fig. 4a–h are provided as a Source Data file