Gene model prediction in P. peruviana . A) The number of P. peruviana cDNAs that (a) can be mapped to both S. lycopersicum and S. tuberosum genomes; (b) have multiple-exon models on both genomes; (c) have at least one common intron position (on the cDNA); (d) all introns positions are the same in gene models from the two genomes. B) For those “common” intron points, the intron lengths in the predicted gene models on the two genomes have big variation. C) A typical example: (a) P. peruviana cDNA Php00a06743.16696 and S. lycopersicum cDNA Solyc01g095570.2.1 have identical gene models on S. lycopersicum chromosome SL2.40ch01. (b) The same P. peruviana cDNA and S. tuberosum cDNA PGSC0003DMT400000597 have identical gene models on S. tuberosum superscaffold PGSC0003DMB000000010. The exon sets of the P. peruviana cDNA in panel A and panel B are identical but the two intron sets have remarkable differences. (c) Nucleotide sequences at the first intron junction. Primers can be designed at the indicated positions to amplify intron regions from the Solanaceae.