Fig. 3
Identification of candidate genes related to phenylpropanoid and lignan biosynthetic pathways in S. chinensis. a. Identification of unigenes homologous to genes related to these two biosynthetic pathways. b. Expression of candidate unigenes in the two pathways in leaf and fruit tissues. After quantifying gene expression from RNA-Seq data derived from the leaves and fruits of S. chinensis (Cheongsoon) with five replicates, the log2-scale fold changes of each of gene between leaf and fruit were calculated. In Figure, each small square cell indicates unigene homologous to gene encoding enzyme involved in the pathways. In addition, expression change of each unigene between leaf and fruit is shown with heatmap. Mark ‘x’ in small square cell indicates no unigene. c. Multiple-sequence alignment of DIR, IGS1, and PLR homologs. Sequence conservation was identified among targeted genes (UniProt accession number: Q9SDR7 for DIR, Q15G13 for IGS1, and O65679 for PLR), the corresponding primary protein domains (dirigent for DIR, PCBER_SDR_a for IGS1, and NmrA-like family for PLR), and the corresponding homologous unigenes. d. Phylogeny of IGS1 homologs on the basis of the relationships among major linages of angiosperms sequenced, including basal angiosperms (GenBank accession number: XP_006859191.1 and XP_020532181.1 Amborella trichopoda and RWR83219.1 and RWR85316.1 for Cinnamomum micranthum), rosids (XP_021900462.1 for Carica papaya, XP_007022888.1 for Theobroma cacao, XP_007213116.1 and XP_007212642.2 for Prunus persica, XP_002310455.1 for Populus trichocarpa, and RVX21189.1 for Vitis vinifera), asterids (Q15GI3.1 for Petunia x hybryda and CAA2957992.1 and CAA2959183.1 for Olea europaea) reported by the Amborella Genome Project [32]. e. Phylogenetic analysis between IGS1 and PLR homologs via the maximum likelihood-based method