Fig. 3: Biosynthetic gene clusters and associated 3D chromosome features.
From: Single-cell multi-omics in the medicinal plant Catharanthus roseus
a, Hi-C contact map generated from mature leaves for a gene cluster consisting of STR, TDC and SLTr (Supplementary Table 6). b, Chemical scheme showing tryptamine, secologanin, strictosidine and secologanin and VIGS for SLTr. Bar heights represent means; error bars represent s.e.m. Each dot represents a sample. P values are based on two-tail Tukey tests and are shown on the graphs. EV, empty vector control. EV, n = 8. VIGS, n = 6. c, Hi-C contact map for a gene cluster consisting of GS1, GS2, THAS2 and PAS. The curve represents the chromosome loop. d, Hi-C contact map for a gene cluster consisting of an array of acetyltransferases. 1, 2 and 3 represent three TADs. Three previously studied biosynthetic genes (MAT, TAT and DAT) are indicated by asterisks. e, Gene expression profiles for acetyltransferases highlighted in c. FPKM: fragments per kilobase exon mapped per million reads. Heatmap represents Hi-C contacts at the 10-kb resolution, where the darker color represents higher Hi-C contacts (a,c,d). Color scales are maxed out at 100 Hi-C contacts per 10 kb. Solid lines and P values represent TAD boundaries detected by HiCKey12. P values are derived from generalized likelihood ratio tests, part of the HiCKey workflow, and are shown on the graphs. See Supplementary Fig. 1 and Supplementary Table 6 for abbreviation definitions.
