Fig. 3
Transcriptome profiling of candidate genes encoding enzymes of the flavonoid core pathway, anthocyanin transporters, P-ATPases and flavonoid regulatory proteins during fruit maturation in R. genevieri (Rg) and R. idaeus cv. Prestige (Ri). a Gene expression was analysed in three developmental stages (unripe, immature and ripe fruits). b to d Candidate genes were identified via homology-based gene mining (BacHBerryGEN [68]) and expression patterns were visualized using the BacHBerryEXP expression browser (tpm and log2 values) [69]. b Candidate genes encoding enzymes of the phenylpropanoid core pathway and modifying proteins: Top panel - R. genevieri homologues: RgPAL-1 (TR124859|c0_g1_i1), RgPAL-2 (TR119394|c2_g1_i1), RgCHS (TR121228|c1_g2_i1), RgCHI-1 (TR87748|c0_g1_i2), RgCHI-2 (TR109085|c3_g1_i1), RgF3H-1 (TR65548|c1_g1_i2), RgF3H-2 (TR99162|c0_g1_i1), RgFNS (TR117515|c0_g1_i1), RgFLS-1 (TR82651|c1_g1_i1), RgFLS-2 (TR89606|c1_g1_i1), RgDFR (TR23878|c0_g1_i1), RgANS-1 (TR79533|c1_g1_i1), RgANS-2 (TR85881|c0_g1_i1), RgLAR-1 (TR97331|c0_g1_i1), RgLAR-2 (TR79474|c0_g3_i1), RgANR (TR77419|c0_g1_i1), RgUFGT (TR99106|c0_g1_i1); Lower panel - R. idaeus cv. Prestige homologues: RiPAL-1 (TR17637|c0_g1_i1), RiPAL-2 (TR60786|c0_g2_i1), RiCHS (TR38621|c0_g1_i3), RiCHI (TR60776|c0_g1_i1), RiF3H-1 (TR22747|c0_g2_i1), RiFNS-1 (TR17254|c0_g1_i1), RiFNS-2 (TR31274|c0_g1_i2), RiFLS (TR76353|c0_g1_i1), RiDFR-1 (TR26907|c0_g1_i1), RiDFR-2 (TR25484|c0_g1_i1), RiANS-1 (TR24906|c0_g1_i1), RiANS-2 (TR19248|c0_g2_i2), RiLAR-1 (TR24256|c0_g1_i1), RiLAR-2 (TR8288|c0_g1_i2), RiLAR-3 (TR58287|c1_g1_i1), RiANR (TR6460|c0_g1_i1), RiUFGT (TR3455|c0_g1_i1). c Candidate anthocyanin ABC and MATE transporters as well as P-ATPases. Top panel - R. genevieri homologues: RgABC-1 (TR71618|c2_g1_i1), RgABC-2 (TR72263|c2_g1_i5), RgABC-3 (TR114784|c2_g1_i2), RgABC-4 (TR73971|c3_g1_i3), RgMATE-1 (TR99523|c1_g1_i1), RgMATE-2 (TR81657|c3_g1_i1), RgMATE-3 (TR86341|c0_g1_i1), RgPH5-1 (TR72443|c2_g1_i1), RgPH5-2 (TR113411|c2_g1_i2), RgPH5-3 (TR72105|c0_g1_i1), RgPH1 (TR107023|c1_g2_i2); Lower panel - R. idaeus cv. Prestige homologues: RiABC-1 (TR41909|c1_g2_i1), RiABC-2 (TR66334|c1_g1_i2), RiABC-3 (TR27015|c1_g4_i3), RiMATE-1 (TR39949|c0_g1_i3), RiMATE-2 (TR11226|c0_g1_i1), RiMATE-3 (TR10226|c0_g1_i1), RiPH5-1 (TR570|c0_g1_i1), RiPH5-2 (TR41268|c0_g1_i1), RiPH1 (TR52475|c0_g1_i6). d Cloned and candidate Rubus regulatory proteins: Top panel - R. genevieri homologues: RgMYB10 (TR103098|c0_g1_i1), RgMYB12 (TR71550|c1_g1_i1), RgMYB6 (TR86812|c0_g1_i1), RgMYB5 (TR80732|c0_g11_i7), RgMYB2 (TR36560|c0_g1_i1), RgMYB1 (TR111295|c2_g2_i1), RgMYB4 (TR32557|c0_g1_i1), RgAN1 (TR110272|c1_g1_i1), RgDEL (TR110629|c1_g1_i1), RgTTG1 (TR29409|c0_g1_i1); Lower panel - R. idaeus cv. Prestige homologues: RiMYB10 (TR49283|c2_g2_i2), RiMYB12 (TR1036|c0_g1_i2), RiMYB6 (TR67691|c0_g1_i2), RiMYB5 (TR48317|c3_g1_i6), RiMYB2 (TR817|c0_g1_i2), RiMYB1 (TR75558|c0_g1_i1), RiMYB4 (TR16747|c0_g1_i1), RiAN1 (TR75681|c0_g1_i1), RiDEL (TR16024|c0_g1_i1) and RiTTG1 (TR7065|c0_g2_i1)