Fig 1.
Fruit samples of the red-fruited raspberry cultivars ‘Anitra’, Glen Ample’ and ‘Veten’ and the apricot-fruited cultivar ‘Varnes’ at three stages of development: (1) unripe (at 25 days post-anthesis), (2) turning (at 30 days post anthesis), and (3) fully mature (35 days post anthesis).
Table 1.
Concentrations (μg g−1 DW) of ten anthocyanin compounds analysed in raspberry (Rubus idaeus) fruit samples at three stages of maturity, ‘unripe’, ‘turning’, and ‘mature’ in four raspberry cultivars, ‘Anitra’, ‘Glen Ample’ and ‘Veten’ (red-fruited) and ‘Varnes’ (apricot-fruited).
Table 2.
Differential expression analysis statistics.
Numbers of down-regulated and up-regulated differentially expressed transcripts for ‘turning’ vs. ‘unripe’ (Tu vs. Un) and ‘mature’ vs. ‘unripe’ (Ma vs. Un) pairwise comparisons revealed in developing fruit of the raspberry cultivars ‘Anitra’, ‘Glen Ample’, ‘Varnes’ and ‘Veten’.
Fig 2.
Gene expression profiles (expressed as transcripts per million mapped reads; TPM) of the anthocyanin pathway genes Phenylalanine lyase (Pal), Chalcone synthase (Chs), Chalcone isomerase (Chi), Flavanone-β3-hydroxylase (F3h), Dihydroflavanol-4-reductase (Dfr), and Anthocyanidin synthase (Ans) in four raspberry cultivars, ‘Anitra’, ‘Glen Ample’, ‘Varnes’, and ‘Veten’, at three stages of fruit maturity; ‘unripe’, ‘turning’, and ‘mature’.
Fig 3.
Coverage plots showing the total number of RNASeq reads mapped to the gene predictions from the ‘Malling Jewel’ genome for the anthocyanin genes Phenylalanine lyase (Pal), Chalcone synthase (Chs), Chalcone isomerase (Chi), Flavanone-β3-hydroxylase (F3h), Dihydroflavanol-4-reductase (Dfr), and Anthocyanidin synthase (Ans) in four raspberry cultivars, ‘Anitra’, ‘Glen Ample’, ‘Varnes’, and ‘Veten’.
The plot of the Ans gene clearly highlights the truncation in the length of the transcribed mRNA in ‘Varnes’.
Fig 4.
Schematic of the ANS gene region in raspberry cultivars ‘Malling Jewel’ and ‘Varnes’ showing (a) the structure of the gene in the ‘Malling Jewel’ reference, the position of the insert sequence in the ‘Varnes’ sequence and the positions and relative sizes of repeat sequences in the insert; (b) the amino acid sequence of the predicted wild-type protein in ‘Malling Jewel’ and the mutant sequence in ‘Varnes’ (key catalytic residues highlighted in blue, mutated residues highlighted in red); and (c) The abundance of RNASeq reads mapping to the four cultivars (‘Anitra’, ‘Glen Ample’, ‘Varnes’ and ‘Veten’) using the gene predictions from the ‘Varnes’ genome sequence (insertion indicated by red bar).
Fig 5.
Diagram showing locations of primers designed to amplify the full-length ANS gene (6.3kb) and the insertion-specific amplicon (1.9kb), and agarose gel showing (a) the PCR amplification of a full-length ANS gene from the cultivars ‘Anitra’, ‘Glen Ample’, ‘Varnes’ and ‘Veten’, showing the presence of the wild-type allele (1,837 bp) in ‘Anitra’, ‘Glen Ample’, and ‘Veten’, and the mutant transposon-containing allele (6,173 bp) in ‘Varnes’; (b) the PCR amplification of an ANS transposon specific amplicon (1,819 bp) in cultivars ‘Varnes’ and ‘Veten’.