Figures (9)  Tables (4)

    • Figure 1. 

      The four fruit colors of hybrids collected in the field.

    • Figure 2. 

      Metabolomic profiling of four fruit types. (a) Pie chart of metabolite class distribution. (b) PCA analysis of metabolites. (c) Heatmap of all detected metabolites.

    • Figure 3. 

      Heat map of main metabolite types related to fruit color and quality. (a) Amino acids, (b) flavonoids, (c) lipids, (d) organoheterocyclic compounds, (e) organic acids and their derivatives, (f) carbohydrates and their derivatives, (g) phenolic acids, in four fruit types.

    • Figure 4. 

      KEGG enriched scatterplot of DAMs in four comparisons. (a) Black vs dark red, (b) black vs yellow, (c) black vs yellow spot, (d) yellow vs dark red, (e) yellow vs yellow spot, (f) yellow spot vs dark red.

    • Figure 5. 

      PCA and Venn profiling of four fruit types in transcriptome. (a) PCA analysis of transcriptome. (b) Venn plot of DEGs.

    • Figure 6. 

      Differential genes classed in heatmaps, subclusters, and expressions in four fruit types. (a) Heatmap of DEGs. (b) Subcluster plots of DEGs.

    • Figure 7. 

      KEGG enriched scatterplot of DEGs in four comparisons. (a) Black vs dark red, (b) black vs yellow, (c) black vs yellow spot, (d) dark red vs yellow, (e) dark red vs yellow spot, (f) yellow vs yellow spot.

    • Figure 8. 

      Correlation network of the top metabolites and genes in four comparisons. (a) Black vs dark red, (b) yellow spots vs dark red, (c) yellow vs yellow spot, (d) yellow vs dark red, (e) black vs yellow spot, (f) black vs yellow.

    • Figure 9. 

      RT-PCR validation of key DEGs in four fruit types. (a) Lba01g01874, (b) Lba01g02344, (c) Lba02g00136, (d) Lba02g00994, (e) Lba03g00118, (f) Lba03g01605, (g) Lba04g01211, (h) Lba05g01557, (i) Lba05g02210, (j) Lba06g01747, (k) Lba06g02033, (l) Lba07g00206, (m) Lba07g00818, (n) Lba07g02052, (o) Lba07g02085, (p) Lba08g02201, (q) Lba11g01391, (r) Lba11g01902. Note: (a)–(r) are the relative expression of 18 genes, A indicates LbaCML38 as the reference gene, B indicates the GAPDH as the reference gene.

    • Compared samples No. of total identified No. of total significantly different No. of significantly up No. of significantly down
      Black vs yellow 993 331 171 160
      Black vs dark red 993 357 187 170
      Black vs yellow_spots 993 313 164 149
      Yellow_spots vs dark red 993 143 59 84
      Yellow vs yellow_spots 993 205 97 108

      Table 1. 

      Detected DAMs in different comparisons.

    • Comparison/DAM Black vs
      dark red      		 Black vs
      yellow      		 Black vs
      yellow_spot      		 Yellow vs
      dark red      		 Yellow vs
      yellow_spot      		 Yellow_spot vs
      dark red
      Amino acid and derivatives 55 75 55 60 46 33
      Flavonoids 52 51 36 18 21 20
      Carbohydrates and its derivatives 48 38 50 26 20 11
      Organic acid and its derivatives 37 29 37 25 21 14
      Phenolic acids 30 23 25 14 11 7
      Organoheterocyclic compounds 22 24 20 13 18 8
      Lipids 19 20 18 20 12 8
      Nucleotide and its derivates 18 9 9 23 15 11
      Phenylpropanoids and polyketides 13 13 7 12 6 1
      Phenols and its derivatives 11 10 12 5 12 11
      Vitamins 11 6 9 9 3 4
      Alkaloids and derivatives 9 8 9 3 0 1
      Phytohormones 8 6 5 8 3 3
      Amines 6 6 8 4 10 3
      Terpenoids 6 2 3 5 6 5
      Alcohols and polyols 5 5 6 3 0 2
      Polyamine 3 3 1 2 0 1
      Benzene and substituted derivatives 2 1 2 2 1 0
      Organooxygen compounds 2 2 1 0 0 0
      Total 357 331 313 252 205 143

      Table 2. 

      Differential metabolites in six comparisons.

    • KEGG term No. meta
      Black vs red Biosynthesis of secondary metabolites 43
      Phenylpropanoid biosynthesis 12
      Galactose metabolism 11
      Amino sugar and nucleotide sugar metabolism 10
      Arginine and proline metabolism 10
      Black vs yellow Biosynthesis of secondary metabolites 50
      ABC transporters 19
      Biosynthesis of amino acids 19
      Phenylpropanoid biosynthesis 13
      Aminoacyl-tRNA biosynthesis 12
      Black vs yellow spot Metabolic pathways 80
      Biosynthesis of secondary metabolites 42
      ABC transporters 19
      Biosynthesis of amino acids 16
      Galactose metabolism 12
      Yellow vs dark red Biosynthesis of amino acids 15
      Pyrimidine metabolism 13
      ABC transporters 12
      Aminoacyl-tRNA biosynthesis 10
      Alanine, aspartate and glutamate metabolism 8
      Yellow vs yellow_spot Metabolic pathways 58
      Pyrimidine metabolism 7
      Carbon metabolism 7
      Tyrosine metabolism 6
      Amino sugar and nucleotide sugar metabolism 6
      Yellow_spot vs dark red Biosynthesis of amino acids 9
      Arginine biosynthesis 7
      ABC transporters 7
      Tyrosine metabolism 4
      Zeatin biosynthesis 4
      No. meta means Number of Metabolites.

      Table 3. 

      Top enriched KEGG term and metabolites number in six comparisons.

    • Compare All Up Down
      Black vs yellow 4,955 1,551 3,404
      Black vs dark red 7,259 2,524 4,735
      Black vs yellow_spot 5,382 1,334 4,048
      Yellow vs dark red 3,642 1,740 1,902
      Yellow vs yellow_spot 321 163 158
      Dark red vs yellow_spot 3,453 1,507 1,946

      Table 4. 

      The number of detected DEGs in six comparisons.