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Additional file 17: Table S10. cDNA sequences of 17 target genes.

Additional file 12: Table S5. Sequences of miRNA primers for real-time PCR.

Additional file 8: Table S1. Statistics of miRNA sequences in pitaya.

Additional file 13: Table S6. Sequences of target genes primers for real-time PCR.

Additional file 5: Figure S5. The sequences of 17 target genes from the two pitaya cultivars. ‘-W’, ‘Guanhuabai’ pitaya. ‘-R’, ‘Guanhuahong’ pitaya. Red lines indicate sequence of target genes primers for real-time PCR. Green lines indicate outer specific primers for nested PCR. Blue lines indicate inner specific primers for nested PCR.

Additional file 6: Figure S6. Transient expressions of miRNAs and their target genes (all). A1-A49, bright field; B1-B49, eGFP; C1-C49, merge; A1-C1, 35 s::eGFP; A2-C2, WT; A3-C3, 35 s::Pre-miR164; A4-C4, 35 s::Pre-Hmo-miR6020; A5-C5, 35 s::HmCYP71A8-like::eGFP; A6-C6, 35 s::positive control HmCYP71A8-like::eGFP; A7-C7, 35 s::negative control HmCYP71A8-like::eGFP; A8-C8, 35 s::HmCYP71A8-like::eGFP+ 35 s::Pre-miR164; A9-C9, 35 s::HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A10-C10, 35 s::positive control HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A11-C11, 35 s::negative control HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A12-C12, 35 s::Pre-Hmo-miR858; A13-C13, 35 s::HmMYB12-like::eGFP; A14-C14, 35 s::positive control HmMYB12-like::eGFP; A15-C15, 35 s::negative control HmMYB12-like::eGFP; A16-C16, 35 s::HmMYB12-like::eGFP+ 35 s::Pre-miR164; A17-C17, 35 s::HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A18-C18, 35 s::positive control HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A19-C19, 35 s::negative control HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A20-C20, 35 s::HmMYBC1-like::eGFP; A21-C21, 35 s::HmMYBC1-like::eGFP+ 35 s::Pre-miR164; A22-C22, 35 s::HmMYBC1-like::eGFP+ 35 s::Pre-Hmo-miR858; A23-C23, 35 s::HmMYB2-like::eGFP; A24-C24, 35 s::HmMYB2-like::eGFP+ 35 s::Pre-miR164; A25-C25, 35 s::HmMYB2-like::eGFP+ 35 s::Pre-Hmo-miR858; A26-C26, 35 s::Pre-Hmo-miR160a; A27-C27, 35 s::Hpcyt P450-like2::eGFP; A28-C28, 35 s::positive control Hpcyt P450-like2::eGFP; A29-C29, 35 s::negative control Hpcyt P450-like2::eGFP; A30-C30, 35 s::Hpcyt P450-like2::eGFP+ 35 s::Pre-miR164; A31-C31, 35 s::Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A32-C32, 35 s::positive control Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A33-C33, 35 s::negative control Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A34-C34, 35 s::Pre-Hmo-novel-2; A35-C35, 35 s::HmCYP83B1-like::eGFP; A36-C36, 35 s::positive control HmCYP83B1-like::eGFP; A37-C37, 35 s::negative control HmCYP83B1-like::eGFP; A38-C38, 35 s::HmCYP83B1-like::eGFP+ 35 s::Pre-miR164; A39-C39, 35 s::HmCYP83B1-like::eGFP+35 s::Pre-Hmo-novel-2; A40-C40, 35 s::positive control HmCYP83B1-like::eGFP+ 35 s::Pre-Hmo-novel-2; A41-C41, 35 s::negative control HmCYP83B1-like::eGFP+ 35 s::Pre-Hmo-novel-2; A42-C42, 35 s::Pre-Hmo-novel-15; A43-C43, 35 s::HmTPST-like::eGFP; A44-C44, 35 s::positive control HmTPST-like::eGFP; A45-C45, 35 s::negative control HmTPST-like::eGFP; A46-C46, 35 s::HmTPST-like::eGFP+ 35 s::Pre-miR164; A47-C47, 35 s::HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15; A48-C48, 35 s::positive control HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15; A49-C49, 35 s::negative control HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15.

Additional file 7: Figure S7. Different fruit developmental stages of ‘Guanhuahong’ (A) and ‘Guanhuabai’ (B) pitayas. A1 and B1, 13 d; A2 and B2, 16 d; A3 and B3, 19 d; A4 and B4, 23 d; A5 and B5, 25 d; A6 and B6, 27 d; A7 and B7, 29 d. Bar = 2.0 cm.

Additional file 7: Figure S7. Different fruit developmental stages of ‘Guanhuahong’ (A) and ‘Guanhuabai’ (B) pitayas. A1 and B1, 13 d; A2 and B2, 16 d; A3 and B3, 19 d; A4 and B4, 23 d; A5 and B5, 25 d; A6 and B6, 27 d; A7 and B7, 29 d. Bar = 2.0 cm.

Additional file 9: Table S2. The information of miRNAs in pitaya.

Additional file 4: Figure S4. Number of miRNA family members in pitaya pulp.

Additional file 1: Figure S1. The length distributions of miRNA fragments in pitaya (unique).

Additional file 10: Table S3. Statistics of gene annotation in six databases.

Additional file 14: Table S7. Sequences of specific primers for 5′RACE.

Additional file 3: Figure S3. GC content distributions of assembled transcripts and genes. A, GC content distributions of transcripts; B, GC content distributions of genes.

Additional file 6: Figure S6. Transient expressions of miRNAs and their target genes (all). A1-A49, bright field; B1-B49, eGFP; C1-C49, merge; A1-C1, 35 s::eGFP; A2-C2, WT; A3-C3, 35 s::Pre-miR164; A4-C4, 35 s::Pre-Hmo-miR6020; A5-C5, 35 s::HmCYP71A8-like::eGFP; A6-C6, 35 s::positive control HmCYP71A8-like::eGFP; A7-C7, 35 s::negative control HmCYP71A8-like::eGFP; A8-C8, 35 s::HmCYP71A8-like::eGFP+ 35 s::Pre-miR164; A9-C9, 35 s::HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A10-C10, 35 s::positive control HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A11-C11, 35 s::negative control HmCYP71A8-like::eGFP+ 35 s::Pre-Hmo-miR6020; A12-C12, 35 s::Pre-Hmo-miR858; A13-C13, 35 s::HmMYB12-like::eGFP; A14-C14, 35 s::positive control HmMYB12-like::eGFP; A15-C15, 35 s::negative control HmMYB12-like::eGFP; A16-C16, 35 s::HmMYB12-like::eGFP+ 35 s::Pre-miR164; A17-C17, 35 s::HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A18-C18, 35 s::positive control HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A19-C19, 35 s::negative control HmMYB12-like::eGFP+ 35 s::Pre-Hmo-miR858; A20-C20, 35 s::HmMYBC1-like::eGFP; A21-C21, 35 s::HmMYBC1-like::eGFP+ 35 s::Pre-miR164; A22-C22, 35 s::HmMYBC1-like::eGFP+ 35 s::Pre-Hmo-miR858; A23-C23, 35 s::HmMYB2-like::eGFP; A24-C24, 35 s::HmMYB2-like::eGFP+ 35 s::Pre-miR164; A25-C25, 35 s::HmMYB2-like::eGFP+ 35 s::Pre-Hmo-miR858; A26-C26, 35 s::Pre-Hmo-miR160a; A27-C27, 35 s::Hpcyt P450-like2::eGFP; A28-C28, 35 s::positive control Hpcyt P450-like2::eGFP; A29-C29, 35 s::negative control Hpcyt P450-like2::eGFP; A30-C30, 35 s::Hpcyt P450-like2::eGFP+ 35 s::Pre-miR164; A31-C31, 35 s::Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A32-C32, 35 s::positive control Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A33-C33, 35 s::negative control Hpcyt P450-like2::eGFP+ 35 s::Pre-Hmo-miR160a; A34-C34, 35 s::Pre-Hmo-novel-2; A35-C35, 35 s::HmCYP83B1-like::eGFP; A36-C36, 35 s::positive control HmCYP83B1-like::eGFP; A37-C37, 35 s::negative control HmCYP83B1-like::eGFP; A38-C38, 35 s::HmCYP83B1-like::eGFP+ 35 s::Pre-miR164; A39-C39, 35 s::HmCYP83B1-like::eGFP+35 s::Pre-Hmo-novel-2; A40-C40, 35 s::positive control HmCYP83B1-like::eGFP+ 35 s::Pre-Hmo-novel-2; A41-C41, 35 s::negative control HmCYP83B1-like::eGFP+ 35 s::Pre-Hmo-novel-2; A42-C42, 35 s::Pre-Hmo-novel-15; A43-C43, 35 s::HmTPST-like::eGFP; A44-C44, 35 s::positive control HmTPST-like::eGFP; A45-C45, 35 s::negative control HmTPST-like::eGFP; A46-C46, 35 s::HmTPST-like::eGFP+ 35 s::Pre-miR164; A47-C47, 35 s::HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15; A48-C48, 35 s::positive control HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15; A49-C49, 35 s::negative control HmTPST-like::eGFP+ 35 s::Pre-Hmo-novel-15.

Additional file 15: Table S8. The information of part RNA-Seq data in pitaya.

Additional file 2: Figure S2. The length distributions of assembled transcripts and genes. A, The length distributions of transcripts; B, The length distributions of genes.

Additional file 9: Table S2. The information of miRNAs in pitaya.

Additional file 11: Table S4. Sequences of miRNA-specific primers for reverse transcription.

Additional file 16: Table S9. Prediction of targets for differentially expression miRNAs in pitaya.

Additional file 4: Figure S4. Number of miRNA family members in pitaya pulp.

Additional file 8: Table S1. Statistics of miRNA sequences in pitaya.