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Table 2 Genes showing similar splicing regulation between Gw and Ri after the véraison time

From: Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

   

IL - Gw

ILD - Gw

IL - Ri

ILD - Ri

Gene IDa

GENE NAME – biological process/function

ASb (region)c

S3

S4

S3 vs S4 (FDR)

S3

S4

S3 vs S4 (FDR)

Vitvi02g00218

BLUS1 - stomatal opening regulation

ES (CDS)

0.69

0.41

0.29 (3.6 E-08)

0.72

0.28

0.43 (0.0 E+00)

Vitvi04g00388

MIEL1 - control of cuticular wax synthesis

IR (5’UTR)

0.56

0.75

−0.19 (4.5 E-06)

0.66

0.82

−0.17 (1.7 E-02)

Vitvi04g01249

PP2C55 - stress signaling

ES (5’UTR)

0.16

0.53

−0.37 (3.6 E-08)

0.21

0.67

−0.46 (0.0 E+00)

Vitvi04g01506

LARP1 - mRNA stabilisation

IR (5’UTR)

0.82

0.66

0.15 (1.1 E-02)

0.78

0.60

0.18 (2.2 E-02)

Vitvi04g02092

DAR1 - cellular expansion regulation

ES (CDS)

0.91

0.70

0.21 (3.8 E-09)

0.92

0.41

0.51 (0.0 E+00)

Vitvi05g00358

ATXN7 - transcription regulation

ES (CDS)

0.94

0.76

0.18 (7.3 E-03)

0.94

0.64

0.30 (8.6 E-06)

Vitvi05g02099

PUM6 - mRNA stabilisation

IR (CDS)

0.85

0.62

0.24 (6.4 E-04)

0.78

0.57

0.21 (6.3 E-03)

Vitvi06g00267

STORAGE PROTEIN-RELATED

ES (5’UTR)

0.10

0.21

−0.10 (8.9 E-02)

0.15

0.34

−0.19 (2.1 E-05)

Vitvi06g00267

STORAGE PROTEIN-RELATED

ES (5’UTR)

0.34

0.59

−0.25 (1.1 E-02)

0.47

0.74

−0.27 (1.8 E-02)

Vitvi07g00031

DRIP1 - water stress regulation

A5SS (5’UTR)

0.84

0.65

0.19 (1.4 E-02)

0.86

0.64

0.22 (2.2 E-02)

Vitvi09g00606

MBD11 - organogenesis and development

IR (5’UTR)

0.91

0.75

0.16 (1.5 E-05)

0.88

0.63

0.25 (2.0 E-11)

Vitvi11g01416

CID5 - endoploidy regulation

ES (5’UTR)

0.57

0.40

0.17 (6.6 E-04)

0.55

0.29

0.26 (1.8 E-08)

Vitvi13g01256

XPO7 - nucleus to cytoplasm RNA transport

IR (5’UTR)

0.49

0.26

0.24 (1.4 E-04)

0.27

0.12

0.15 (7.8 E-02)

Vitvi14g01295

FBD PROTEIN - nuclear processes

ES (5’UTR)

0.39

0.59

−0.20 (7.4 E-02)

0.25

0.68

−0.43 (0.0 E+00)

Vitvi17g00561

ABCA1 - membrane lipid transport

ES (CDS)

0.82

0.50

0.32 (1.7 E-05)

0.84

0.57

0.27 (7.6 E-04)

Vitvi18g00597

ITPK3 - phytic acid synthesis

ES (CDS)

0.03

0.13

−0.09 (4.5 E-02)

0.02

0.25

−0.23 (0.0 E+00)

Vitvi18g00927

LPCAT1 - phospholipid biosynthesis

IR (CDS)

0.73

0.52

0.22 (3.4 E-05)

0.69

0.49

0.20 (1.9 E-02)

  1. Splicing regulation occurred between S3 (soft berry at mid-véraison) and S4 (mid-ripening). The values of IL and ILD (significant at FDR ≤ 0.05) were means of three biological replicates
  2. aaccording to the VCost.v3 genome annotation
  3. bAS type, comprising A3SS, A5SS, ES and IR events
  4. cregion affected by the AS event (3′-UTR, 5′-UTR or CDS)