Vitis vinifera; grape

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Data set added in Release #19, Dec 2012, based on Fasoli et al (2012)

Fasoli et al (2012). The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program. The Plant Cell Online. doi: 10.1105/tpc.112.100230.

Background: The authors developed a genome-wide transcriptome atlas of grapevine (Vitis vinifera cv Corvina, clone 48)) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed ∼91% of the predicted grapevine genes.

To identify and characterize organ-specific genes, the authors constructed a reduced 38-sample data set, excluding from the analysis samples with redundant organ identity and those collected during senescence and withering (see Supplemental Data Set 2)

Annotations based on Supplemental Data Set 2: Organ-specific transcripts_S2

The samples were mapped to PO ids representing the plant structures and plant growth stages used.

PO anatomy and growth stage mapping table:

Organ Organ Stage Anatomy PO ID Anatomy PO name Growth Stage PO ID Growth Stage PO name comments
latent bud E-L 23 PO:0004709axillary budPO:0025529bud dormancy stage
winter bud E-L 1PO:0004709axillary budPO:0025529bud dormancy stage
bud swell E-L 2PO:0004709axillary budPO:0025531bud swell stage
bud burst (green tip) E-L 4PO:0004709axillary budPO:0025532bud burst stage
green berry E-L 29-32 PO:0009001fruitPO:0025501fruit formation stagepost-fruit set, before véraison
red berry E-L 35-36 PO:0009001fruitPO:0025502fruit ripening stage
green rachis E-L 14 PO:0025242infructescence axis PO:0007089stem elongation stage
red rachis E-L 43 PO:0025242infructescence axis PO:0007017sporophyte senescent stage
leaf E-L 14, 29, 43 PO:0009025vascular leafPO:0001050leaf development stage
root n/a PO:0009005rootPO:0007520root development stage
carpel E-L 20/E-L 23 PO:0009030carpelPO:0007016whole plant flowering stagepool of carpels from undisclosed flowers at 10% and 50% open flowers
petal E-L 20/E-L 23PO:0009032petalPO:0007016whole plant flowering stagepool of petals from undisclosed flowers at 10% and 50% open flowers
stamen E-L 20/E-L 23 PO:0009029stamenPO:0007016whole plant flowering stagepool of stamens from undisclosed flowers at 10% and 50% open flowers
pollen E-L 25PO:0025281pollenPO:0007052FL.03 3/4 of flowers open stagepollen from disclosed flowers at more than 50% open flowers
stem EL-14 to 43PO:0025073branchPO:0028002sporophyte development stage
Seed-fruit set (FS) E-L 29PO:0009010seedPO:0025501fruit formation stage
Seed- post-fruit set (PFS) E-L 32PO:0009010seedPO:0025501fruit formation stage
Seed- véraison (V)E-L 35PO:0009010seedPO:0025502fruit ripening stage
Seed- mid-ripening (MR) E-L 36PO:0009010seedPO:0025502fruit ripening stage
tendril E-L 14-29PO:0025361leaf tendril PO:0001050leaf development stage
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