Vitis vinifera; grape

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