Vitis vinifera; grape

From Plant Ontology Wiki
Jump to navigationJump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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