Difference between revisions of "Vitis vinifera; grape"
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Data set added in Release #19, Dec 2012, based on Fasoli et al (2012) | Data set added in Release #19, Dec 2012, based on Fasoli et al (2012) | ||
− | [http://www.plantcell.org/content/24/9/3489.abstract 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 | + | [http://www.plantcell.org/content/24/9/3489.abstract 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: | Background: | ||
− | The authors developed a genome-wide | + | 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) | 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) | ||
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Annotations based on [http://www.plantcell.org/content/24/9/3489/suppl/DC1 Supplemental Data Set 2]: Organ-specific transcripts_S2 | Annotations based on [http://www.plantcell.org/content/24/9/3489/suppl/DC1 Supplemental Data Set 2]: Organ-specific transcripts_S2 | ||
− | The | + | The samples were mapped to PO ids representing the plant structures and plant growth stages used. |
'''PO anatomy and growth stage mapping table:''' | '''PO anatomy and growth stage mapping table:''' | ||
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| align="center" style="background:#f0f0f0;"|'''Anatomy PO ID''' | | align="center" style="background:#f0f0f0;"|'''Anatomy PO ID''' | ||
| align="center" style="background:#f0f0f0;"|'''Anatomy PO name''' | | align="center" style="background:#f0f0f0;"|'''Anatomy PO name''' | ||
− | | align="center" style="background:#f0f0f0;"|'''Stage PO ID''' | + | | align="center" style="background:#f0f0f0;"|'''Growth Stage PO ID''' |
− | | align="center" style="background:#f0f0f0;"|'''Stage PO name | + | | align="center" style="background:#f0f0f0;"|'''Growth Stage PO name''' |
− | |||
| align="center" style="background:#f0f0f0;"|'''comments''' | | align="center" style="background:#f0f0f0;"|'''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|||| | ||
|- | |- | ||
− | |||
|} | |} | ||
Latest revision as of 19:55, 27 December 2012
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 |