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)
  
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[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 transcriptomic atlas of grapevine (Vitis vinifera) 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.
+
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)
Line 10: Line 10:
 
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
  
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The 38 samples were mapped to PO ids representing the plant structures and plant growth stages used.   
+
The samples were mapped to PO ids representing the plant structures and plant growth stages used.   
  
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----
+
'''PO anatomy and growth stage mapping table:'''
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Legends:
 
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#Gene ID: RAP-japan/IRGSP rice gene locus ID
 
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#Cultivar: Nipponbare
 
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#Gene data: Derived from supplementary tables ST2-ST25
 
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#PO:annotations: best match to the sample description in the following tables. If required the PO annotations to growth stages were done to #both the organ/structure specific development stages and the whole plant growth stages. Every sample has PO whole plant growth stage #annotations.
 
−
----
 
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'''PO anatomy and growth stage annotations table:'''
 
 
{| {{table}}
 
{| {{table}}
−
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
+
| align="center" style="background:#f0f0f0;"|'''Organ'''
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| align="center" style="background:#f0f0f0;"|'''Dataset'''
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| align="center" style="background:#f0f0f0;"|'''Organ Stage'''
 
| align="center" style="background:#f0f0f0;"|'''Anatomy PO ID'''
 
| align="center" style="background:#f0f0f0;"|'''Anatomy PO ID'''
−
| align="center" style="background:#f0f0f0;"|'''growth stage PO ID'''
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| align="center" style="background:#f0f0f0;"|'''Anatomy PO name'''
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| align="center" style="background:#f0f0f0;"|'''growth stage PO ID'''
+
| align="center" style="background:#f0f0f0;"|'''Growth Stage PO ID'''
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| align="center" style="background:#f0f0f0;"|''''''
+
| align="center" style="background:#f0f0f0;"|'''Growth Stage PO name'''
 
| align="center" style="background:#f0f0f0;"|'''comments'''
 
| align="center" style="background:#f0f0f0;"|'''comments'''
 
|-
 
|-
−
| Anther at premeiosis stage, replicate 1_LMD sample||Pre_anther||PO:0009066||PO:0001004||PO:0007130||||
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|latent bud  ||E-L 23 ||PO:0004709||axillary bud||PO:0025529||bud dormancy stage||||
 
|-
 
|-
−
| Anther_0.3-0.6 mm ||Anther_0.3-0.6 mm||PO:0009066||PO:0001004||PO:0007130||||
+
|winter bud  ||E-L 1||PO:0004709||axillary bud||PO:0025529||bud dormancy stage||||
 
|-
 
|-
−
| Anther_0.7-1.0 mm ||Anther_0.7-1.0 mm||PO:0009066||PO:0001004||PO:0007130||||
+
|bud swell  ||E-L 2||PO:0004709||axillary bud||PO:0025531||bud swell stage||||
 
|-
 
|-
−
| Anther_1.2-1.5 mm ||Anther_1.2-1.5 mm||PO:0009066||PO:0001004||PO:0007130||||
+
|bud burst (green tip)  ||E-L 4||PO:0004709||axillary bud||PO:0025532||bud burst stage||||
 
|-
 
|-
−
| Anther_1.6-2.0 mm ||Anther_1.6-2.0 mm||PO:0009066||PO:0001004||PO:0007130||||
+
|green berry  ||E-L 29-32  ||PO:0009001||fruit||PO:0025501||fruit formation stage||post-fruit set, before véraison||||
 
|-
 
|-
−
| Embryo_07 DAF ||Embryo_07 DAF ||PO:0009009||PO:0001095||PO:0007042||||At 5 DAP embryo differentiating the first leaf primordium
+
|red berry  ||E-L 35-36  ||PO:0009001||fruit||PO:0025502||fruit ripening stage||||
 
|-
 
|-
−
| Embryo_10 DAF ||Embryo_10 DAF ||PO:0009009||PO:0001081||PO:0007042||||Morphologically completed 10 DAP embryo
+
|green rachis ||E-L 14  ||PO:0025242||infructescence axis  ||PO:0007089||stem elongation stage||||
 
|-
 
|-
−
| Embryo_14 DAF ||Embryo_14 DAF ||PO:0009009||PO:0001081||PO:0007042||||milk stage
+
|red rachis ||E-L 43  ||PO:0025242||infructescence axis  ||PO:0007017||sporophyte senescent stage||||
 
|-
 
|-
−
| Embryo_28 DAF ||Embryo_28 DAF ||PO:0009009||PO:0001081||PO:0007010||||dough
+
|leaf  ||E-L 14, 29, 43  ||PO:0009025||vascular leaf||PO:0001050||leaf development stage||||
 
|-
 
|-
−
| Embryo_42 DAF ||Embryo_42 DAF ||PO:0009009||PO:0001081||PO:0007050||||
+
|root  || n/a  ||PO:0009005||root||PO:0007520||root development stage||||
 
|-
 
|-
−
| Endosperm_07 DAF ||Endosperm_07 DAF ||PO:0009089||PO:0007633||PO:0007042||||
+
|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||||
 
|-
 
|-
−
| Endosperm_10 DAF ||Endosperm_10 DAF ||PO:0009089||PO:0007633||PO:0007042||||
+
|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||||
 
|-
 
|-
−
| Endosperm_14 DAF ||Endosperm_14 DAF ||PO:0009089||PO:0007633||PO:0007042||||
+
|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||||
 
|-
 
|-
−
| Endosperm_28 DAF ||Endosperm_28 DAF ||PO:0009089||PO:0007633||PO:0007010||||
+
|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||
 
|-
 
|-
−
| Endosperm_42 DAF ||Endosperm_42 DAF ||PO:0009089||PO:0007633||PO:0007050||||
+
|stem  || EL-14 to 43||PO:0025073||branch||PO:0028002||sporophyte development stage||||
 
|-
 
|-
−
| Inflorescence_0.6-1.0 mm ||Inflorescence_0.6-1.0 mm||PO:0009049 ||PO:0001083||PO:0007006||||
+
|Seed-fruit set (FS) ||E-L 29||PO:0009010||seed||PO:0025501||fruit formation stage||||
 
|-
 
|-
−
| Inflorescence_3.0-4.0 mm ||Inflorescence_3.0-4.0 mm||PO:0009049 ||PO:0001083||PO:0007006||||
+
|Seed- post-fruit set (PFS) ||E-L 32||PO:0009010||seed||PO:0025501||fruit formation stage||||
 
|-
 
|-
−
| Inflorescence_5.0-10.0 mm ||Inflorescence_5.0-10 mm||PO:0009049 ||PO:0001083||PO:0007006||||
+
|Seed- véraison (V)||E-L 35||PO:0009010||seed||PO:0025502||fruit ripening stage||||
 
|-
 
|-
−
| Leaf blade_reproductive_00:00 ||LeafBlade_76DAT_24:00||PO:0020039||-||PO:0007130||||
+
|Seed- mid-ripening (MR) ||E-L 36||PO:0009010||seed||PO:0025502||fruit ripening stage||||
 
|-
 
|-
−
| Leaf blade_reproductive_12:00 ||LeafBlade_76DAT_12:00||PO:0020039||-||PO:0007130||||
+
|tendril  ||E-L 14-29||PO:0025361||leaf tendril|| PO:0001050||leaf development stage||||
 
|-
 
|-
−
| Leaf blade_ripening_00:00 ||LeafBlade_125DAT_24:00||PO:0020039||-||PO:0007010||||
 
−
|-
 
−
| Leaf blade_ripening_12:00 ||LeafBlade_125DAT_12:00||PO:0020039||-||PO:0007010||||
 
−
|-
 
−
| Leaf blade_vegetative_00:00 ||LeafBlade_27DAT_24:00||PO:0020039||-||PO:0007134||||
 
−
|-
 
−
| Leaf blade_vegetative_12:00 ||LeafBlade_27DAT_12:00||PO:0020039||-||PO:0007134||||
 
−
|-
 
−
| Leaf sheath_reproductive_00:00 ||LeafSheath_76DAT_24:00||PO:0020104||-||PO:0007130||||
 
−
|-
 
−
| Leaf sheath_reproductive_12:00 ||LeafSheath_76DAT_12:00||PO:0020104||-||PO:0007130||||
 
−
|-
 
−
| Leaf sheath_vegetative_00:00 ||LeafSheath_27DAT_24:00||PO:0020104||-||PO:0007134||||
 
−
|-
 
−
| Leaf sheath_vegetative_12:00 ||LeafSheath_27DAT_12:00||PO:0020104||-||PO:0007134||||
 
−
|-
 
−
| Lemma_1.5-2.0 mm floret ||Lemma_1.5-2.0 mm floret||PO:0009037||PO:0001047||PO:0007130||||
 
−
|-
 
−
| Lemma_4.0-5.0 mm floret ||Lemma_4.0-5.0 mm floret||PO:0009037||PO:0001047||PO:0007130||||
 
−
|-
 
−
| Lemma_7.0 mm floret ||Lemma_7.0 mm floret||PO:0009037||PO:0001047||PO:0007130||||
 
−
|-
 
−
| Microspore at meiosis stage, replicate 1_LMD sample||MEI-microspore||PO:0020048||PO:0001009||PO:0007130||||
 
−
|-
 
−
| Microspore at tetrad stage, replicate 1_LMD sample||TET-microspore||PO:0000032||PO:0001029||PO:0007130||||
 
−
|-
 
−
| Microspore at uninuclear stage, replicate 1_LMD sample||UN-microspore||PO:0020048||PO:0001012 |  PO:0001013||PO:0007130||||
 
−
|-
 
−
| Ovary_01 DAF ||Ovary_01 DAF ||PO:0009072||-||PO:0007042||||
 
−
|-
 
−
| Ovary_03 DAF ||Ovary_03 DAF ||PO:0009072||-||PO:0007042||||
 
−
|-
 
−
| Ovary_05 DAF ||Ovary_05 DAF ||PO:0009072||-||PO:0007042||||
 
−
|-
 
−
| Ovary_07 DAF ||Ovary_07 DAF ||PO:0009072||-||PO:0007042||||
 
−
|-
 
−
| Palea_1.5-2.0 mm floret ||Palea_1.5-2.0 mm floret||PO:0009038 ||PO:0001048||PO:0007130||||
 
−
|-
 
−
| Palea_4.0-5.0 mm floret ||Palea_4.0-5.0 mm floret||PO:0009038 ||PO:0001048||PO:0007130||||
 
−
|-
 
−
| Palea_7.0 mm floret ||Palea_7.0 mm floret||PO:0009038 ||PO:0001048||PO:0007130||||
 
−
|-
 
−
| Pistil_10-14 cm panicle ||Pistil_10-14 cm inflorescence||PO:0009030||PO:0007606||PO:0007130||||
 
−
|-
 
−
| Pistil_14-18 cm panicle ||Pistil_14-18 cm inflorescence||PO:0009030||PO:0007606||PO:0007130||||
 
−
|-
 
−
| Pistil_5-10 cm panicle ||Pistil_05-10 cm inflorescence||PO:0009030||PO:0007606||PO:0007130||||
 
−
|-
 
−
| Pollen at bicelluar stage, replicate 1_LMD sample||BC-pollen||PO:0025281||PO:0001059||PO:0007130||||
 
−
|-
 
−
| Pollen at tricelluar stage, replicate 1_LMD sample||TC-pollen||PO:0025281||PO:0001015||PO:0007130||||
 
−
|-
 
−
| Root_reproductive_00:00 ||Root_76DAT_24:00||PO:0009005||-||PO:0007130||||
 
−
|-
 
−
| Root_reproductive_12:00 ||Root_76DAT_12:00||PO:0009005||-||PO:0007130||||
 
−
|-
 
−
| Root_vegetative_00:00 ||Root_27DAT_24:00||PO:0009005||-||PO:0007134||||
 
−
|-
 
−
| Root_vegetative_12:00 ||Root_27DAT_12:00||PO:0009005||-||PO:0007134||||
 
−
|-
 
−
| Stem_reproductive_00:00 ||Stem_83DAT_24:00||PO:0009047||-||PO:0007130||||
 
−
|-
 
−
| Stem_reproductive_12:00 ||Stem_83DAT_12:00||PO:0009047||-||PO:0007130||||
 
−
|-
 
−
| Stem_ripening_00:00 ||Stem_90DAT_24:00||PO:0009047||PO:0007010||PO:0007010||||
 
−
|-
 
−
| Stem_ripening_12:00 ||Stem_90DAT_12:00||PO:0009047||PO:0007010||PO:0007010||||
 
−
|-
 
−
| Tapetum at meiosis stage, replicate 1_LMD sample||MEI-tapetum||PO:0009071 ||PO:0001009||PO:0007130||||
 
−
|-
 
−
| Tapetum at tetrad stage, replicate 1_LMD sample||TET-tapetum||PO:0009071 ||PO:0001029||PO:0007130||||
 
−
|-
 
−
| Tapetum at uninuclear stage, replicate 1_LMD sample||UN-tapetum||PO:0009071 ||PO:0001013||PO:0007130||||
 
−
|-
 
−
|
 
 
|}
 
|}
  

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
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