Difference between revisions of "Vitis vinifera; grape"
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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;"|'''comments''' | | align="center" style="background:#f0f0f0;"|'''comments''' | ||
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Revision as of 16:45, 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 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.
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 38 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 | growth stage PO ID | comments |
| Anther at premeiosis stage, replicate 1_LMD sample | Pre_anther | PO:0009066 | PO:0001004 | PO:0007130 | |||
| Anther_0.3-0.6 mm | Anther_0.3-0.6 mm | PO:0009066 | PO:0001004 | PO:0007130 | |||
| Anther_0.7-1.0 mm | Anther_0.7-1.0 mm | PO:0009066 | PO:0001004 | PO:0007130 | |||
| Anther_1.2-1.5 mm | Anther_1.2-1.5 mm | PO:0009066 | PO:0001004 | PO:0007130 | |||
| Anther_1.6-2.0 mm | Anther_1.6-2.0 mm | PO:0009066 | PO:0001004 | PO:0007130 | |||
| Embryo_07 DAF | Embryo_07 DAF | PO:0009009 | PO:0001095 | PO:0007042 | At 5 DAP embryo differentiating the first leaf primordium | ||
| Embryo_10 DAF | Embryo_10 DAF | PO:0009009 | PO:0001081 | PO:0007042 | Morphologically completed 10 DAP embryo | ||
| Embryo_14 DAF | Embryo_14 DAF | PO:0009009 | PO:0001081 | PO:0007042 | milk stage | ||
| Embryo_28 DAF | Embryo_28 DAF | PO:0009009 | PO:0001081 | PO:0007010 | dough | ||
| Embryo_42 DAF | Embryo_42 DAF | PO:0009009 | PO:0001081 | PO:0007050 | |||
| Endosperm_07 DAF | Endosperm_07 DAF | PO:0009089 | PO:0007633 | PO:0007042 | |||
| Endosperm_10 DAF | Endosperm_10 DAF | PO:0009089 | PO:0007633 | PO:0007042 | |||
| Endosperm_14 DAF | Endosperm_14 DAF | PO:0009089 | PO:0007633 | PO:0007042 | |||
| Endosperm_28 DAF | Endosperm_28 DAF | PO:0009089 | PO:0007633 | PO:0007010 | |||
| Endosperm_42 DAF | Endosperm_42 DAF | PO:0009089 | PO:0007633 | PO:0007050 | |||
| Inflorescence_0.6-1.0 mm | Inflorescence_0.6-1.0 mm | PO:0009049 | PO:0001083 | PO:0007006 | |||
| Inflorescence_3.0-4.0 mm | Inflorescence_3.0-4.0 mm | PO:0009049 | PO:0001083 | PO:0007006 | |||
| Inflorescence_5.0-10.0 mm | Inflorescence_5.0-10 mm | PO:0009049 | PO:0001083 | PO:0007006 | |||
| Leaf blade_reproductive_00:00 | LeafBlade_76DAT_24:00 | PO:0020039 | - | PO:0007130 | |||
| Leaf blade_reproductive_12:00 | LeafBlade_76DAT_12:00 | PO:0020039 | - | PO:0007130 | |||
| 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: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 | |||
