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marcelakareymarcelakarey
authoredSep 30, 2021
Update Release 2---2021-09-15.md
added bioproject id and data availability col
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‎grapevine/Release 2---2021-09-15.md

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@@ -55,19 +55,19 @@ The set consists of 10 studies with baseline expression (REFS?) and 23 baseline
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These were projected from curated Japonica rice pathways and are linked to [Gramene’s Plant Reactome](https://plantreactome.gramene.org/PathwayBrowser/#/SPECIES=9030216).
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## Statistics {#statistics}
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| Species | Classification | Note | Assembly | Literature reference | Accession | Expression | Phylogenetic Trees | Pathways |
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|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
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| *Vitis vinifera* L. ssp. *vinifera* Pinot noir PN40024 v3 | Eudicotyledons | Dicot reference | IGGP_12x (**V3**) | [Jaillon *et al* (2007)](https://www.nature.com/articles/nature06148) | GCA_000003745.2 | Search only | Y | Search only |
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| *Vitis vinifera* L. ssp. *vinifera* Pinot noir PN40024 v4 | Eudicotyledons | Dicot reference | v1 (**V4**) | [INTEGRAPE](http://www.integrape.eu/index.php/resources/genomes/genome-accessions) | PN40024_40X_REF_AnnoV2 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Cabernet Sauvignon clone FPS08 | Eudicotyledons | | Cabernet_Sauvignon | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) & [Chin *et al* (2016)](https://www.nature.com/articles/nmeth.4035) | VvCabSauv08_v1 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Carménère clone FPS02 | Eudicotyledons | | Carmenere | [Minio *et al* (2019)](https://www.g3journal.org/content/9/5/1331) | VvCarFPS02VCR702_v1 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Chardonnay clone FPS04 | Eudicotyledons | | Carmenere | [Zou *et al* (2020)](https://www.nature.com/articles/s41467-019-14280-1) | VvChar04_v1 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* interspecific crossing Concord PI588077 | Eudicotyledons | | VvCabSauv08_v1 | [Zou *et al* (2020)](https://www.nature.com/articles/s41467-019-14280-1) | 10x201806 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Flame Seedless clone Parlier | Eudicotyledons | | pacbio201806 | [Zou *et al* (2020)](https://www.nature.com/articles/s41467-019-14280-1) | | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Merlot clone FPS15 | Eudicotyledons | | Merlot | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) | VITVvi_vMerlFPS15_v1.1 | - | Y | - |
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| *Vitis vinifera* L. ssp. *vinifera* Zinfandel clone FPS03 | Eudicotyledons | | Zinfandel | [Vondras *et al* (2019)](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6211-2) | VvZin03_v1 | - | Y | - |
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| *Vitis vinifera* L. ssp. *sylvestris* C1-2 (Badouin et al, 2020) | Eudicotyledons | | Sylvestris_C1-2 | [Badouin *et al* (2020)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02131-y) | Sylvestris_C1-2 | - | Y | - |
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| *Vitis vinifera* L. ssp. *sylvestris* DVIT3351.27 (Ren1 male) | Eudicotyledons | | Sylvestris_DVIT3351.27 | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) | VITVvi_sDVIT3351.27_v1.1 | - | Y | - |
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| Species | Classification | Note | Assembly | Literature reference | Accession | Expression | Phylogenetic Trees | Pathways | BioProject or Genomics Data Source|
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|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
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| *Vitis vinifera* L. ssp. *vinifera* Pinot noir PN40024 v3 | Eudicotyledons | Dicot reference | IGGP_12x (**V3**) | [Jaillon *et al* (2007)](https://www.nature.com/articles/nature06148) | GCA_000003745.2 | Search only | Y | Search only | - |
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| *Vitis vinifera* L. ssp. *vinifera* Pinot noir PN40024 v4 | Eudicotyledons | Dicot reference | v1 (**V4**) | [INTEGRAPE](https://integrape.eu/resources/genes-genomes/genome-accessions/) | PN40024_40X_REF_AnnoV2 | - | Y | - | - |
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| *Vitis vinifera* L. ssp. *vinifera* Cabernet Sauvignon clone FPS08 | Eudicotyledons | | Cabernet_Sauvignon | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) & [Chin *et al* (2016)](https://www.nature.com/articles/nmeth.4035) | VvCabSauv08_v1 | - | Y | - | [PRJNA593045](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593045), [Data](https://doi.org/10.5281/zenodo.3827985), [PRJNA316730](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA316730), [PRJNA433195](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA433195) & [Cantu Lab](http://cantulab.github.io/data.html) |
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| *Vitis vinifera* L. ssp. *vinifera* Carménère clone FPS02 | Eudicotyledons | | Carmenere | [Minio *et al* (2019)](https://www.g3journal.org/content/9/5/1331) | VvCarFPS02VCR702_v1 | - | Y | - | [PRJNA517468](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517468, [Cantu Lab](http://cantulab.github.io/data.html) |
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| *Vitis vinifera* L. ssp. *vinifera* Chardonnay clone FPS04 | Eudicotyledons | | Chardonnay | [Zou *et al* (2019)](https://www.nature.com/articles/s41477-019-0507-8) | VvChar04_v1 | - | Y | - | [PRJNA550461](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA550461) |
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| *Vitis vinifera* L. ssp. *vinifera* interspecific crossing Concord PI588077 | Eudicotyledons | | 10x201806 | [Zou *et al* (2020)](https://www.nature.com/articles/s41467-019-14280-1) | 10x201806 | - | Y | - | [PRJNA281110](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA281110) |
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| *Vitis vinifera* L. ssp. *vinifera* Flame Seedless clone Parlier | Eudicotyledons | | pacbio201806 | [Zou *et al* (2020)](https://www.nature.com/articles/s41467-019-14280-1) | | - | Y | - | [PRJNA281110](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA281110) |
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| *Vitis vinifera* L. ssp. *vinifera* Merlot clone FPS15 | Eudicotyledons | | Merlot | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) | VITVvi_vMerlFPS15_v1.1 | - | Y | - | [PRJNA593045](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593045), [Data](https://doi.org/10.5281/zenodo.3827985) |
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| *Vitis vinifera* L. ssp. *vinifera* Zinfandel clone FPS03 | Eudicotyledons | | Zinfandel | [Vondras *et al* (2019)](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6211-2) | VvZin03_v1 | - | Y | - | [PRJNA527006]((https://www.ncbi.nlm.nih.gov/bioproject/PRJNA527006) & [Cantu Lab](http://cantulab.github.io/data.html) |
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| *Vitis vinifera* L. ssp. *sylvestris* C1-2 (Badouin et al, 2020) | Eudicotyledons | | Sylvestris_C1-2 | [Badouin *et al* (2020)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02131-y) | Sylvestris_C1-2 | - | Y | - | [PRJEB37020](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB37020) |
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| *Vitis vinifera* L. ssp. *sylvestris* DVIT3351.27 (Ren1 male) | Eudicotyledons | | Sylvestris_DVIT3351.27 | [Massonnet *et al* (2020)](https://www.nature.com/articles/s41467-020-16700-z) | VITVvi_sDVIT3351.27_v1.1 | - | Y | - | [PRJNA593045](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593045), [Data](https://doi.org/10.5281/zenodo.3827985) |
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## References {#references}
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