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Hello Everyone,<span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><br>
<br>
The Gramene project team is pleased to announce its Release #60
with the <a
href="http://ensembl.gramene.org/genome_browser/index.html"
target="_top">Genome section</a> providing access to
information on 2,162,056 genes and 58 reference plant genomes.
It includes new reference genome of <em>Arabidopsis halleri</em>
and updates to several existing genomes. 1,891,391
protein-coding genes are organized in 93,194 gene families. The
<a href="http://plantreactome.gramene.org" target="_top">Plant
Reactome</a>, Gramene's pathway portal </span></span><span
style="color:rgb(0, 0, 0); font-family:arial,helvetica,sans-serif;
font-size:14px">hosts pathway projections for 79 species ranging
from unicellular autotrophs to higher plants. </span><span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">In this release,</span></span> <span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)">we have extended orthology-based
pathway projections for 1 new species: </span><span
style="background-color:transparent"><em><a
href="http://plants.ensembl.org/Arabidopsis_halleri"
style="color: rgb(68, 68, 68); box-sizing: border-box;
text-decoration-line: none; background-color: transparent;
transition: all 0.3s ease-out 0s;" target="_top"><span
style="color:rgb(0, 0, 0)">Arabidopsis halleri</span></a></em></span><span
style="background-color:transparent"><em>, and </em></span><span
style="color:rgb(0, 0, 0)">revised pathways for </span><em><a
href="http://plants.ensembl.org/Solanum_lycopersicum/Info/Index"
style="color: rgb(153, 51, 0); box-sizing: border-box;
text-decoration-line: none; background-color: transparent;
transition: all 0.3s ease-out 0s;" target="_top"><span
style="color:rgb(0, 0, 0)">several species,</span></a></em><span
style="color:rgb(0, 0, 0)"> based on their recent genome
updates; </span></span></span><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">added 10 new
curated pathways for reference species <em>Oryza sativa</em>
(total curated reference pathways are <span style="color:rgb(0,
0, 0)">293)</span>. </span></span>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Gramene is a
curated, open-source, integrated data resource for comparative
functional genomics in crops and model plant species. The
genome databases were built in direct collaboration with
Ensembl Plants and the Plant Reactome database was produced in
collaboration with the Reactome project.</span></span></p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>GENOMES</strong> </span></span></p>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>New
genomes: </strong></span></span>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Arabidopsis_halleri/Info/Index"
href="http://ensembl.gramene.org/Arabidopsis_halleri/Info/Index"
style="color: rgb(204, 54, 0);"><span
style="color:#0000FF">Arabidopsis halleri</span></a></em>:
assembly <a
data-cke-saved-href="https://www.ebi.ac.uk/ena/data/view/GCA_900078215"
href="https://www.ebi.ac.uk/ena/data/view/GCA_900078215" rel="external"
style="color: rgb(51, 71, 140); background-position:
right center; background-repeat: no-repeat;
padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">GCA_900078215</a>,
annotation <a
data-cke-saved-href="https://datadryad.org/resource/doi:10.5061/dryad.gn4hh?show=full"
href="https://datadryad.org/resource/doi:10.5061/dryad.gn4hh?show=full"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">doi:10.5061/dryad.gn4hh.</a></span></span></li>
</ul>
</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>Updated
genomes:</strong></span></span></li>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Aegilops_tauschii/Info/Index"
href="http://ensembl.gramene.org/Aegilops_tauschii/Info/Index"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Aegilops tauschii</span></a></em><span
style="color:#0000FF">:</span> updated assembly and
annotation to version Aet v4.0 (<a
data-cke-saved-href="https://www.ebi.ac.uk/ena/data/view/GCA_002575655"
href="https://www.ebi.ac.uk/ena/data/view/GCA_002575655"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">GCA_002575655</a>).</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Solanum_lycopersicum"
href="http://ensembl.gramene.org/Solanum_lycopersicum"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Solanum lycopersicum</span></a></em>:
updated assembly (<a
data-cke-saved-href="https://www.ebi.ac.uk/ena/data/view/GCA_000188115.3"
href="https://www.ebi.ac.uk/ena/data/view/GCA_000188115.3"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">GCA_000188115.3</a>)
and annotation (ITAG3.0, except unplaced genes).</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Glycine_max"
href="http://ensembl.gramene.org/Glycine_max"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Glycine max</span></a>:</em> updated
assembly (<a
data-cke-saved-href="https://www.ebi.ac.uk/ena/data/view/GCA_000004515.4"
href="https://www.ebi.ac.uk/ena/data/view/GCA_000004515.4"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">GCA_000004515.4</a>)
and annotation (Rel. 137, Version 4, Glycine_max_v2.1)</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Vigna_radiata"
href="http://ensembl.gramene.org/Vigna_radiata"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Vigna radiata</span></a></em>:
updated annotation (vigra.VC1973A.gnm6.ann1.M1Qs)</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><a
data-cke-saved-href="http://ensembl.gramene.org/Vigna_radiata"
href="http://ensembl.gramene.org/Vigna_radiata"><span
style="color:#0000FF"><em>Physcomitrella patens</em></span></a>:
updated annotation (<a
data-cke-saved-href="https://genomevolution.org/coge/ExperimentView.pl?eid=11065"
href="https://genomevolution.org/coge/ExperimentView.pl?eid=11065"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">V3.3</a>)</span></span>.</li>
</ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>New
& Updated data: <br>
</strong></span></span></li>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Triticum_aestivum/Info/Index"
href="http://ensembl.gramene.org/Triticum_aestivum/Info/Index"
style="color: rgb(204, 54, 0);"><span
style="color:#0000FF">Triticum aestivum</span></a></em>:
Inter-Homeologous Variants (IHVs) were added.</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Lupinus_angustifolius"
href="http://ensembl.gramene.org/Lupinus_angustifolius" style="color:
rgb(51, 71, 140);"><span style="color:#0000FF">Lupinus
angustifolius</span></a></em>: genes from previous
release were added</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Arabidopsis_thaliana"
href="http://ensembl.gramene.org/Arabidopsis_thaliana"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Arabidopsis thaliana</span>:</a></em> TAIR10
is now the unique source of ncRNA annotations.</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Nicotiana_attenuata"
href="http://ensembl.gramene.org/Nicotiana_attenuata"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Nicotiana attenuata</span></a></em>:
mapped microarray probes were updated</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><em><a
data-cke-saved-href="http://ensembl.gramene.org/Zea_mays"
href="http://ensembl.gramene.org/Zea_mays"
style="color: rgb(51, 71, 140);"><span
style="color:#0000FF">Zea mays</span>:</a></em> mapped
microarray probes were updated</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><a
data-cke-saved-href="http://ensembl.gramene.org/biomart/martview/"
href="http://ensembl.gramene.org/biomart/martview/">BioMarts</a>
for all gene and variation data</span></span>.</li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Updated <a
data-cke-saved-href="ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/split_genes/"
href="ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/split_genes/"><span
style="color:#0000FF">split gene predictions</span></a>
from <a
data-cke-saved-href="http://ensemblgenomes.org/info/data/peptide_compara"
href="http://ensemblgenomes.org/info/data/peptide_compara"
rel="external">peptide comparative genomics</a>.</span></span></li>
</ul>
</ul>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>Updated
software:</strong> <strong>Updated genome browser,
database schema, and API to <a
data-cke-saved-href="http://www.ensembl.info/2019/01/09/ensembl-95-is-out/"
href="http://www.ensembl.info/2019/01/09/ensembl-95-is-out/"
rel="external" style="color: rgb(51, 71, 140);
background-position: right center; background-repeat:
no-repeat; padding-right: 12px; background-image:
url("data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%0A%20%20%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%0A%20%20%20%20%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23ffffff%22%20stroke%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%3Cg%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%23697ec9%22%2F%3E%0A%20%20%20%20%20%20%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23ffffff%22%2F%3E%0A%20%20%20%20%3C%2Fg%3E%0A%20%20%3C%2Fg%3E%0A%3C%2Fsvg%3E%0A");">Ensembl
95 software</a>.</strong></span></span></li>
</ul>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>PATHWAYS</strong> (<a
data-cke-saved-href="http://plantreactome.gramene.org"
href="http://plantreactome.gramene.org"><span
style="color:#0000FF">Plant Reactome</span></a>): </span></span></p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">For details
see: <a
data-cke-saved-href="http://plantreactomedev.oicr.on.ca/index.php?option=com_content&view=article&id=66&Itemid=360&lang=en"
href="http://plantreactomedev.oicr.on.ca/index.php?option=com_content&view=article&id=66&Itemid=360&lang=en"><span
style="color:#0000FF">Plant Reactome Release Summary</span></a>
- Version 17 (Gramene r60): Here is the summary of updates
made to plant pathways.</span></span></p>
<ul>
<li><span style="color:#000000"><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong>Website
and coding updates</strong></span></span></span> : <span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)"> The latest Plant Reactome
pathway data has been re-indexed and made available via
Gramene search.</span></span></span></li>
</ul>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:#000000"><strong>Curation of reference rice
pathways:</strong></span><span style="color:rgb(0, 128,
0)"><strong> </strong></span></span></span>W<span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)">e have added 10 newly curated
pathways and 3 "container" pathways, and updated 2
existing pathways, resulting in a total of 293 reference
rice pathways.</span></span></span></li>
</ul>
<ul>
<li>
<h3><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)"><strong>New Pathways</strong>:</span></span></span></h3>
</li>
</ul>
<blockquote>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Regulation
of embryo development</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Maternal
tissue PCD</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Cell cycle
regulation</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Aleurone
layer formation</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Regulatory
network of nutrient accumulation</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Regulation
of seed size</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Regulation
of leaf development</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"> HSFA7/
HSFA6B-regulatory network-induced by drought and ABA.</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">SNAC1
transcription network involved in drought and salinity
tolerance</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">Arsenic
uptake and detoxification</span></span></li>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"> </span></span>Regulatory
Network of Nutrient Accumulation</span></span></li>
</ul>
</blockquote>
<ul>
<li>
<h3><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><strong><span
style="background-color:transparent; color:rgb(0, 0,
0)">Updated/renamed </span><span
style="background-color:transparent; color:rgb(0, 0,
0)">pathways:</span></strong></span></span></h3>
</li>
</ul>
<blockquote>
<ul>
<li><span style="font-family:arial,helvetica,sans-serif"><span
style="background-color:transparent; color:rgb(0, 0, 0)"> Flower
development</span></span></li>
<li><span style="font-family:arial,helvetica,sans-serif"><span
style="background-color:transparent; color:rgb(0, 0, 0)"></span><span
style="background-color:transparent; color:rgb(0, 0, 0)">
Thiosulfate disproportionation III (rhodanese)</span></span></li>
</ul>
</blockquote>
<ul>
<li><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)"><strong>Pathway Projections:</strong></span><span
style="color:rgb(0, 128, 0)"><strong> </strong></span></span></span><span
style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><span
style="color:rgb(0, 0, 0)">We have extended
orthology-based pathway projections for 1 new species: </span><a
data-cke-saved-href="http://plants.ensembl.org/Arabidopsis_halleri"
href="http://plants.ensembl.org/Arabidopsis_halleri"
style="box-sizing: border-box; color: rgb(68, 68, 68);
text-decoration-line: none; background-color: transparent;
transition: all 0.3s ease-out 0s;"><span
style="color:#000000"><em>Arabidopsis halleri</em></span></a><span
style="color:rgb(0, 0, 0)">. Plant Reactome now hosts
pathway projections for 79 species ranging from
unicellular autotrophs to higher plants. In addition, we
have</span> <span style="color:rgb(0, 0, 0)">revised
pathways for </span><a
data-cke-saved-href="http://plants.ensembl.org/Solanum_lycopersicum/Info/Index"
href="http://plants.ensembl.org/Solanum_lycopersicum/Info/Index"
style="box-sizing: border-box; color: rgb(153, 51, 0);
text-decoration-line: none; background-color: transparent;
transition: all 0.3s ease-out 0s;"><span
style="color:#000000"><em>several species</em></span></a><span
style="color:#000000"> based on their recent genome
updates (see genome section).</span></span></span></li>
</ul>
<p class="rteindent1"><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">The Plant
Reactome increasingly includes curated regulatory and
developmental pathways, which require more reference DNA and
RNA sequence elements, in addition to the traditional
protein-coding elements. These sequence elements are not
included in Reactome orthoinference at this time, although we
are actively working to enhance the projection process to
include these elements on projected pathways in future
releases.</span></span></p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"> Please let us
know if you have questions or suggestions. </span></span><br>
</p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif">The Gramene
Team <br>
<a class="moz-txt-link-abbreviated" href="http://www.gramene.org">www.gramene.org</a>.</span></span><br>
</p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"></span></span></p>
<p><span style="font-size:14px"><span
style="font-family:arial,helvetica,sans-serif"><br>
</span></span></p>
<pre class="moz-signature" cols="72">--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA
Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: <a class="moz-txt-link-abbreviated" href="mailto:jaiswalp@oregonstate.edu">jaiswalp@oregonstate.edu</a>
Web: <a class="moz-txt-link-freetext" href="http://jaiswallab.cgrb.oregonstate.edu">http://jaiswallab.cgrb.oregonstate.edu</a>
<a class="moz-txt-link-freetext" href="http://icbo-conference.org">http://icbo-conference.org</a></pre>
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