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<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">Dear
Researchers,</span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">The Gramene
team is pleased to announce its <a
href="http://news.gramene.org/release-notes-62"
moz-do-not-send="true">Release #62 </a><span
style="color:blue"></span>with updates to its <a
href="http://ensembl.gramene.org/genome_browser/index.html"
moz-do-not-send="true">Genome portal</a>, Pathway portal <a
href="https://plantreactome.gramene.org/index.php?lang=en"
moz-do-not-send="true">Plant Reactome</a> and the
infrastructure. The genome portal hosts 67 plant genomes with
six new species and an updated chocolate tree genome. The<span
style="color:black;mso-themecolor:text1"> Plant Reactome,</span>
hosts pathways for 97 species. The Plant Reactome has extended
orthology-based pathway projections for 15 new species; added
six newly curated pathways and updated 11 pathways in the
reference species <i>Oryza sativa </i>(resulting in a total of
306 rice pathways). In the following sections, we provide a
summary of updates to the Gramene Knowledgebase. We also share
four new publications highlighting major Gramene updates over
the last two years and discuss new efforts by Gramene on
community engagement in biocuration of plant genes and pathways.</span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">The <a
href="http://gramene.org/" moz-do-not-send="true">Gramene </a>is
a curated, open-source, integrated data resource for comparative
functional genomics in crops and model plant species. The <a
href="http://ensembl.gramene.org/genome_browser/index.html"
moz-do-not-send="true">plant genome databases</a> were
co-produced in direct collaboration with <a
href="https://plants.ensembl.org/index.html"
moz-do-not-send="true">Ensembl Plants</a>, and the <a
href="https://plantreactome.gramene.org/index.php?lang=en"
moz-do-not-send="true">Plant Reactome </a>database was
produced in collaboration with the <a
href="https://reactome.org/" moz-do-not-send="true">Reactome </a>project.
The National Science Foundation, USA provided core funding for
the project.</span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">Updates
in the Genome Portal:<span style="mso-spacerun:yes"> </span></span></b><span
style="font-size:12.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""><a
href="http://news.gramene.org/release-notes-62"
moz-do-not-send="true">Release #62</a> includes six new
reference genomes and one updated genome. Overall, the Genome
section providing access to information <span
style="color:black">96,607 </span>Gene families comprising <span
style="color:black">2,146,774 </span>individual genes from 67
plant genomes with <span style="color:black">2,365,624</span>
input proteins. </span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:darkgreen">New genomes</span></b><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman"">:</span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Robusta coffee (<a
href="http://ensembl.gramene.org/Coffea_canephora"
moz-do-not-send="true"><i>Coffea canephora</i></a>):
assembly and annotation <a
href="https://www.ebi.ac.uk/ena/data/view/GCA_900059795.1"
moz-do-not-send="true"><span style="color:#444444">GCA_900059795.1</span></a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Hot pepper (<a
href="http://ensembl.gramene.org/Capsicum_annuum"
moz-do-not-send="true"><i>Capsicum annuum</i></a><span
style="color:blue">)</span>: assembly and annotation <a
href="https://www.ebi.ac.uk/ena/data/view/GCA_000512255.2"
moz-do-not-send="true"><span style="color:#444444">GCA_000512255.2</span></a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Global artichoke (<a
href="http://ensembl.gramene.org/Cynara_cardunculus"
moz-do-not-send="true"><i>Cynara cardunculus</i></a><span
style="color:blue">)</span>: assembly and annotation <a
href="https://www.ebi.ac.uk/ena/data/view/GCA_001531365.1"
moz-do-not-send="true"><span style="color:#444444">GCA_001531365.1</span></a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Eragrostis tef (<a
href="http://ensembl.gramene.org/Eragrostis_tef"
moz-do-not-send="true"><i>Eragrostis tef</i></a>): assembly
from ENA (<a
href="https://www.ebi.ac.uk/ena/data/view/GCA_000970635.1"
moz-do-not-send="true"><span style="color:#444444">GCA_000970635.1</span></a>)
and <a href="http://130.92.252.158/tef/version1/"
moz-do-not-send="true"><span style="color:#444444">community
annotation</span></a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Durum wheat (<a
href="http://ensembl.gramene.org/Triticum_turgidum"
moz-do-not-send="true"><i>Triticum turgidum</i></a>,
tetraploid AABB).</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l1 level1 lfo6;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Common liverwort (<a
href="http://ensembl.gramene.org/Marchantia_polymorpha"
moz-do-not-send="true"><i>Marchantia polymorpha</i></a>):
assembly and annotation <a
href="https://www.ebi.ac.uk/ena/data/view/GCA_003032435.1"
moz-do-not-send="true"><span style="color:#444444">GCA_003032435.1</span></a>.</span></li>
</ul>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:darkgreen">Updated genomes</span></b><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">:</span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l3 level1 lfo1;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Criollo cocoa, cacao or chocolate
tree (<a href="http://ensembl.gramene.org/Theobroma_cacao"
moz-do-not-send="true"><i>Theobroma cacao</i></a>): assembly
update <a
href="https://www.ebi.ac.uk/ena/data/view/GCA_000208745.2"
moz-do-not-send="true"><span style="color:#444444">GCA_000208745.2</span></a>.</span></li>
</ul>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:darkgreen">New & Updated data: </span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">New whole genome alignments for
robusta coffee (<i>Coffea canefora</i>), hot pepper (<i>Capsicum
annuum</i>), global artichoke (<i>Cynara cardunculus</i>),
eragrostis tef (<i>Eragrostis tef</i>), durum wheat (<i>Triticum
turgidum</i>), common liverwort (<i>Marchantia polymorpha</i>),
and chocolate tree (<i>Theobroma cacao</i>); see summary <a
href="http://ensembl.gramene.org/compara_analyses.html"
moz-do-not-send="true">here</a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">New synteny data for robusta
coffee (<i>Coffea canefora</i>), hot pepper (<i>Capsicum
annuum</i>), and chocolate tree (<i>Theobroma cacao</i>);
see summary <a
href="http://ensembl.gramene.org/compara_analyses.html"
moz-do-not-send="true">here</a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Updated <a
href="ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/split_genes/"
moz-do-not-send="true">split gene predictions</a><span
style="color:blue"> </span>from <a
href="http://ensemblgenomes.org/info/data/peptide_compara"
moz-do-not-send="true">peptide comparative genomics</a>.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">The Pan-taxonomic Compara set of
gene trees was updated with two new plant species added (<i>Marchantia
polymorpha</i> and <i>Brachypodium distachyon</i>), and one
removed (<i>Chondrus crispus</i>).</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Updated metadata for wheat
EMS-induced mutations.</span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l0 level1 lfo2;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">KASP marker information for the
TILLING population is being displayed on the genetic variation
pages for wheat.</span></li>
</ul>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">Updates
in the Pathway Portal (Plant Reactome): </span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">Plant
Reactome is the pathway knowledgebase of Gramene. We utilize the
Reactome pathway data model to represent plant metabolic,
transport and signaling pathways, developmental processes, organ
differentiation, and transcriptional regulatory networks. Manual
biocuration is conducted in the reference species rice (<i>O.
sativa</i>) and pathways are then projected via gene
orthology to other species, including single-cell
photoautotrophs, lower plants, and higher plants. </span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#2A2A2A">We continue to leverage the resources
made available in the Powered-by-CyVerse virtual server
environment by providing the Plant Reactome database mirror (</span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""><a
href="https://plantreactome.cyverse.org/"
moz-do-not-send="true"><span style="color:#006FB7;border:none
windowtext 1.0pt;mso-border-alt:none windowtext 0in;
padding:0in">https://plantreactome.cyverse.org</span></a><span
style="color:#2A2A2A">) to facilitate training, education, and
integration with the CyVerse platform and user community. </span></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">This
release represents a significant expansion in the number of
curated pathways, projected species, and associated inferred
pathways, reactions, and genes (~25% data increase). Plant
Reactome now hosts pathway projections for 97 plant species (a
list of available species are available in the <a
href="https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=108&Itemid=360&lang=en"
moz-do-not-send="true">content summary</a>). </span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:green">Curation of reference rice pathways</span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman"">We have
added 6 newly curated pathways, 11 updated pathways, and 2
"container" pathways, resulting in a total of 306 reference rice
pathways. </span></p>
<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><b style="mso-bidi-font-weight:normal"><span
style="font-size:12.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman"">New Pathways:</span></b></p>
<ul>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""> </span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B">Cell Cycle <a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640760"
moz-do-not-send="true"><span style="color:#1F8FDE">G1 Phase</span></a></span><span
style="font-size:12.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""></span></li>
<ul>
<li><span style="font-size:12.0pt;font-family:"Courier
New";mso-fareast-font-family:"Courier New""><span
style="mso-list:Ignore"><span style="font:7.0pt
"Times New Roman""> </span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE">G1/S
Transition</span></a></span><span style="font-size:
12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""></span></li>
<ul>
<li> <span style="font-size:12.0pt;
font-family:Wingdings;mso-fareast-font-family:Wingdings;mso-bidi-font-family:
Wingdings"><span style="mso-list:Ignore"><span
style="font:7.0pt "Times New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE">Assembly
of pre-replication complex</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE"></span></a></span></li>
<li><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE">Activation
of pre-replication complex</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE"></span></a></span></li>
<li><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887"
moz-do-not-send="true"><span style="color:#1F8FDE">G1/S-specific
transcription</span></a></span><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol"><span style="mso-list:Ignore"></span></span></li>
</ul>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt
"Times New Roman""> </span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9641042"
moz-do-not-send="true"><span style="color:#1F8FDE">OsNAC5
transcription network involved in drought and high
salinity tolerance</span></a></span><span
style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times New
Roman""></span></li>
</ul>
</ul>
<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal"><b style="mso-bidi-font-weight:normal"><span
style="font-size:12.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman"">Updated Pathways:</span></b></p>
<ul>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""> </span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119502"
moz-do-not-send="true"><span style="color:#1F8FDE">Allantoin
degradation</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""> </span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119309"
moz-do-not-send="true"><span style="color:#1F8FDE">Aminopropanol
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
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style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119410"
moz-do-not-send="true"><span style="color:#1F8FDE">Ascorbate
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119287"
moz-do-not-send="true"><span style="color:#1F8FDE">Vitamin E
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119263"
moz-do-not-send="true"><span style="color:#1F8FDE">Arginine
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119553"
moz-do-not-send="true"><span style="color:#1F8FDE">Asparagine
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119567"
moz-do-not-send="true"><span style="color:#1F8FDE">Beta-alanine
biosynthesis I</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119297"
moz-do-not-send="true"><span style="color:#1F8FDE">Beta-alanine
biosynthesis III</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119506"
moz-do-not-send="true"><span style="color:#1F8FDE">Tyrosine
degradation I</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119443"
moz-do-not-send="true"><span style="color:#1F8FDE">Ammonia
assimilation cycle</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li><span
style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span
style="mso-list:Ignore"><span style="font:7.0pt "Times
New Roman""></span></span></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:#3B3B3B"><a
href="https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119407"
moz-do-not-send="true"><span style="color:#1F8FDE">Ureide
biosynthesis</span></a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
</ul>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:green">Pathway Projection to other species</span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman";color:black">We
have extended orthology-based pathway projections for 15 new
species. Plant Reactome now hosts pathway projections for 97
species ranging from unicellular autotrophs to higher plants
(for a list of available species in Plant Reactome click <a
href="https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=108&Itemid=360&lang=en"
moz-do-not-send="true">here</a>).</span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New
Roman";color:black">Recent Publications:</span></b><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></p>
<ol start="1" type="1">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l4 level1 lfo3;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Naithani S., P. Gupta, J. Preece,
P. D'Eustachio, J. Elser, J. Kiff, P. Garg, D.A. Dikeman$,
A.J. Olson, S. Wei, M.K. Tello-Ruiz, J. Cook, A. Fabregat, T.
Cheng, E. Bolton, A.F. Muñoz-Pomer, S. Mohammed, I.
Papatheodorou, L. Stein, D. Ware, and P. Jaiswal (2019). Plant
Reactome: A knowledgebase and resource for comparative pathway
analysis.<i> Nucleic Acids Res. <a
href="https://doi.org/10.1093/nar/gkz996"
moz-do-not-send="true">https://doi.org/10.1093/nar/gkz996</a><span
style="color:blue">.</span></i></span></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal;mso-list:l4 level1 lfo3;tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman"">Howe K.L., B. Contreras-Moreira,
N. De Silva, G. Maslen, W. Akanni, J. Allen, J.
Alvarez-Jarreta, M. Barba, D.M. Bolser, L. Cambell, M.
Carbajo, M. Chakiachvili, M. Christensen, C. Cummins, A.
Cuzick, P. Davis, S. Fexova, A. Gall, N. George, L. Gil, P.
Gupta, K. E. Hammond-Kosack, E. Haskell, S. E. Hunt, P.
Jaiswal, S. H. Janacek, P. J. Kersey, N. Langridge, U.
Maheswari, T. Maurel, M. D. McDowall, B. Moore, M. Muffato, G.
Naamati, S. Naithani, A. Olson, I. Papatheodorou, M. Patricio,
M. Paulini, H. Pedro, E. Perry, J. Preece, M. Rosello, M.
Russell, V. Sitnik, D. M. Staines, J. Stein, M. K. Tello-Ruiz,
S. J. Trevanion, M. Urban, S. Wei, D. Ware, G. Williams, A. D.
Yates, P. Flicek (2019). Ensembl Genomes 2020—enabling
non-vertebrate genomic research. Nucleic Acids Res., gkz890, <a
href="https://doi.org/10.1093/nar/gkz890"
moz-do-not-send="true">https://doi.org/10.1093/nar/gkz890</a></span></li>
<li class="MsoNormal"
style="color:black;mso-themecolor:text1;mso-margin-top-alt:
auto;mso-margin-bottom-alt:auto;line-height:normal;mso-list:l4
level1 lfo3; tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
mso-fareast-font-family:"Times New Roman""><a
moz-do-not-send="true"><span
style="color:black;mso-themecolor:text1;text-decoration:none;text-underline:
none">Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao
P, et al. (2019) Double triage to identify poorly
annotated genes in maize: The missing link in community
curation. PLOS ONE 14(10): e0224086</span></a> </span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;color:windowtext"><a
href="https://doi.org/10.1371/journal.pone.0224086"
target="_top" moz-do-not-send="true">https://doi.org/10.1371/journal.pone.0224086</a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
<li class="MsoNormal"
style="color:black;mso-themecolor:text1;mso-margin-top-alt:
auto;mso-margin-bottom-alt:auto;line-height:normal;mso-list:l4
level1 lfo3; tab-stops:list .5in"><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;
color:windowtext">Naithani S, Gupta P, <span
style="mso-spacerun:yes"> </span>Preece J, Garg P, Fraser V,
Padgitt-Cobb LK, Martin M, Vining K, Jaiswal P, Involving
community in genes and pathway curation, <span
style="font-family:"Arial",sans-serif">Database</span>,
Volume 2019, 2019, bay146, <a
href="https://doi.org/10.1093/database/bay146"
moz-do-not-send="true">https://doi.org/10.1093/database/bay146</a></span><span
style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-font-family:
"Times New Roman""></span></li>
</ol>
<span style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman"">Please let us know if you have any questions or
suggestions.</span><span style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""><br>
<br>
The Gramene Team</span><br>
<span style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""></span><span style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""></span><span style="font-size:12.0pt;font-family:
"Arial",sans-serif;mso-fareast-font-family:"Times
New Roman""><a href="http://www.gramene.org/" target="_top"
moz-do-not-send="true"><span style="color:#444444">www.gramene.org</span></a>.</span>
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style="font-size:12.0pt;line-height:107%;font-family:
"Arial",sans-serif"> </span></p>
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<w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" Priority="39" Name="Table Grid"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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<w:LsdException Locked="false" Priority="61" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1"/>
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<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/>
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<w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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<w:LsdException Locked="false" Priority="30" QFormat="true"
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<w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
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<w:LsdException Locked="false" Priority="52"
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<w:LsdException Locked="false" Priority="46"
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<w:LsdException Locked="false" Priority="52"
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<w:LsdException Locked="false" Priority="46"
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<w:LsdException Locked="false" Priority="52"
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<w:LsdException Locked="false" Priority="52"
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<w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
<w:LsdException Locked="false" Priority="51"
Name="List Table 6 Colorful Accent 5"/>
<w:LsdException Locked="false" Priority="52"
Name="List Table 7 Colorful Accent 5"/>
<w:LsdException Locked="false" Priority="46"
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<w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
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<w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
<w:LsdException Locked="false" Priority="51"
Name="List Table 6 Colorful Accent 6"/>
<w:LsdException Locked="false" Priority="52"
Name="List Table 7 Colorful Accent 6"/>
</w:LatentStyles>
</xml><![endif]--><!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
        {mso-style-name:"Table Normal";
        mso-tstyle-rowband-size:0;
        mso-tstyle-colband-size:0;
        mso-style-noshow:yes;
        mso-style-priority:99;
        mso-style-parent:"";
        mso-padding-alt:0in 5.4pt 0in 5.4pt;
        mso-para-margin-top:0in;
        mso-para-margin-right:0in;
        mso-para-margin-bottom:8.0pt;
        mso-para-margin-left:0in;
        line-height:107%;
        mso-pagination:widow-orphan;
        font-size:11.0pt;
        font-family:"Calibri",sans-serif;
        mso-ascii-font-family:Calibri;
        mso-ascii-theme-font:minor-latin;
        mso-hansi-font-family:Calibri;
        mso-hansi-theme-font:minor-latin;
        mso-bidi-font-family:"Times New Roman";
        mso-bidi-theme-font:minor-bidi;}
</style>
<![endif]-->
</body>
</html>