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<p style="margin:0in;text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black">Xenbase Newsletter
<span class="spelle">Autumn|Fall</span> 2024 [text version] <o:p></o:p></span></b></p>
<p style="margin:0in;text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black"><o:p> </o:p></span></b></p>
<p style="margin:0in;text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black">Open PDF to see figures/tables</span></b></p>
<p style="margin:0in;text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black"> </span></b></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">NEW TOOL Xenbase Simple Synteny Search: 16,000
<i>Xenopus</i> synteny maps!<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">Synteny, the conserved order of genes on a chromosome, carries valuable information for comparative genomics, phylogenetics and informs gene nomenclature. We have generated
new synteny maps comparing <i>X. tropicalis, X.</i> <i>laevis</i> L and <i>X.</i>
<i>laevis</i> S sub-genomes, Human, mouse and chick. The maps are based on explicit orthology assertions, combined with symbol matching. Each map shows the gene of interest at center, in yellow, flanked by 5 upstream and 5 downstream gene models. Orthologs/paralogs
are shown in same color, connecting matched gene symbols by same-colored lines. <o:p>
</o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">Try it here:
</span><span style="font-size:12.0pt;font-family:"Georgia",serif;color:#0070C0"><a href="https://www.xenbase.org/xenbase/static/gene/synteny.jsp"><span style="color:#0070C0">https://www.xenbase.org/xenbase/static/gene/synteny.jsp</span></a></span><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">
Just enter a gene symbol, hit search. It’s not perfect, and LOC genes are currently excluded from the serch, though they do show up in the maps. We are working to expand coverage- the next version will integrate reciprocal BLAST and InParanoid to resolve
orthology for more genes. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">Test it out and tell us if you find any bugs:
</span><span style="font-size:12.0pt;font-family:"Georgia",serif;color:#0070C0"><a href="mailto:Xenbase@cchmc.org"><span style="color:#0070C0">Xenbase@cchmc.org</span></a>
</span><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black"> </span></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">REGISTER NOW for XRET 20224:
</span></b><b><i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">Xenopus</span></i></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> Resources and Emerging Technologies Meeting @ NXR, Woods Hole MA.
</span></b><b><span style="font-family:"Georgia",serif;color:#3A7C22"> Registration closing soon!!</span></b></p>
<p class="MsoNormal"><b><span style="font-family:"Georgia",serif;color:black">When:
</span></b><b><span style="font-family:"Georgia",serif;color:#212529">Fri, October 11, 2024 — Mon, October 14, 2024</span></b></p>
<p class="MsoNormal"><span style="font-family:"Georgia",serif;color:#212529">Register here:
</span><span style="font-family:"Georgia",serif"><a href="https://www.mbl.edu/research/resources-research-facilities/national-xenopus-resource/workshops-and-meetings">https://www.mbl.edu/research/resources-research-facilities/national-xenopus-resource/workshops-and-meetings</a></span></p>
<p class="MsoNormal"><span style="font-family:"Georgia",serif;color:#212529"> </span></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">WORKSHOP</span></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> GO Jamboree at XRET: Community Curation</span></b><span style="font-family:"Georgia",serif;color:black">
</span><b><span style="font-family:"Georgia",serif;color:#3A7C22">for</span></b><span style="font-family:"Georgia",serif;color:#3A7C22">
</span><b><i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">Xenopus
</span></i></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">genes</span></b></p>
<p class="MsoNormal"><span style="font-family:"Georgia",serif;color:black">In the 2024
<i>Xenopus</i> researcher survey, 63% of people said YES, they would be happy to annotate the genes they work on for GO! A community curation workshop will be held on the last day of the XRET meeting in Woods Holes MA.
</span><span style="font-family:"Georgia",serif;color:#202124;background:white">We will train you to use a simple GO annotation tool (called
</span><b><span style="font-family:"Georgia",serif;color:#202124">GOAT</span></b><span style="font-family:"Georgia",serif;color:#202124;background:white">) to annotate the genes you know best </span><span style="font-family:"Georgia",serif;color:#202124">using
GO, from your own papers. Just bring your laptop! GO <i>Xenopus</i>! In preparation, register for an ORCID
</span><span style="font-family:"Georgia",serif"><a href="https://info.orcid.org/what-is-orcid/">here</a><span style="color:#202124">.
<b>No need to register for the workshop itself- everyone is welcome!</b> </span></span></p>
<p class="MsoNormal"><b><span style="font-family:"Georgia",serif;color:#3A7C22">When: Monday 9-10.30am Monday October 14<sup>th</sup>, 2024, XRET Woods Hole.</span></b></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black"> </span></p>
<p style="margin:0in;text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">NEW ANATOMY RESOURCE</span></b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">
</span><i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">Xenopus</span></i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> 3D anatomy atlas module from Jakub
<span class="spelle">Harnos</span>’ Lab (Masaryk University, Czech Republic) now on Xenbase.</span></p>
<p style="margin:0in;text-align:justify"><span style="font-family:"Georgia",serif;color:#212529">High-quality X-ray microtomography images cover the lifespan of the African Clawed Frog in unprecedented detail were recently published in
<span class="spelle">Gigascience</span> (</span><span style="font-family:"Georgia",serif"><span class="MsoHyperlink">doi: 10.1093/gigascience/giae037</span><span style="color:#212529">) and shared with Xenbase, to share with you!
<span class="grame">A</span></span><span class="grame"><span style="color:black">ll of</span></span><span style="color:black"> the
<span class="spelle">microCT</span> data files from this open access resource can be downloaded from Xenbase server.
<b>Access the <i>Xenopus</i> 3D atlas files here:</b> </span><a href="https://bigfrog2.xenbase.org/pub/xenbase/images/Laznovsky_3D_Atlas/"><span style="color:#1155CC;background:white">https://bigfrog2.xenbase.org/pub/xenbase/images/Laznovsky_3D_Atlas/</span></a><span style="color:#232333;background:white"> </span><span style="color:black"> </span></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red"> </span></p>
<p class="MsoNormal" style="text-align:justify"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">NEW XENOPUS BOOK</span></b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">
</span><b><i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">Xenopus Normal Table Redux.
</span></i></b></p>
<p class="MsoNormal" style="text-align:justify"><b><span style="font-family:"Georgia",serif;color:#3A7C22">Edited by Peter
<span class="spelle">Vize</span>. Illustrated by Natalya Zahn<i>.</i></span></b><b><i><span style="font-family:"Georgia",serif;color:red">
</span></i></b><span style="font-family:"Georgia",serif;color:black">A reworked version of
<span class="spelle">Nieuwkoop</span> & Faber’s classic text, the new <i>Xenopus</i>
<i>Normal Table Redux</i> merges the beauty, <span class="grame">art</span> and science of Natalya Zahn’s extraordinary nature illustrations with the wisdom and richness of the 1956 N&F text, supplemented by new stages (e.g., oogenesis,
<span class="spelle">metamorphs</span>), views, internal and external staging details, and molecular markers.
<b>The volume itself is also a work of art!</b> Limited to just 100 copies, it is hand sewn and bound by artist and lecturer Adj. Prof. Sydney
<span class="spelle">Vize</span> (yes, Peter’s daughter!), in a flat large format (12x9.5inches/ 30.5x24cm; 14pt font) that lays flat when opened. It is produced in 4 colors on luxurious egg-shell textured 80lb Neenah paper and will be priced at $300 USD. First
copies will be available in October. To reserve your copy, please contact Peter <span class="spelle">
Vize</span> directly: </span><span style="font-family:"Georgia",serif"><a href="mailto:pvize@ucalgary.ca">pvize@ucalgary.ca</a></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black"> </span></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">LAST CHANCE!
</span></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">The 2024 Xenbase -<i>Xenopus</i> Research community survey.</span></b></p>
<p class="MsoNormal"><span style="font-family:"Georgia",serif;color:black">Thank you to everyone who has replied to our survey questions- you’ve given us lots of great feedback and new ideas… but we’d like to hear from even
<b><i>more</i></b> people. The <b>survey is closing soon</b>, so if you can spare us a few minutes, please t</span><span style="font-family:"Georgia",serif;color:#212529">ake it today:
</span><span style="font-family:"Georgia",serif"><a href="https://forms.gle/5WFANQTKA6TuSyg67">https://forms.gle/5WFANQTKA6TuSyg67</a></span></p>
<p style="margin:0in;text-align:justify"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> </span></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">LATEST</span></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> v10
<i>Xenopus</i> Genome Files for Download</span></b></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-family:"Georgia",serif">In collaboration with of colleague
<span class="spelle">Taejoon</span> Kwon (UNIST, Rep. Korea), Xenbase has made new downloadable files which you can use for high-throughput data analysis (RNA-Seq and
<span class="spelle">ChIP</span>-Seq) and gene list for GO enrichment. These ‘clean’ files and the most up-to-date gene reports available.
</span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-family:"Georgia",serif">We highly recommend you use v10
<i>Xenopus</i> genome and proteome files for data analysis! </span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-family:"Georgia",serif"> </span></p>
<p style="margin:0in;text-align:justify"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:black">See PDF for scannable QR codes</span></p>
<p style="margin:0in;text-align:justify"><span style="font-family:"Georgia",serif">Click links below to download specific files.( X. laevis files on left, X. tropicalis on right)
</span></p>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black">Release notes detailing the sources for the data:</span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></p>
<pre style="margin-left:.5in"><span style="font-family:"Georgia",serif"> <a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/RELEASE.xenLae10.2024_06"><span style="font-size:10.5pt;color:#0070C0">RELEASE.xenLae10.2024_06</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/RELEASE.xenTro10.2024_06"><span style="font-size:10.5pt;color:#0070C0">RELEASE.xenTro10.2024_06</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span></pre>
<pre style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></pre>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black">GFF3 with all non-coding RNAs removed:</span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></p>
<pre><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3.gz"><span style="font-size:10.5pt;color:#0070C0">xenLae10.xb2024_06.sorted.gff3.gz</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3.gz"><span style="font-size:10.5pt;color:#0070C0">xenTro10.xb2024_06.sorted.gff3.gz</span></a></span></pre>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></p>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black">FASTA file for CDS in the GFF3:</span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></p>
<pre><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_cds.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenLae10.xb2024_06.sorted.gff3_cds.fa.gz</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_cds.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenTro10.xb2024_06.sorted.gff3_cds.fa.gz</span></a></span></pre>
<pre style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></pre>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black">FASTA
<span style="background:white">file of protein for CDS in the </span>GFF3:</span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></p>
<pre><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_prot.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenLae10.xb2024_06.sorted.gff3_prot.fa.gz</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_prot.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenTro10.xb2024_06.sorted.gff3_prot.fa.gz</span></a></span></pre>
<pre><span style="font-family:"Georgia",serif;color:black"> </span></pre>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black">FASTA
<span style="background:white">file of mRNA transcripts in the </span>GFF3:</span></b></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black;background:white"> </span></p>
<pre><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_tx.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenLae10.xb2024_06.sorted.gff3_tx.fa.gz</span></a></span><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_tx.fa.gz"><span style="font-size:10.5pt;color:#0070C0">xenTro10.xb2024_06.sorted.gff3_tx.fa.gz</span></a></span></pre>
<pre style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black"> </span></pre>
<pre style="margin-left:.5in"><b><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black;background:white">GTF version of the GFF file:</span></b></pre>
<pre style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:black;background:white"> </span></pre>
<pre style="margin-left:.5in"><span style="font-family:"Georgia",serif;color:#0070C0"> </span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gtf.gz"><span style="font-size:10.5pt;color:#0070C0">xenLae10.xb2024_06.sorted.gtf.gz</span></a></span><span class="MsoHyperlink"><span style="font-size:10.5pt;font-family:"Georgia",serif;color:#0070C0;text-decoration:none"> </span></span><span style="font-family:"Georgia",serif"><a href="https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gtf.gz"><span style="font-size:10.5pt;color:#0070C0">xenTro10.xb2024_06.sorted.gtf.gz</span></a></span></pre>
<p style="margin:0in;text-align:justify"><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22"> </span></p>
<p class="MsoNormal"><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:red">UPDATE</span></b><b><i><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">
</span></i></b><b><span style="font-size:14.0pt;font-family:"Georgia",serif;color:#3A7C22">FYI
<i>Xenopus</i> v10 gene model annotation improvements by Xenbase. </span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">For
<i>X. tropicalis</i>, from Jan23 to Jan24, we increased the number of fully annotated genes by 2,103; and we partially curated more than 7,000 more genes, leaving only 800 unannotated/uncharacterized genes in the v10.1 genome.</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Georgia",serif;color:black">For
<i>X. laevis</i>, we fully annotated 4,961 genes, and improved names and mappings for 2,568 genes.
</span><span style="font-family:"Georgia",serif;color:black">Our work to further improve
<i>X. laevis</i> annotations (naming models, mapping orthologs, associating proteins) is ongoing. The latest genome stats will be released in the winter Xenbase newsletter- stay tuned!</span></p>
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