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<p class="MsoNormal"><span style="font-size:11.0pt">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Please join us in <b>Marley 230 at 4:00 PM today</b> for a seminar presented by
<b>Md Nafis Ul Alam</b>, School of Plant Sciences, University of Arizona. <b>Dr. Dario Copetti</b> will serve as the host.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Zoom link: <a href="https://arizona.zoom.us/j/84253432688">
https://arizona.zoom.us/j/84253432688</a> (password: <b>SPLS2025</b>).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Refreshments will be provided in the Marley Lobby at 3:30 PM.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt">Title: Universal orthologs infer deep phylogenies and improve genome quality assessments<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt">Abstract</span></b><span style="font-size:11.0pt">: Universal single-copy orthologs are the most stable components of genomes. Although they are routinely used for studying evolutionary histories and assessing
new assemblies, current methods do not incorporate information from available genomic data. Here, we first determine the influence of evolutionary history on universal gene content in plants, fungi and animals. We find that across 11,098 genomes comprising
2,606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of their BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs likely
as an artifact of whole genome duplication events. Secondly, we investigate the extent of taxonomic congruence in BUSCO whole-genome phylogenies. For 275 suitable families out of 543 tested, sites evolving at higher rates produce up to 23.84% more taxonomically
concordant, and up to 32.25% less terminally variable phylogenies compared to lower-rate sites. We find topological differences between BUSCO concatenated and coalescent trees to be marginal and conclude that higher rate sites from concatenated alignments
produce the most congruent and least variable phylogenies. Finally, we show that BUSCO misannotations can lead to misrepresentations of assembly quality. To overcome this issue, we filter a Curated set of BUSCOs (CUSCOs) that provide up to 6.99% fewer false
positives compared to the standard BUSCO search and introduce novel methods for comparing assemblies using BUSCO synteny. Overall, we highlight the importance of considering evolutionary histories during assembly evaluations and release the UniPhy software
toolkit that reconstructs consistent phylogenies and reports phylogenetically informed assembly assessments.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Courier New";mso-ligatures:none">===============================================================<br>
</span><b><span style="font-size:20.0pt;font-family:"Vladimir Script";mso-ligatures:none">Zhongguo Xiong</span></b><span style="font-size:10.0pt;font-family:"Courier New";mso-ligatures:none"> <br>
School of Plant Sciences BIO5 Institute<br>
BIO5 Email: <span style="color:blue"><a href="mailto:zxiong@arizona.edu"><span style="color:blue">zxiong@arizona.edu</span></a></span>
<br>
Phone: (520)-621-9869<br>
Forbes 303, P.O. box 210036 Fax: (520)-621-7186<br>
University of Arizona <br>
Tucson, AZ 85721-0036 <span style="color:blue"><a href="http://ag.arizona.edu/~zxiong"><span style="color:blue">http://ag.arizona.edu/~zxiong</span></a></span><br>
===============================================================</span><span style="font-size:11.0pt;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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