<html><body><div style="font-family: verdana,helvetica,sans-serif; font-size: 12pt; color: #000000"><div>Dear Xenopus community,</div><div> Here is an announcement from Richard Harland regarding the upcoming DB special issue on Xenopus genomes.</div><div><br></div><div>marko</div><div><br></div><div><div class="WordSection1"><p align="center" style="text-align: center; margin: 0px;" data-mce-style="text-align: center; margin: 0px;"><b><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Update on Developmental Biology special Xenopus genome issue</span></b></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"> </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">The submission of the <i>X. laevis</i> genome manuscript has been delayed, so as to optimize the chromosome scale assembly. We have pushed back the deadline for submission of manuscripts, which use or enrich the genomics of <i>Xenopus</i> or other amphibians, to the end of October. People can take advantage of this delay to further hone their ideas, or discuss them at the MBL PI meeting.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">If you have ideas, or plans for manuscripts that exploit either the <i>X. tropicalis</i>, the <i>X. laevis</i>, or indeed other amphibian genomes, then Developmental Biology would be very happy to consider them.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Please send a paragraph on your plans to Richard Harland, then the journal can further plan this special issue. If you are doing some whole genome analysis that may not be covered in the <i>X. laevis</i> genome paper, let Richard know and he would be happy to share plans for the main manuscript with you.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">We prefer that people use the new assembly of record for <i>Xenopus</i> <i>laevis</i> (version 9.1). This is now available, along with annotation, on the Xenbase server, in both browser and downloadable formats. The assembly is a chromosome scale reassembly of version 7.1, so any analysis you have previously done should in principle be able to be “lifted over” to the new coordinates. However, we will accept alignments to the 7.1 assembly.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">The <i>X. laevis</i> 9.1 assembly improves on previous version by capturing >90% of the assembled sequence into 18 pseudomolecules representing the 18 chromosomes of <i>X. laevis</i>. These have been named based off of their orthology to <i>X. tropicalis</i> and unique evolutionary history. The v7.2 assembly was improved by Dovetail, using their proprietary Chicago reads followed by Hi-C data to measure DNA-DNA interactions and assemble scaffolds large enough to be ordered/oriented by BAC-FISH and synteny to X. tropicalis. Regions with important genes that were affected by gaps were replaced by high quality BAC sequences.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">A new <i>X. tropicalis</i> assembly is also available at Xenbase.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">The new <i>X. tropicalis</i> v9.0 assembly improves on previous versions by utilizing Dovetail’s Chicago reads to reorient small segments of <i>X. tropicalis</i> chromosomes whose orientation could not be discerned by the genetic map. Additional extrachromosomal sequence has been assigned to chromosomes. Improvements to the <i>X. laevis</i> transcriptome, which is used as a sister taxon, have also improved models in the <i>X. tropicalis</i> genome.</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"> </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Please contact:</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"> </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Richard Harland</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Editor, Developmental Biology</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><a href="mailto:harland@berkeley.edu" data-mce-href="mailto:harland@berkeley.edu"><span style="font-size: 11.0pt; font-family: Arial; color: windowtext; text-decoration: none;" data-mce-style="font-size: 11.0pt; font-family: Arial; color: windowtext; text-decoration: none;">harland@berkeley.edu</span></a><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">University of California, Berkeley</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Department of Molecular & Cell Biology</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">142 Life Sciences Addition #3200</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Berkeley, CA 94720-3200</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"> </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">I have received proposals (abstracts) for submission from:</span></p></div><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br clear="all" style="page-break-before: auto;" data-mce-style="page-break-before: auto;"> </span><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Amy Sater</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Michael Zuber</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Ron Stewart</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Ken Cho</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Hajime Ogino</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Shuji Takahashi</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Toshiaka Tanaka</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Masanori Taira</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Akira Hikoska</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Naoto Ueno</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Marko Horb</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Grant Wheeler</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Michael Klymkowsky</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Minoru Watanabe</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Mariko Kondo</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Richard Harland</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Qinghua Tao</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Derek Stemple</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;">Dan Rokhsar</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11.0pt; font-family: Arial;" data-mce-style="font-size: 11.0pt; font-family: Arial;"><br></span></p></div><div><span name="x"></span>---------------------------------------------------------------------------------------<br>Marko Horb, Ph.D.<br>Director, National Xenopus Resource (NXR)<br>Marine Biological Laboratory<br>7 MBL Street<br>Woods Hole, MA 02543<br><div><br></div>Email: xenopus@mbl.edu<br>Office: 508-289-7627<br>Cell: 508-564-3764<br><div><br></div>http://www.mbl.edu/xenopus<br>https://twitter.com/xenopusnxr<span name="x"></span><br></div><div><br></div></div></body></html>