<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Christina<div class=""><br class=""></div><div class="">Many thanks for the inquiry, and I think we can provide a useful answer!</div><div class=""><br class=""></div><div class="">Rebecca Heald’s lab uses them, and has obtained them originally from the pet shop, though of course they are now under the oversight of the IACUC.<div class=""><br class=""></div><div class="">There is a genome sequence, well assembled, as part of a bigger survey of frog sequences, and chromatin/sequence structure. one can find it by googling, or click <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_019447015.1/" class="">this link</a>. Here is the biorXiv manuscript <a href="https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1" class="">https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1</a></div><div class=""><br class=""></div><div class="">Maybe all those sequences should be hosted by Xenbase as well as NIH? Xenbase does host a browser for 26 aligned amphibian genomes as an option on theX. tropicalis v10 genome browser, including the extremely basal Ascaphus truei, and a urodele outgroup ( See screenshot below). I also have access to a more manageable set of files one can run on one’s own machine (which needs a lot of RAM), let me know if you want it or if Xenbase should host the raw .maf files. That alignment has other vertebrate outgroups. </div><div class=""><br class=""></div><div class=""> I feel it would be useful to have a Vista/ecrbrowser hosted, but someone would have to generate the resource from the aligned sequences</div><div class=""><br class=""></div><div class=""><a href="https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1" class="">https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1</a></div><div class=""><br class=""></div><div class="">I should apologize for the long delay in getting this into the formal literature. As often happens with these big projects, there are annoying loose ends that are difficult to tie up after people go out into the real world. But all the resources are linked in the manuscript. However, there are many nice biological nuggets in there, so everybody should do a journal club on it!</div><div class=""><br class=""></div><div class="">to whet your appetite, here is the whole genome alignment showing the extraordinary synteny between frogs, and how rare it is to rearrange chromosomes in the course of the one billion years combined branch length in the figure</div><div class=""><br class=""></div><div class="">See you at the Xenopus meeting!</div><div class=""><br class=""></div><div class="">Richard</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="5B330FAC-F55A-4055-8A0E-8924A3FCBD63" src="cid:0F444FF0-B59E-4E15-88B2-8577AA777D75" class=""><img apple-inline="yes" id="87F1DC9B-899F-4AB5-9CE0-79B64D3E834D" src="cid:0AC9E78A-8ABC-47EE-833E-066DC155DF3A" class=""></div><div class=""><br class=""></div><br class=""><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: "Lucida Grande"; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: "Lucida Grande"; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class="">Richard Harland FRS<br class="">C.H. Li Distinguished Professor and Senior Associate Dean in the Division of Biological Sciences.<br class="">Department of Molecular and Cell Biology<br class="">Division of Genetics, Genomics and Development<br class=""><br class="">mailing address <br class="">Department of Molecular and Cell Biology <br class="">University of California <br class="">163 Life Sciences Addition #3200 <br class="">BERKELEY, CALIFORNIA 94720-3200 <br class=""><br class="">(510) 643-7830<br class=""><a href="mailto:harland@berkeley.edu" class="">harland@berkeley.edu</a><br class="">lab web site http://mcb.berkeley.edu/labs/harland/<br class="">lab 571 LSA</div></span></div></span></div>
</div>
<div><br class=""><blockquote type="cite" class=""><div class="">On Feb 22, 2023, at 11:07 AM, James-Zorn, Christina <<a href="mailto:Christina.James_Zorn@cchmc.org" class="">Christina.James_Zorn@cchmc.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class="">Greetings Xenopus peeps!<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">Does anyone in the Xenopus and/or Zebrafish community also work with the Afri</span><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><p style="margin-top: 0in;" class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">can Dwarf Frogs, genus<span class="apple-converted-space"> </span><em class=""><span style="font-family: Arial, sans-serif;" class="">Hymenochirus</span></em><span class="apple-converted-space"> </span>?<o:p class=""></o:p></span></p><p style="margin-top: 0in;" class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">If not you, do you know of anyone who does?<o:p class=""></o:p></span></p><p style="caret-color: rgb(34, 34, 34); font-variant-caps: normal; text-align: start; -webkit-text-stroke-width: 0px; word-spacing: 0px;" class=""><em class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">Hymenochirus</span></em><span class="apple-converted-space"><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class=""> </span></span><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">are quite similar to<span class="apple-converted-space"> </span><em class=""><span style="font-family: Arial, sans-serif;" class="">Xenopus tropicalis</span></em>, are popular in the pet trade, and have an egg size similar to that of zebrafish.<o:p class=""></o:p></span></p><p style="caret-color: rgb(34, 34, 34); font-variant-caps: normal; text-align: start; -webkit-text-stroke-width: 0px; word-spacing: 0px;" class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">I’m looking for a university lab that would be interested in doing some contract genomics work ( probably CRISPR/TALEN gene knockout) for a biotech company in the USA.<o:p class=""></o:p></span></p><p style="caret-color: rgb(34, 34, 34); font-variant-caps: normal; text-align: start; -webkit-text-stroke-width: 0px; word-spacing: 0px;" class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">Let me know if you have any leads. email:<span class="apple-converted-space"> </span><a href="mailto:xenbase@cchmc.org" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">xenbase@cchmc.org</a><o:p class=""></o:p></span></p><p class=""><span style="font-size: 11.5pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34);" class="">Thanks!<br class="">Christina@ Xenbase<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></p></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Xenopus mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:Xenopus@lists.mbl.edu" style="color: rgb(5, 99, 193); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Xenopus@lists.mbl.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://lists.mbl.edu/mailman/listinfo/xenopus" style="color: rgb(5, 99, 193); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://lists.mbl.edu/mailman/listinfo/xenopus</a></div></blockquote></div><br class=""></div></body></html>