[Xenopus] Labs that work with Hymenochirus ?

[Richard Harland]

Dear Christina

Many thanks for the inquiry, and I think we can provide a useful answer!

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.

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 this link <https://www.ncbi.nlm.nih.gov/assembly/GCA_019447015.1/>.  Here is the biorXiv manuscript https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1 <https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1>

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.   

 I feel it would be useful to have a Vista/ecrbrowser hosted, but someone would have to generate the resource from the aligned sequences

https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1 <https://www.biorxiv.org/content/10.1101/2021.10.18.464293v1>

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!

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

See you at the Xenopus meeting!

Richard








Richard Harland FRS
C.H. Li Distinguished Professor and Senior Associate Dean in the Division of Biological Sciences.
Department of Molecular and Cell Biology
Division of Genetics, Genomics and Development

mailing address 
Department of Molecular and Cell Biology 
University of California       
163 Life Sciences Addition #3200 
BERKELEY, CALIFORNIA 94720-3200 

(510) 643-7830
harland at berkeley.edu
lab web site http://mcb.berkeley.edu/labs/harland/
lab 571 LSA

> On Feb 22, 2023, at 11:07 AM, James-Zorn, Christina <Christina.James_Zorn at cchmc.org> wrote:
> 
> Greetings Xenopus peeps!
>  
> Does anyone in the Xenopus and/or Zebrafish community also work with the Afri
>  
> can Dwarf Frogs, genus Hymenochirus ?
> 
> If not you, do you know of anyone who does?
> 
> Hymenochirus are quite similar to Xenopus tropicalis, are popular in the pet trade, and have an egg size similar to that of zebrafish.
> 
> 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.
> 
> Let me know if you have any leads. email: xenbase at cchmc.org <mailto:xenbase at cchmc.org>
> Thanks!
> Christina@ Xenbase 
> 
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