[Feedback] Site Feedback: Marchantia genome update

[Marcela K. Monaco]

Hello Dulce,

Unfortunately we can only host genomes (i.e., genome assembly and gene
annotation) that have been previously submitted to the INSDC (ENA, NCBI or
DDBJ). Version 1 is the only one available in any of these repositories. It
is very tricky to map things after 5 rounds of modifications (v1 <--> v6)
but that might be the only way you would be able to use Plant Reactome
pathways.  Unless the V6 assembly and annotation for *Marchantia polymorpha*
is submitted to the INSDC (preferably the ENA), we would not be able to
update it in Gramene.

If it helps, I noticed that gene names in the latest version 3.1 in
Phytozome seem to correspond to those in v1 after replacing the Mapoly###
prefix with MARPO_### but you would need to (BLAST) align them to confirm
this.  See for example:

https://phytozome-next.jgi.doe.gov/report/transcript/Mpolymorpha_v3_1/Mapoly0001s0006.1
and
https://ensembl.gramene.org/Marchantia_polymorpha/Transcript/Domains?db=core;g=MARPO_0001s0006;r=KZ772673:61451-62686;t=PTQ49917

Regards,

Marcela

On Tue, May 3, 2022 at 4:55 PM feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         : No referrer
>
> Subject     : Marchantia genome update
>
> Name        : Dulce Flores
>
> Email       : floresmtzdulce at gmail.com
>
> Organization: Universidad Veracruzana
>
> Comments    : Hello, I am interested in performing an analysis with
> Marchantia polymorpha, I work with Marchantia.info and the most recent
> version is 6. But when I try to use plantreactome.gramene, the only version
> is 1 and I cannot perform my analysis. I would like to know if it is
> possible to update the Marchantia polymorpha genome version
> Best regards
>
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.warelab.org_bugs_view.php-3Fid-3D6139&d=DwIBaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NTJkpUcuPGSVWXBMVfPABpI&m=vPzqHrL04DMltw9iKyoVDzfuT_QXQRF-LmgYieBSVxHOYmhWyPRs5ms_GnXoVnVe&s=g7zD6QStnfOY7IV9ZqV5jOYJWjFIKfBnJfWeT4chKKo&e=
>


-- 

Marcela Karey Tello-Ruiz, PhD
Computational Science Manager and Education, Outreach & Training Lead
Cold Spring Harbor Laboratory
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/feedback/attachments/20220504/f8b2b2f8/attachment.html>