Zymoseptoria genome manual re-annotation project at ENSEMBL

​Dear colleagues working on Zymoseptoria genomics,

An exciting time has come for us to start the curation of Zymoseptoria genome annotation for strain IPO323. The European Bio-informatics Institute (EBI) has put in place a Web Apollo platform, where you will be able to make changes to gene models (fused genes, split genes, wrong start, wrong stop, wrong intron, RNAseq based 5’-UTRs and 3’-UTRS) as well as adding new gene models (new genes, novel splice variants). 

EBI has kindly offered to organize a webinar, in which they will demonstrate how to use their Web Apollo platform and how data will become visible at the Ensembl platform. The webinar will be offered in the next few weeks. Please fill in your preferred times and dates in the following Doodle poll and we will select a time which suits the most interested users.

In order to give you access to the Web Apollo platform, you will also need to register as a user. For every person participating in the annotation, please provide us name, institution and contact email address. 

We will forward this information to EBI for bulk pre-registration. Anyone who does not pre-register at this moment can register later through the website www.phytopathDB.org/zymoseptoria. PhytoPath is a BBSRC-funded project at EBI whose goals include the capture of annotations from communities. Our activity will thus be a part of the PhytoPath project. Our Web Apollo instance is located at http://cap.ensemblgenomes.org/zymoseptoria, where you perform annotation tasks. For a user guide of WebApollo, visit http://genomearchitect.org/web_apollo_user_guide. 

EBI staff will demonstrate how to use the most important functionalities of this platform in a webinar. After that webinar, and with some help of the user guide, you will probably learn quite quickly how cool and convenient Web Apollo is. 

Precise instructions for the annotation (when and how to change gene models, what information to add) will follow soon. For volunteer teams an analysis of given chromosomal region from the start to the very end will be organized. We will prepare the list of genomic regions for each volunteer lab. Other teams may annotate only genes related to their specific expertise and interest (they will have to register for a category of genes). 

The annotation results will become available on the public Ensembl Fungi site as a separate track in the browser. The plan is to “harvest” the annotations made in WebApollo by community members on a regular (daily) basis and make them available through the public site the next day. At the end of the annotation process (Christmas 2017), EBI will incorporate all the changes (new and modified gene models) into the main annotation release. We then plan to draft a community manuscript (likely target journal Genome Announcements- but other options also possible) describing the update.

We hope that that you are equally excited as we are to get the process started. Please respond to this message (replies to both Jason and Marc-Henri please), even if you do NOT wish to participate in the annotation process, so that it is clear to us who is in or out. Also, please check the list of recipients of this message. If you know anyone in the community who has NOT received this message, but might be interested to participate, feel free to forward this message to them. 

We look forward to a productive annotation process and an enjoyable interaction with all of you.

Jason and Marc-Henri