Following our discussions in Zürich 6-7 September 2018, we are updating you now on the process to improve the IPO323 annotation.
You can view the currently available annotations here.
The genome browser allows you to visualize a wealth of additional annotation and RNAseq mapping tracks. Please let Marc-Henri (email@example.com) know if you have additional data that would be useful to display.
It would be very helpful if individual research groups would verify and correct their most important gene sets that they depend on (e.g. effectors, MFS, favorite gene). Obviously, groups are welcome to suggest changes to any wrongly annotated or missing gene. To make changes to the current core gene set, please contact Marc-Henri Lebrun (firstname.lastname@example.org). There is a dedicated Apollo webpage similar to the cap.ensemblgenome page described above that will allow you to make changes. You will need a username and password (many community members do already have access to the platform) to be able to change the gene model.
As discussed in Zürich, we want to release an improved version of the annotationfollowing a community discussion at the International Symposium on Cereal LeafBlights 22-24 May 2019 (Dublin, Ireland). The new annotation will replace thecurrent one on Ensembl and will be deposited in EBI-NCBI archives. Pleas note that the current annotation is still basedon the original annotation available from the JGI (Goodwin et al. 2011, PLOSGenetics).
Thank you all for your contributions.
With best wishes, Marc-Henri Lebrun and Daniel Croll
PS: The Ensembl team has also released a blog post advertising our efforts:
"The gene set for Zymoseptoria tritici, a wheat plant pathogen causing sectorial leaf blotch, is currently under review by a team of Z. tritici researchers. This is a collaborative effort (supported by EnsemblFungi) using an easy web-based tool called Apollo and hopes to consolidate and improve the existing gene sets. If you would like to get involved, please contact Marc-Henri Lebrun from the National Institute of Agricultural Research (INRA) in France (email@example.com) to get started."
For updates on the annotation process, visit the blog.
Chromosome two of Zt reference strain IPO323. Figure from Goodwin et al 2011 https://doi.org/10.1371/journal.pgen.1002070.g001