Update from EuPathDB:

We are pleased to announce the release of FungiDB 34

New data in this release
Genome Sequence and Annotation: these annotated genomes appear for the first time in FungiDB.
·        Clavispora lusitaniae ATCC 42720 – Butler G et al.
·        Magnaporthe oryzae BR32 – Chiapello et al.
·        Uncinocarpus reesii 1704 – Sharpton et al.
·        Zymoseptoria tritici IPO323 – Grandaubert et al. and Goodwin et al.

RNA Sequencing data
·        Characterization of light regulated genes – Wu et al.
·        Transcriptome of Magnaporthe oryzae isolates collected from Bangladeshi fields – Islam et al.
·        Transcriptome of Magnaporthe oryzae isolates collected from Bangladeshi fields (aligned to BR32) – Islam et al.
·        The Cryptococcus neoformans transcriptome at the site of human meningitis (paired-end data) – Chen et al.
·        The Cryptococcus neoformans transcriptome at the site of human meningitis (single-read data) – Chen et al.

Proteomics data
·        Phosphoproteome in non-limiting conditions – Fusarium graminearum phosphoproteome in non-limiting conditions. Rampitsch et al.

Chip-seq data
·        ADV-1 gene targets ChIP-seq – ADV-1 functions to generate distinct temporal dynamics of target genes in Neurospora crassa. Dekhang et al.


Neurospora crassa e-Compendium
PubMed IDs from Neurospora crassa e-Compendium by Alan Radford and Matt Sachs have been loaded for Neurospora crassa OR74A. The list of loaded publications is available.


New features in this release

REVIGO direct link
EuPathDB now offers a direct link from gene ontology (GO) enrichment results to REVIGO, a tool that provides GO term summarization and visualization. To access this feature first run a GO term enrichment using the 'Analyze Results' option from any gene search result. Then click on the 'Start Revigo Analysis' link (upper right hand side of enrichment results) to populate the REVIGO submission page with your GO enrichment results from EuPathDB. Follow instructions on the REVIGO page to complete your analysis.

External database links
·        In a collaborative effort between FungiDB and PHI-Base, FungiDB gene pages now contain links to PHI-Base for 47 fungal organisms.
·        In a collaborative effort between FungiDB and JGI, FungiDB Aspergillus nidulans gene pages now contain links to JGI record pages.
 
Interpreting RNA Seq data on FungiDB
         
     Gene page expression graphs as well as all GBrowse coverage plots display data from uniquely aligned reads, which align to one location only.  This may under-represent expression for genes that are duplicated in the genome. See this news item to learn more about how to view non-unique reads and improvements planned for future releases.

As always, Contact Us with questions or concerns.

Sincerely,

The EuPathDB Team

http://eupathdb.org/eupathdb/
https://www.facebook.com/eupathdb/
https://twitter.com/eupathdb

List of 4075 genes selected by D. Studholme at Exeter 
Helder has just sent you a list of 4075 genes selected by D. Studholme since they have not any of the following three obvious potential problems:

(1)    Missing stop codon (i.e. final predicted exon lacks and in-frame stop codon; given that no UTRs are annotated, then I assume that the final codon should contain an in-frame stop codon).
(2)    Multiple possible ATG start codons. In other words, it is possible that the gene model has the wrong start codon.
(3)    Very short first exon.
This selection does not imply that these 4075 gene models are right, but here is no obvious evidence that they are wrong. Therefore, they were prioritised by Exeter for their ORFeome project.

We agreed in July to have a look the first 600 of these genes (20 for each annotator) as a pilot study in order to have your feedback on the actual settings of Zt WEB Apollo site, before opening it to the community. These genes are likely more easy to check than a random selection.

Transposons
When annotating, please check that the gene you are working on do not contain an open reading frame from a transposon using the track  . Transposon ORFs are difficult to annotate and are therefore excluded from the community annotation process

Homology track
Use it for comparison to other well annotated fungal genomes

RNAseq tracks
Use first the bw tracks of RR files. If not sufficient find the best samples in other tracks. 
Overall, select only few RNAseq tracks, ie those for which your gene display a sufficient number of reads (>20), and if possible RNAseq conditions in which the neighboring genes are not expressed. Indeed, the gene coding part of Zt genome is compact, and frequently there is an overlap of the RNAseq reads among neighboring genes, making difficult to define the start of its 5’UTR and end of its 3’UTR. 

Gene naming (to give to the curated gene in the main track)
We agreed in July to use the number defined by WUR (track), using the prefix ZtWA for
Zymoseptoria tritici Web Apollo. 
For example 
JGI annotation   being wrong (introns not supported by RNAseq data in this case), the Wageningen model  is chosen for the used-created annotation track and renamed ZtWA_66101. 
This topics will be further discussed at Kiel in September 2017. 

Feedback
We need your feedback on the tracks displayed (are they all useful or not?), do we need additional ones? What are the problems you have encountered? 
You can use the google sheet sent by Helder to leave on line your comment gene per gene. We will open a dedicated mailing list so you could send questions/comments to all annotators early next week.

​Marc-Henri Lebrun

​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