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The Glanville fritillary butterfly (Melitaea cinxia) is an ecological model for studying how organisms live in spatially structured habitats. This seminal system, initiated by late Professor Ilkka Hanski in the early 90’s with the still ongoing survey of the the occupancy of the butterfly in the network of meadows in the Åland islands (the classic metapopulation of the butterfly), has become pioneering also in studying the genetic and evolutionary processes resulting from habitat fragmentation. The first version of the Glanville fritillary genome was published in 2014 as the third butterfly genome published in the world, and the first eukaryotic genome sequenced in Finland. We are now in the process of improving upon this work with version 2 of the genome.
|Placed onto chromosomes (MB)||283||484|
|BUSCO (% complete and single copy, euk)||84.5||94.3|
Details of these steps are in the basic annotation guide above
1. You will receive a list of genes to annotate form Daniel Blande. If you have not received a list please contact daniel.blande (at) helsinki.fi
2. Open your received list of genes and login to main annotation server (Apollo)
3. Locate a gene model in Apollo from your gene list
4. Make relevant evidence tracks visible in the Apollo view
5. Add annotation to the User-created annotation area
6. Get the cDNA sequence of your annotation and perform BLASTX alignment
7. Perform multiple alignment against the best BLASTX hits
8. Set correct exon lengths and add missing exons into your annotation
9. Edit information of your annotation and move on to next gene on your list
10. Once you’re done with the annotations for the day, logout from Apollo
11. Once your whole gene list is finished and commented, send it back to daniel.blande (at) helsinki.fi . You may also request a new gene list at the same time. Select a new gene family and send a list of identifiers.
Support available during and post-annotation at:
daniel.blande (at) helsinki.fi
juhana.kammonen (at) helsinki.fi
Slack instant messaging: https://mcinxiaannota-ctk7011.slack.com/
1. Login to the Apollo service fails. After entering username and password the browser returns to the login page
2. Features such as scaffold coordinates are missing from the main annotation view
The Apollo server may be crowded during the annotation phase (there are 30+ people performing annotations). This may cause some loading of scripts to take a long time or even your browser to warn about this. Logout / re-login may help here. Apollo saves the location of your session so that when the user makes a re-login, the view and location within the genome will be the same as when logging out.
We have completed the manual annotation phase of the M. cinxia genome project. Thank you to everyone who was involved in the annotation. In total 1232 genes (1448 transcripts) have been annotated across a variety of gene families.
The prize winners for completing the most annotations were Janina, Tarja and Anne.