A few tool updates

I’m working to make more data available in the genome browsers for fungi. One is adding in the Primer information from the Neurospora KO project to the Neurospora browser to indicate the position and primer sequences for all the gene knockouts being (or already) constructed.  At least 60% of the genes have been knocked out and are available from the FGSC.

We’re also integrating SNP data using the HapMap glyphs in which you can see one way to view this information in the Genome Browser for Coccidioides.  Working on other information including PhastCons conservation profiles and other information in our development server and hope to make this public soon.

Coprinopsis cinereus genome annotation updated

Coprinus cinereus genome projectThe Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.

 

This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next week.  Additional work to annotate the “Kinome” by the Broad team provides some promising new insight to this genome annotation as well.

We’re using this updated genome assembly address questions about evolution of genome structure by studying syntenic conservation and aspects of crossing over points during meiosis.  The C. cinereus system has long been used as model for fungal development and morphogensis of mushrooms as it is straightforward to induce mushroom fruiting in the laboratory.  It also a model for studying meiosis due to the synchronized meiosis occurring in the cells in the cap of the mushroom.

Happy genome shrooming.

Please be sure of your mushroom’s identity before eating

Amanita PhalloidesSFChronicle has an article on musroom poisining from Amanita phalloides over this holiday season. They come in a variety of colors during their development depending on moisture and their surroundings. These are definitely beautiful and attractive mushrooms, but they are not to be eaten! Please be sure of what you are have found before eating. Waiting for that spore print is worth it when in doubt (at all!).  Get a copy of a good book especially if you are collecting in a new environment.

Also see Richard Eshelman’s survial from a mushroom poisoning experience.

Eigenfactors of mycology journals

Eigenfactor.org computes journal’s influence (akin to Impact Factor).  Here’s a plot of the influence and number of articles in journals classified as “Mycology”.  It shows bubbles representing eigenfactor and the lines are the representation of change over time – the animation is much more informative so click over to see it play out. Unfortunately a few mycology journals like Fungal Genetics and Biology/Experimental Mycology aren’t included.

Mycology Journals influence over time From http://eigenfactor.org
Mycology Journals influence over time. From http://eigenfactor.org