All posts by Jason Stajich

Assistant Professor at UC Riverside

Godzilla fungi

CNN reports on a giant (25 ft tall) prehistoric fungus classified by C. Kevin Boyce and collegues. Also see U Chicago press release and Softpedia articles about the manuscript entitled Devonian landscape heterogeneity recorded by a giant fungus published in Geology describing the Prototaxites fossil.  It has apparently been studied for quite a long time (150 years) to no avail as to whether it was fungus, algae, or lichen prior to this study.

[Thanks Annie].

More Neurospora genomes

We got word last week from the JGI that our DNA for Neurospora tetrasperma and N. discreta have passed QC and library QC and are on their way to being sequenced. The center also plans to do some EST sequencing to improve gene calling abilities.

Why more Neurospora genomes? The sequencing proposal discussed these species as a model system for evolutionary and ecological genetics. It will allow us and others to test several hypotheses about the molecular evolution of things like genome defense in Neurospora and to understand more about the evolutionary history of the model organism N. crassa.

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Orthology detection software

Blogging about Peer-Reviewed Research A paper in PLoS One, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, reports a new approach to assess the performance of automated orthology detection. These authors also wrote the OrthoMCL (2006 DB paper, 2003 algorithm paper) which uses MCL to build orthologous gene families. The authors discuss the trade-offs between highly sensitive specific tree-based methods and fast but less sensitive approaches of the Best-Reciprocal-Hits from BLAST or FASTA or some of the hybrid approaches. The authors employ Latent Class Analysis (LCA) to aid in “evaluation and optimization of a comprehensive set of orthology detection methods, providing a guide for selecting methods and appropriate parameters”. LCA is also the statistical basis for feature choice in combing gene predictions into a single set of gene calls in GLEAN written by many of the same authors including Aaron Mackey.

I’ve been reading a lot of orthology and gene tree-species tree reconcilation papers lately, some are listed in Ian Holmes’s group as well as listing some of the software on the BioPerl site. This also follows with on our Phyloinformatics hackathon work which we are trying to formalize in some more documentation for phyloinformatics pipelines to support some of the described use cases. I’m also applying some of this to a tutorial I’m teaching at ISMB2007 this summer.

Puccinia black stem rust disease spreading

The New Scientist has an article about the spread of black stem rust caused by Puccinia graminis. We briefly mentioned the 1st release of a Puccinia genome in January. Some more links about the spread of the Ug99 virulent strain.

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Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

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Fungal Genetics 2007 summary

A Fungal Genetics 2007 summary.
Wow. What a meeting! I am still exhausted and not just because of the very late Saturday night dancing at the close of the conference. I will just say anyone who thinks scientists are boring people should witness the passion researchers have for their science and in sharing it with other people. Not to mention that some know how to put on their dancing shoes and let loose. Because of the atmosphere at the Asilomar conference center, it really did feel like I was at a super fun science camp that culminated with a rock band and dancing in the big hall.

I am also digesting the science from the talks and social interactions with a variety of people enthusiastic about mycology, genomes, and evolution (which could be a conference unto itsself). There were presentations on a lot of really great topics, from symbiosis between mycorhizal fungi and plants (Laccaria bicolor) to cell wall structure in Cryptococcus. I got to meet so many people who are making an impact in the fungal community both in their research and in the resources provide online. I will try and re-cap so I can remember everything I saw.

Continue reading Fungal Genetics 2007 summary

Hello, do I know you?

Blogging about Peer-Reviewed ResearchSelf and non-self recognition is important for fungi when hyphae interact fuse if they should compartmentalize and undergo apoptosis to kill the heterokaryoton or exchange nutrients. This process is part of cell defense and to limit to the movement of mycoviruses.

A paper in PLOS ONE describes the Genesis of Fungal Non-Self Repertoire. This kind of work goes on down the hall from us as well in the Glass lab among others. This recent paper describes het genes, which contain WD40 repeats and different combinations of these help control specificity. There is of course a diverse literature on this subject especially in Neurospora, and I’m not reviewing it here, but it is an imporant process in understanding how fungi interact with their environment.