The Hyphal Tip

Report concludes that a fungal genome database is of “the highest priority”.

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

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The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons

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Another asexual species of fungi also has evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).

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A paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi.  RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae.  However, I think this study is the first to describe RIP in a putatively asexual fungus.  The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium.  A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.  

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Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. 

There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence traces.

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Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

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The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.

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A review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.

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While many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789″.

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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”.

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