P. chrysogenum genome

BBC news and GTO report the sequence of P. chrysogenum, will be published in October in Nat Biotechnology in a project based at the biotech company DSM. P. chrysogenum being the mold that fortuitously contaminated Dr Fleming’s bacterial plates.

The 13,500 reported genes in the press release is quite bit larger than relatives in the Aspergillus clade (~10,000 genes) so it will be intriguing to see what’s going on here and if there will be interesting examples of horizontal transfer like what has been investigated in Aspergillus oryzae. I am unclear as to whether the selected strain is a wild isolate or represents an industrial strain, but look forward to reading the full account of the genome.

Factoid – Most of the industrial fungal genome papers have seen publication in Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete chrysosporium).

Edit: 1-Oct-2008, Jonathan Badger, an author on the paper, blogs about the paper and links to the pre-print available on NBT site.

Escaping the dung pile quickly: Speedy Pilobolus spores

ResearchBlogging.orgSporangiophore discharge in the fungus <em/>Pilobolus kleinii captured with high speed video. In a paper appearing today in PLoS One, “The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi” Nicholas Money and colleagues including 6 undergraduates and 3 graduate students, have measured the speed of flight of spores discharging from several Ascomycete and Zygomycete dung fungi including Pilobolus kleinii, Basidiobolus ranarum, Podospora anserina, and Ascobolus immersus. The team used high speed cameras that recorded at 250,000 frames per second and were able to capture spores being launched at 25 meters per second at accelerations of 180,000 g. The publication also provides multimedia including a video of the spore discharge slowed down and set to music. Nik and Mark Fisher both presented portions of the work at the Mycological Society of America 2008 meeting this summer and showed clips of these dramatic videos, so it was great to see this in print shortly following the meeting.

By way of the press release the major findings from this work show that

… the discharge mechanisms in fungi are powered by the same levels of pressure that are characteristic of the cells that make up the feeding colonies of fungi. Therefore, the long flights enjoyed by spores result not from unusually high pressure, but from the way in which explosive pressure loss is linked to the propulsion of the spores. There appear to be some similarities between the escape of the spores and the expulsion of ink droplets through nozzles on inkjet printers.

As Dr Money has described in a humorous and humble manner before in his Mr Bloomfield’s Orchard, some of the coolest and fundamental observations about spore flight and discharge, from Buller to the present, have come from simple and careful observations of fungi. In this case they have used a new tools of ultra high speed photography to capture events. Some of the previous work from the Money lab on this front include a demonstration that conidia are actively launched and rather than being passively released by low velocity airflow in the toxic indoor mold Stachybotrys (Tucker et al FGB 2007; free at PMC)

Yafetto L, Carroll L, Cui Y, Davis DJ, Fischer MWF,Henterly AC,, Kessler JD, Kilroy HA, Shidler JB, Stolze-Rybczynski JL, Sugawara Z, Money NP (2008). The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi PLoS One, 3 (9) DOI: 10.1371/journal.pone.0003237

Fungi on Science Friday

NPR’s Science Friday covered fungi with several myco-luminaries on the radiowaves including:

The show also speaks with Gavin Sherlock on recently published work on the origins of lager yeast.

A brief history of lager yeast

Some tasty research if you are of the set who enjoy a good pint of beer. GenomeWebNews reports on a study in Genome Research by Barbara Dunn and Gavin Sherlock at Stanford, looking at the history of lager yeast Saccharomyces pastorianus, a hybrid of S. cerevisiae and S. bayanus. Using array Comparative Genome Hybridization (aCGH) they trace the history of S. pastorianus lager strains to show that they sort into two distinct groups indicating there might have been at least two independent origins of the hybrid strain/species both derived from an ale yeast.

The CGH data also indicates there have been many genome rearrangements and aneuploidies after the hybridization providing an interesting picture of recent post-allopolyploidy changes in two independent experiments. Lots more delicious genome evolution details in the paper, so drink up!

Gene prediction without training?

A new paper in Genome Research from Borodovsky lab at Georgia Tech provides an improved ab initio gene prediction building on their previous program GeneMark called GeneMark.hmm ES.  This application doesn’t require a training set when building models for gene prediction in fungal genomes and reports to have as good or better sensitivity and specificity than most of the commonly used ab initio programs. They are picking up on proviously described insights about fungal gene structures and introns which is the lack of a necessary branch site and varying degrees of conservation of splice-sites in most intron rich fungi (Schwartz et al, 2008) and that these intron sizes remain short across the fungi (Stajich et al. 2007).

In practice it should simplify the initial genome annotation protocols used and could really streamline the procedures. It doesn’t replace the need to gathering EST sequence data that can also be used generate a training set in an automated fashion.  EST and transcriptional evidence is still very important for identification of UTR and alternative splicing isoforms.

Hopefully these data from the predictions will integrate into the Cryptococcus and Coprinus genome annotations that are undergoing an update at the Broad.  We’ll see how well this performs on a couple of the Chytrid genome sequences we are working on as well.

Attend Fungal Genetics 2009!

If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month.  Budding (and conidiating) artists can also submit a Logo design so we have cool T-shirts to wear.

25th Fungal Genetics Conference Registration and Program

The Fungal Genetics Policy Committee invites you to attend the 25th Fungal Genetics Conference, sponsored by the Genetics Society of America.   The meeting will be held March  17-22, 2009 at the Asilomar Conference Center, Pacific Grove, California (near Monterey, California).

The FGSC is pleased to announce that the scientific program and registration information are available online at the FGSC website

Registration for the meeting will take place online at the FGSC and GSA websites from October 27th-December 12th.

Financial aid applications are due November 14th.

Abstract submission deadlines are the same as the registration deadlines, from October 27th to December 12.

LOGOS – Please Submit your artwork

We are also pleased to invite the submission of logos for the meeting. Past logos are available for review

The winner will receive a complimentary t-shirt.

Please send logos to the FGSC by October 17, 2008.