The Hyphal Tip

Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches' broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different from other basidiomycete fungi and are lineage specific expansions will help determine if these families played a role in the adaptation of this plant pathogen.

This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches' broom disease.

See related:

• Will you always be able to satisfy that chocolate craving?
• Theobroma cacao to be sequenced, Oompa Loompa genome to follow.

Jorge MC Mondego, Marcelo F Carazzolle, Gustavo GL Costa, Eduardo F Formighieri, Lucas P Parizzi, Johana Rincones, Carolina Cotomacci, Dirce M Carraro, Anderson F Cunha, Helaine Carrer, Ramon O Vidal, Raissa C Estrela, Odalys Garcia, Daniela PT Thomazella, Bruno V de Oliveira, Acassia BL Pires, Maria Carolina S Rio, Marcos Renato R Araujo, Marcos H de Moraes, Luis AB Castro, Karina P Gramacho, Marilda S Goncalves, Jose P Moura Neto, Aristoteles Goes Neto, Luciana V Barbosa, Mark J Guiltinan, Bryan A Bailey, Lyndel W Meinhardt, Julio CM Cascardo, Goncalo AG Pereira (2008). A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-548

The DNA sequence of Melampsora larici-populina has been determined by the U.S. Department of Energy DOE Joint Genome Institute (DOE JGI). Annotations of the v1.0 assembly of Melampsora laricis-populina are publicly available at http://www.jgi.doe.gov/Melampsora.

Genome Technology highlights the very cool thing about next-gen sequencing - it puts the power in the hands of the researchers to explore genome sequence and doesn't limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke's Institute for Genome Sciences and Policy through their next-gen sequencing program.

A Brevia piece in Science today describes efforts to describe the causal agent in white-nose syndrome (WNS) in bats which appears to be contributing to bat decline. According to the authors, previous work had described an uncharacterized fungus associated with bats that showed signs of being sick with WNS.

Trying a little experiment here. I've started a wiki page for jobs that fall into the general category of genomics, fungi, and evolution and added a tab link to this at the top of the blog site. At this point I am only posting academic positions (Faculty and postdoctoral positions) but it may be possible to include industry and government postings if there is sufficient interest.

You are welcome to sign up for a wiki account and add links for other positions.

Registration opens today for the 25th Fungal Genetics conference at Asilomar. The preliminary program is also available with a great slate of speakers already lined up and plenty of opportunity for many students and postdocs to present their work.

The 24th conference help in 2007 was great and expect a similar great opportunity for sharing science and networking with the fungal genetics community.

Related links

• Attend Fungal Genetics 2009!
• Fungal Genetics 2007 summary

Nature news picked up an article that a Stachybotrys sp. can remove sulfur from crude oil and which would be more efficient than traditional chemical and heat methods. You may remember that some Stachybotrys are a nasty black indoor mold that can cause indoor air quality problems. It will be quite interesting to see more about this particular species once it has been better followed up.

A paper (Park et al, BMC Genomics) from Fungal Bioinformatics Lab at Seoul University in South Korea describes their new "Fungal P450 Database". The database contains sequence, names, and genome links for P450's (or Cytochrome P450s) identified by similarity and phylogenetic classification from genome annotations.

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.

Mike Challen asks for anyone with Agaricus bisporus ESTs, BAC data, or mapping information to send them in the direction of the JGI to aid in the assembly and annotation of this mushroom genome.