The Hyphal Tip

Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:

Allomyces macrogynus (Blastocladiomycota “Chytrid”)
Capsaspora owczarzaki (Ichthyosporea)

Already available data from

Monosiga brevicolis (JGI)
Batrachochytrium dendrobatidis (JGI, BI) (Chytridiomycota)

Still in progress (BI)

Amastigomonas sp
Amoebidium parasiticum
Nuclearia simplex
Salpingoeca or [...]

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Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though.

“Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
NYT Science article sort of summarizing the good, bad, and ugly of fungi [...]

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Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. In homage to his earlier street art we’ll discuss the growing Aspergillus genome posse.

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Postia placenta genome is now published in early edition of PNAS. Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters cannot break down lignin while white rotters (like the previously sequenced Phanerochaete chrysosporium). This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author – go Diego!).

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The 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 [...]

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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 [...]

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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.

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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.

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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.

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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 [...]

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