The Hyphal Tip: Fungal Genomes and Comparative Genomics

Looks like the USDA, Mars (the candy company), and IBM are partnering up to sequence the Cacao plants genome for everyone to use. Here is the article over at BBC News.

This month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:

The [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.

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

Neil has a great summary of the results from the Platypus genome sequencing project.

Ewan Birney and Ensembl (the other/original genome browser depending on if you are a UCSC junkie) have started blogging a bit more about what is going on under the proverbial hood over there in Hinxton.  There are some great nuggets talking about what are some of the current problems.  These bite-sized comments should be a great glimpse into how Ensembl works

The Broad Institute has made available the Schizosaccharomyces octosporus genome sequence producing another model system (S.pombe) with several related species for comparative genomics.  I believe S. octosporus genome was entirely sequenced with 454 technology.   The other genome sequences in the Taphrina clade include the S. japonicus genome. S. octosporus is pretty interesting as it grows filamentously and is 8-spored unlike

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

Interesting blog post that mentions N. crassa and RIP

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.