The Hyphal Tip: Fungal Genomes and Comparative Genomics

The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.

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.

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.

I've been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

• FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds - so a database of these enzymes

The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of 05-Feb-2008

Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I've been remiss in reviewing the paper myself, but they've created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut. Chris and Tom took some more Coprinus pictures while I was away from the lab.

The Saccharomyces Genome Database has deployed a wiki for gene annotation from the community.  This should be an interesting experiment in how information can flow from the community into these databases.

It seems intuitive enough that the size of an organism's genome should be related to its evolutionary complexity. As a general rule, this tends to be true. But look within a class of organisms and you'll find a great deal of genome size - also known as a C-value - variation. A newt's genome, for example, is ten times the size of a frog’s. This discrepancy between genome size and evolutionary complexity is known as the C-value paradox and it has long captured the imagination of biologists. Genome sequencing and annotation have revealed that a great amount of an organism's genome is non-coding, suggesting that a great deal of genetic content may be gained or lost without affecting the so-called "evolutionary complexity" of the organism (though whether this non-coding DNA is truly "junk" is still up for debate). In a recent Nucleic Acids Research paper, Gregory et al introduce another toolset to aid in our understand of genome size: the genome size databases. Three separate databases catalog the genome size statistics for various Plants, Animals and Fungi respectively, collectively covering >10,000 species. While various methods of estimating genome size may produce conflicting estimates of genome size (caveat emptor!), these tools should serve to help guide analyses and experiments of genome size evolution. Specifically, by enabling comparisons of genome size across multiple phylogenetic levels, these datasets should facilitate a better understanding of where the genome size/complexity relationship falls off. As an interesting side note, the authors mention a few particular findings in fungi. The histogram of genome size in Fungi (see the figure) tends to be tighter than in Plants and Animals, with almost all taxa within the range of 1C or 10-60 Mb of DNA. That said, a few species appear to exhibit considerable intraspecific variation. While this may be due to the aforementioned methodological errors, the authors consider that dikaryotic hybrids and heterokaryotes may contribute to this observation. It seems that we may only be scratching the surface of genome size variation in Fungi and if genome size is indeed rapidly evolving in Fungi, they may serve to as good models to study this evolutionary phenomenon.

In a recent Microbiology Mini-Review, Meriel Jones catalogs both the potential benefits and problems that arise from fungal genome sequencing.