The Hyphal Tip: Fungal Genomes and Comparative Genomics

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.

A paper in Nature this week describes how a few mutations can alter the interactions between species in a biofilm from competitive to cooperative system. This is a great study that goes from start to finish on studying community interactions, looking at an evolved phenotype, and understanding the genetic and physiological basis for the adaptation. Acinetobacter sp. and Pseudomonas putida were raised in a carbon-limited environment with only benzyl alcohol as the carbon source. Acinetobacter can processes the benzyl alcohol, while P. putida is unable to. Acinetobacter takes up the bezyl alcohol and secretes benzoate that P. putida can then use as a carbon source. The research group propagated these in chemostats and looked at different starting concentrations of the organisms. They found that evolved P. putida had a different morphology and did several experiments to determine the relative fitness of the derived and ancestral genotype. They went on to also map the mutations in P. putida and found two independent mutations in wapH (I think this is the right gene)—a gene involved in lipopolysaccharide (LPS) biosynthesis. They then engineered the ancestral strain to have a mutation in P. putida and found the rough colony phenotype morphology indistinguishable from the strain derived from experimental evolution. There are various evolutionary and niche adaptation implications arising from this study. One application to mycology is to how lichens evolved in that an algael cell and a fungal cell must communicate and cooperate.

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

The JGI has previously released A.niger strain ATCC 1015 sequence in November 2005.

The Baylor sequencing center has published the genome of two honey bee pathogens. Bayolor and collaborators recently published a slew of honey bee genome papers and it is great that they have also chosen to follow up on the parasites as well.

Ants, fungi, and bacteria I have to admit that I am fascinated by co-evolution of symbiotic and mutalistic systems. A review by Richard Robinson gives an overview. A great example is the mutalism between ants and fungi where the ants cultivate the fungi for food.

The FGI and the Broad Institute have released the 7X genome assembly of Puccinia graminis f. sp tritici in roughly 4500 contigs. This represents the first rust fungus to be sequenced.

Sally Otto and colleagues have identified that populations of laboratory yeast strains convereged on diploidy in this study. This is nicely consistent with the observation that most wild strains isolated from the environment are diploid.

A recent paper identifies "Twenty-five repetitive elements ... in the genomes of the arbuscular mycorrhizal (AM) fungi Gigaspora margarita, Gig. rosea and Glomus mosseae".

The JGI has released the Phycomyces blakesleeanus genome. This represents the second Zygomycete genome sequence that has been released in addition to Rhizopus oryzae that was released by the Broad Institute last year. We are now getting a better look at the basal fungal genomes including the Chytrids and Zygomycetes.