Tag Archives: lichen

Lichen genome projects and the power shift prompted by next-gen sequencing

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. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues.

This isn’t the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has taken a while to get going because of some logistical problems getting the DNA (and any problems are amplified because it takes a long time to get new material since lichens grow very slow).

The transfer of the power for researchers to be able to quick exploratory whole-genome sequencing with next-gen and eventually, high quality genome sequences from next-gen sequencing is predicted to transform how this kind of science gets done. It means we’ll probably just sequence a mutant strain instead of trying to map the mutation – this is happening already in anecdotal stories in worms and in our work in mushrooms. N.B. this is done after a mutagenized strain has been cleaned up a bit to insure we’re looking for one or only a few mutations based on some crosses – but that is part of standard genetic approaches anyways.

This fast,cheap,whole-genome-sequencing is also the stuff of personal genomics, but for basic research it will also mean that a first pass exploring gene repertoire of an organism will be a multi-week instead of multi-year project. I just hope we’re training enough people who can efficiently extract the information from all this data with solid bioinformatics, computational, data-oriented programming, and statistical skills to support all the labs that will want to take this approach. You’ll need a life-vest to swim in the big data pool for a while until more tools are developed that can be deployed by non-experts.

Experimental cooperative evolution

Blogging about Peer-Reviewed ResearchA 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.

Tripartate symbioses with fungi

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. There are more layers to the relationship as a fungal parasite (Escovopsis) attacks the cultivated fungi, and a bacteria. Several researchers have studied the coevolution of these studies including Ulrich Mueller and Cameron Currie. Currie and Mueller have published several great studies describing the patterns of coevolution and the nature of the cooperation.
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