Tag Archives: Joint Genome Institute

2012 Workshop Series in Microbial Genomics & Metagenomics at JGI

There’s another series of workshops for both microbial genomics and metagenomics presented by the U.S. Department of Energy’s Joint Genome Institute in 2012.   These workshops include two days of seminars and three days of hands-on tutorials for both microbial genomics and metagenomics.  These workshops are centered on the use of the following bioinformatic tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB.  Registration for this workshop can be found here.

7th Annual Joint Genome Institute Users Meeting 2012

Recently announced, the Joint Genome Institute – US Department of Energy is planning to have their annual meeting in Walnut Creek, California, during the dates of March 20th to 22nd.  Registration is now open.  This should be another great meeting and includes another impressive array of speakers.

JGI’s Microbial Genomics & Metagenomics Workshops

The U.S. Department of Energy’s Joint Genome Institute has offered numerous workshops for both microbial genomics and metagenomics over the past two years, and registration for the last workshop for 2011 is now open.  This last five day workshop of 2011 includes two days of seminars and three days of hands-on tutorials for both microbial genomics and metagenomic and using the following bioinformatic tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB.  Registration for this workshop can be found here.

Lessons Learned from Ectomycorrhizal Fungal Genome Sequencing

Genome sequencing has provided us with an amazing amount of information regarding organismal biology and mycorrhizal fungi are some of the most interesting of the organisms who have had their genomes sequenced.  Maybe I am a little partial to these fungi because I study them intimately, but new sequencing technology has made this an exciting time for people like me.

Ectomycorrhizal fungi are a polyphyletic group of organisms which form a symbiotic association with the roots of tree species (the word ‘mycorrhizal’ literally means plant-fungal unions).  This association has typically been recognized by the exchange of nutrients and water from the fungus to the plant and the exchange of sugars derived from photosynthesis from the plant to the fungus.  Although ectomycorrhizal fungi only form mycorrhizae  with 3% of plant species (arbuscular and other mycorrhizal fungi associate with approximately 92% of plants), these associations are with a diverse array of plant lineages, including the Betulaceae, Cistaceae, Dipterocarpaceae, Fabaceae, Fagaceae, Myrtaceae, Pinaceae, and Saleceae.  Plants in these families cover almost the entire portion of boreal, temperate, Mediterranean, and sub-tropical woodlands, so their importance is significant.  It’s very interesting to note that these associations have independently arisen at least eight times within the angiosperms and between six and eight times in the gymnosperms.  Mycorrhizal associations are thought to have originated when plants and fungi climbed onto land together (more on that here).

The sequencing of both fungal and plant genomes over the last few years has led to greater understanding of how these organisms interact during their mutualistic associations.  Although genome sequencing has addressed some long established questions, there are many more questions that have arisen from these sequencing efforts.  This recent review in Trends in Genetics by Jonathan Plett and Francis Martin of INRA-Nancy, two of my collaborators, addresses the current state of our knowledge of  the ectomycorrhizal symbiosis and poses directions for future research in this vital research area.

Currently, only two ectomycorrhizal fungal genomes (Basidiomycete mushroom Laccaria bicolor & Ascomycete truffle Tuber melanosporum) have been sequenced, but other fungi (see the Mycorrhizal Genomes Project) are scheduled to be sequenced by the Martin Lab through JGI.  With a genome size of 65 Mb Laccaria bicolor has the largest amount of protein coding regions of any sequenced fungus, and Tuber melanosporum has the largest genome of any sequenced fungus at 125 Mb but has one of the least dense genomes.

The nature of mutualistic symbiotic relationships imply that both organisms benefit from the association and both ectomycorrhizal fungi and their host plants fulfill this criteria.  Unlike saprotrophic fungi, ectomycorrhizal fungi are very poorly suited to degrade cellulosic plant material, but they are able to access soil nutrients via a large biological toolbox of secreted proteases and phosphorus transporters.  Both Laccaria bicolor and Tuber melanosporum, which have very different genomes, exhibit a very similar suite of symbiosis-induced nutrient cycling enzymes, which suggest that providing nutrients to the host plant is a key defining feature of ectomycorrhizal fungi.  Interestingly, Laccaria bicolor and Tuber melanosporum rely on differing mechanisms of interacting with their host and acquiring carbon from the environment.  Laccaria bicolor appears to be less dependent on the host and more active at acquiring carbon from the soil substrates and, as a result, may act as a weak saprotroph in the environment.  Tuber melansporum is more aggressive in its colonization of plant roots and does not appear to be able to acquire carbon from the soil and therefore is more dependent on the host for its survival.

Information gathered from fungal genomes suggests that a majority of the biochemical and genetic control over the initiation of the mycorrhizal association comes from the fungal partner, which makes sense given that the fungus has more energy to gain from the association.  Most mycorrhizal fungi are unable to acquire carbon from the environment so they are completely reliant on hand outs from their host plants.  It appears that mutualistic fungi share similar mechanisms with pathogenic fungi and bacteria when interacting with plants, including the use of small secreted proteins which interact directly with plant cells.

With the sheer amount of genomic data being generated it’s an exciting time to be a scientist, especially one who studies mycorrhizal fungi.  Over the next few years, especially with sequencing projects scheduled for completion, we will have even more data to shed light on the amazing biological associations of plants and microbes.

(Above Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA)

Cranking Out Fungal Genomes

In the last two weeks, JGI have released 4 new fungal genomes:

  • Septoria musiva (teliomorph: Mycosphaerella populorum) – leaf and stem pathogen on forest trees
  • Rhodotorula graminis (Basidiomycete yeast) – widespread environmental sample and plant endophyte
  • Hansenula polymorpha (syn: Pichia angusta) – methylotrophic yeast industrially important in fermentations
  • Wolfiporia cocos (brown rot Basidiomycete fungus) – important root pathogen and Native American food staple

There is a lot of data to sort through on their website.  Hop to it!