The genome sequence of the basidiomycete fungus Laccaria bicolor S238N-H82
The DOE Joint Genome
Institute and the Laccaria Genome Consortium have publicly released the draft sequence of the ectomycorrhizal fungus Laccaria bicolor S238N-H82 in July 2006. This ectomycorrhizal basidiomycete was chosen because it is heavily studied, ecologically relevant and is used in large-scale inoculation of seedlings in forest nurseries.
The genomic sequencing work has been conducted by scientists (I Grigoriev et al.) at the Department of Energy's Joint Genome Institute in Walnut Creek, California. A network of laboratories including the Tree-Microbe Interactions Unit (INRA-Nancy), the Bioinformatics & Evolutionary Genomics Division (Gent University), the University of Alabama, the Microbial Ecology Department (Lund University) and additional teams (Tuebingen University, Göttingen University, Lyon University) is involved in EST sequencing, and the machine and manual annotations.
A whole-genome shotgun approach has been used to sequence the Laccaria genome. Genomic DNA has been fragmented into pieces of 3, 8 and 40-kb, cloned into a plasmid and fosmid vectors, amplified, and sequence reads generated from about 830,000 sub-clones. Sequence reads have been assembled into larger contiguous regions by Harris Shapiro at JGI and these further assembled onto fosmid-end sequenced scaffolds. The Stanford Human Genome Center (Jane Grimwood et al.) is performing finishing work on the draft genome. Final assembly will be accomplished using supplemental information from physical and genetic maps. All sequence data will be freely available to the scientific community.
- In February 2004, high quality DNA from the monokaryotic strain H82 of Laccaria bicolor S238N has been dispatched by F Martin (INRA-Nancy) and G Podila (University of Alabama) to JGI.
- In July 2004, 3kb- and 8 kb-genomic libraries of high quality DNA from strain S238N-H82 have been prepared at JGI.
- In September 2004, a 40-kb fosmid library of high quality DNA from strain S238N-H82 has been prepared. Based on preliminary screening and sequencing the size of the genome was estimated to be in the 60 Mb range.
- In January 2005, JGI has finished about 200 Mb sequencing of S238N-H82 mostly from 3 kb- and 8 kb-libraries.
- In February 2005, JGI has uploaded 833,392 raw single-pass reads of L. bicolor S238N-H82 to NCBI Trace Archive section.
- In March 2005, JGI has released the first assembly draft of L. bicolor S238N-H82 (see "The Laccaria Genome: An Update" for details).
- In June 2005, JGI uploaded 39,000 new ESTs to the JGI database. The clustering of JGI + INRA + Génoscope Laccaria ESTs gave rise to 14,300 unigenes, i.e. approx. 70% of the putative genome models. See Laccaria dbEST.
- At the end of July 2005, JGI and Ghent/INRA-Nancy run their annotation pipelines on the Laccaria genome assembly. The two sets of gene callers gave a similar raw estimate of the number of gene models, i.e. 18-20K.
- On October 13, 2005, the JGI (Igor Grigoriev et al.) has completed automated annotation of v1.0 of Laccaria bicolor genome. JGI Genome portal is available to the community of annotators at http://shake.jgi-psf.org/lacbi1/lacbi1.home.html. The current draft release, version 1.0, includes 20,614 predicted gene models that were functionally annotated using the JGI annotation pipeline.
- The complete Laccaria genome sequence was announced July 23, 2006, at the Fifth International Conference on Mycorrhiza in Granada, Spain by the International Laccaria consortium. See the Press release: "DOE JGI Sequences, Releases Genome of Symbiotic Tree Fungus". The JGI Laccaria Genome portal is now available at: http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html.
- Publication: The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008 Mar 6;452(7183):88-92.
- The Stanford Human Genome Sequencing Center, in collaboration with JGI, has carried out additional sequencing to close up the repetitive gaps and fix misassembled regions (J. Grimwood et al., unpublished results). In June 2008, this finished sequence has been anchored to L. bicolor genetic map. In this finished and anchored version of the assembly, the 20 largest scaffolds contain 80% of the total 60.583 Mbp of sequence. The largest assembled scaffolds with telomeric ends are 4.6 and 5.1 Mbp and likely correspond to chromosomes.
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