Annotation of the Laccaria bicolor genome for protein-coding and non-coding RNA genes and their possible interactions in the onset of mycorrhizal symbiosis

The ectomycorrhizal fungus Laccaria bicolor plays an important role in forest ecology, the planetary carbon and nitrogen cycles, and environmental remediation as a mutualist symbiotic partner with a variety of tree species. Because of its importance, the DOE Joint Genome Institute selected it for sequencing as part of a larger project to sequence Populus trichocarpa and Glomus intraradices. This dissertation describes the annotation of the L. bicolor genome for protein coding, transfer RNA, ribosomal RNA, small-nucleolar RNA, and micro-RNA genes, and subsequent analyses of the gene models focusing on possible roles in symbiosis. A total of 18,429 protein coding gene models was identified and provided to the analysis consortium where they were used to develop a consensus model set. These gene predictions show a GC content distribution that is broader than the human genome and also includes many short introns. The gene models were searched for second messenger genes yielding a total of 57 G-protein, 117 GPCR, and 247 kinase genes. A total of 297 tRNA genes representing 51 of 61 possible anticodons was identified. High copy numbers of cysteine, aspartic acid, and glycine tRNA genes were found relative to the related species Coprinus cinereus and Ustilago maydis. The extra copies are likely to be tRNA-derived SINEs miscalled as genes based on the miscalculation of their secondary structure. A correspondence analysis of the codon usage indicates that the most important bias effects are compositional bias related to the broad GC content distribution and hydrophobicity indicating an adaption for transmembrane proteins. No complete rRNA operons were identified although many components were identified. A total of 22 snRNAs was identified including three copies of the U1 snRNA reported for the first time here in filamentous fungi. A search for micro-RNAs, unreported in any fungi, was accomplished by searching for genes in the biogenesis pathways and sequences that match the known characteristics of miRNAs in animal species. Although no conclusive evidence was found, 64 sequences were found that meet some of the known criteria and are prime candidates for biochemical assay.