Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 9, 2012
Publication Date: April 1, 2012
Citation: Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Burgess, S.C., Diehl, S.V. 2012. Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 78(7):2272-81.
Interpretive Summary: Next generation, short-read sequencing technology has provided the opportunity to explore unique gene expression from a variety of organisms. In this case, we sequenced a fungus that is resistant to copper and can rot wood. This experiment had two goals. The first was to prove that assemblies of the small genomes of fungus could be made with short-read methodology. The second was to build a gene catalog that could be used to investigate genes involved in lignocelluloses decay. This resource will be valuable for future studies of gene function in fungus like Fibroporia rediculosa.
The practical capability of short read sequencing for whole genome gene prediction was investigated for Fibroporia radiculosa, a copper-tolerant basidiomycete fungus that causes brown rot decay of wood. Illumina GAIIX reads from a single run of a paired-end library (75 nt read length, 300 bp insert size) were filtered to three levels of stringency. The original and the three filtered datasets were each assembled with Velvet. By combining a Venn analysis with histograms of read quality, we were able to identify a "best" assembly. This assembly had a genome size of 33.6 Mb, N50 = 65.8 kb for k = 51, max contig length of 347 kb, 9262 gene predictions, and 5407 genes with gene ontology annotations. Detection of 187 genes with putative roles in the decay of lignocellulose demonstrates that we have created a valuable molecular resource for future studies in functional genomics.