Genome Sequencing and Analysis in Traditional Chinese Medicine Ganoderma sinense

The genome of a model medicinal macrofungus, Ganoderma lucidum (GanLu), has recently been sequenced. Here we report the genome sequence of Ganoderma sinense (GanSi), the same as GanLu, which is an important traditional Chinese medicine, producing a large number of triterpenoids and polysaccharides. The genome sequencing using 454 and Illumina generated a genome assembly with 48.96Mb genome size about 55.58% GC content, which was anchored to the optical maps and 12 chromosomes spanned 48.63Mb. About 16,949 gene models was predicted using MAKER software, of which 80% was annotated by public nucleotide and protein databases. A total of 10.6% repeat sequences were identified using REPET. Some important genes were corrected in manual. We identified 19 genes from upstream of triterpene biosynthesis by homology alignment and collected 228 cytochrome P450s including 38 subfamilies, some of which may also be related to the triterpene biosynthesis. Phylogenetic analysis suggests the taxonomic status of Ganoderma in polyporales by the use of single copy genes. Genome comparison of GanSi and GanLu suggest the difference of them in genome structure. The differential expression of three phases including mycelia, primordial and fruiting bodies showed the high expression of genes in primordial and fruiting bodies. Also, the genome-wide regulation mechanism will be elucidated by DNA methylation and small RNA analysis. In conclusion, genome sequencing and analysis of G. sinense provided useful resources to elucidate the mechanism of the biosynthetic of pathways of fungal natural products and its regulation mechanism.