Bioinformatics Analysis of Expressed Genes in Ganoderma lucidum

• Main Authors: Wei-Hsiang Hsieh, 謝威翔
• Other Authors: Ueng-Cheng Yang
• Format: Others
• Language: zh-TW
• Published: 2006
• Online Access: http://ndltd.ncl.edu.tw/handle/49310103526875658575

碩士 === 國立陽明大學 === 生物資訊研究所 === 94 === Ling-Chi (Ganoderma lucidum) is one of the traditional Chinese herbs. The recent studies have revealed that polysaccharides, triterpenes, and some microelements in Ling-Chi have several interesting effects, such as anti-tumor, hypoglycemic, hypocholesterol, and immuno-stimulation. The genome and expressed sequence tag (EST) analyses are useful in identifying the genes involved in the biosynthesis of polysaccharides or triterpenes. Ling-Chi genome project have sequenced the draft sequence by shotgun method. In order to discover the expressed genes, the EST project has completed the sequencing of 47,122 EST sequences in 2005. The redundancy of the EST sequences was removed by two steps. The EST sequences were assembled and then be compared with the known protein sequences of other species. Those sequences that match the same protein were merged and got 9,697 tentative unique genes (TUG-1). The possible functions and reaction pathways of these TUG’s were annotated by using the sequence similarity to known proteins. On the basis of literature survey and sequence analysis, I identified 46 genes that might be involved in the polysaccharide biosynthesis in Ling-Chi. Moreover, 20 genes among the 46 genes, which are very similar to the known genes in the database, were annotated further. The gene structure, the predicted protein sequences, the putative protein domains of these genes were summarized for functional studies. In additional to annotating the function of Ling-Chi genes, EST sequences can also be applied to verify the gene structure predicted by programs, to estimate the gene numbers, to provide the order of genomic contigs, and to find the putative paralogous genes of Ling-Chi. Selected examples are discussed to demonstrate the feasibility of such approaches.