Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia

• Format: Thesis
• Language: English; English
• Published: 2012
• Subjects: SB183-317 Field crops Including cereals, forage crops, grasses, legumes, root crops, sugar plants, textile plants, alkaloidal plants, medicinal plants
• Online Access: https://eprints.ums.edu.my/id/eprint/38636/1/ABSTRACT.pdf; https://eprints.ums.edu.my/id/eprint/38636/2/FULLTEXT.pdf; https://eprints.ums.edu.my/id/eprint/38636/

Four types of preparation were done prior to de novo sequencing of Ganoderma sp. causing basal stem rot in oil palm located in Sabah, Malaysia. Firstly, at least 12 μg of DNA with the ratio of OD260 to OD2so between 1. 7 and 2.0 was obtained from the mycelia of Ganoerma sp. strain C in order to be sent for de novo sequencing. Secondly, the DNA sequencing of PCR amplified region of ITSl, 5.8S rDNA and ITS2 of the four strains of Ganoderma sp. was conducted, revealing that strain A was actually identical to strain E. Both strains were much closely related to strain B than to strain C. Regardless, all the strains were considered to be of the same species when they were compared to the more well-known G. /ucidum. BLAST revealed that the identification of the strains could not be done due to the limited genetic information regarding the species in Genbank database. All of the sequences were submitted to the database and given the accession numbers, therefore freely allowing others to analyze the DNA sequence in the database. The workflow of SOAP, AbySS and Velvet was prepared and tested with the paired-end sequences of human 18 chromosome 12 to compare the contigs produced by them. Unfortunately, no clones containing DNA of Ganoderma sp. were successfully produced. All the preparations were done in anticipation that the assembly and analysis of the de novo sequences of Ganoderma sp. would be hastened.