Genotyping Using Illumina MiSeq Amplicon Sequencing in Ganoderma

Ganoderma boninense, a basidiomycete white rot fungus, is a serious pathogen encountered by the oil palm industry in South East Asia. It causes the devastating basal stem rot (BSR) and upper stem rot (USR) disease in oil palm. Research efforts have been contributed by various parties such as the industry players, government entities and academicians to detect and tackle this deadly pathogen. DNA markers, such as single nucleotide polymorphisms (SNPs), will be useful for the detection of this pathogen.  Towards this end, ACGT has sequenced the whole genomes of pathogenic and non-pathogenic Ganoderma. By performing comparative genomic analysis, SNPs that can differentiate between pathogenic and non-pathogenic Ganoderma were identified. In this study, Illumina MiSeq sequencing platform was used to perform amplicon sequencing for these SNPs.  The workflow and analysis of amplicon sequencing have been optimised. It was shown that the amplicon sequencing results are reproducible, proving that Illumina MiSeq can serve as a genotyping platform for the diagnosis of the Ganoderma disease.