Ganoderma boninense is a telluric lignicolous basidiomycete and the causal agent of basal stem rot, one of the most devastating diseases of the oil palm (Elaeis guineensis). While the fight against G. boninense is of major concern in Southeast Asia, little information is available regarding the genetic diversity and evolutionary history of the fungus. In this context, the development of an informative molecular marker set to characterize the diversity of G. boninense is a key step towards understanding the biology of this pathogen. A G. boninense draft genome sequence of 63 Mbp, assembled using 454 and Illumina sequencing technology, was used to identify and develop a set of microsatellite markers (simple sequence repeats, SSRs). A total of 2487 SSRs were identified, for which 145 SSR primer pairs were designed. These SSRs are characterized by di-to hexanucleotide motifs with 5 to 34 repetitions. Ninety-seven SSR loci were successfully amplified on an initial small set of G. boninense isolates from Indonesia. A collection of 107 isolates from several regions in Southeast Asia were screened to characterize each locus for allele number, polymorphism information criterion and the presence or absence of null alleles at each locus. These results allowed us to propose an effective set of 17 SSRs for studying genetic diversity within G. boninense.
To date,
Ganoderma boninense
is known to be the causal agent of basal stem rot (BSR) disease in oil palm (
Elaeis guineensis
). This disease causes rotting in the roots, basal and upper stem of oil palm. Infection causes progressive destruction of the basal tissues at the oil palm trunk and internal dry rotting, particularly at the intersection between the bole and trunk. Molecular responses of oil palm during infection are not well study although this information is crucial to strategize effective measures to control or eliminate BSR. Here we report three sets of transcriptome data from samples of near-rot section of basal stem tissue of oil palm tree infected with
G. boninense
(IPIT), healthy section of basal stem tissue of the same
G. boninense
infected palm (IPHT) and the healthy section of basal stem tissue of the healthy palm (HPHT). The raw reads were deposited into NCBI database and can be accessed via BioProject accession number PRJNA530030.
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