Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis. We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences.

The oil palm conventional breeding is faced with many challenges, including the long breeding cycle and limited genetic variations available from the existing breeding populations. Recent genomic research revealed the genetic properties of various oil palm populations and could be exploited by recombining favorable alleles through molecular breeding and selection. In aimed to discover high quality single nucleotide polymorphisms (SNPs) sampled from 236 diverse genetic backgrounds palms, a paired-end ddRAD-sequencing was employed to discover allelic variations. Whole 195.62 Gb clean data were generated using ddRAD-seq. After stringent filtering, 8 189 SNPs in the annotated genes were discovered based on the oil palm EG05 reference genome. The high polymorphism rate was observed across the assayed populations, whereby 29 % of loci showed moderate to high putative impact on amino acid changes in silico as predicted by SnpEff software. The Angola and Deli origins seemed to have undergone inbreeding as reflected by the fixation index and the lower observed heterozygosity compared to expected heterozygosity. Assessment of genetic stratification and structure was not strong enough to differentiate the core breeding materials according to their prior genetic backgrounds. The results demonstrated the robustness and high-throuputness of ddRAD sequencing method for SNP discovery.

Here, we report the complete sequence of the mitochondrial (mt) genome of Ganoderma boninense that assembled as a single circular double-stranded DNA (dsDNA) of 86,549 bp with a G+C content of 26.81%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNA subunits, 4 hypothetical proteins, and 5 homing endonucleases.

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Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.