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.

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.

No abstract

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.

Ganoderma boninense is the dominant fungal pathogen in causing Basal Stem Rot (BSR) disease on oil palm. The whole genome of this fungus was sequenced using PacBio RS II platforms to gain the whole-genome shotgun libraries. These libraries were smoothed with Illumina Hiseq 4000 paired end sequencing to polish the genome assembly. Subsequently, a combination of Dovetail Chicago and HiC libraries with the HiRise assembly pipeline revealed the 12 pseudo-chromosomes of G. boninense. This is the first report of chromosomal-scale genome assembly for the most important fungal pathogen on oil palm.

Increasing of dry areas for Oil Palm plantation due to climate change led the breeders to develop drought stress, tolerant palm. Characterization of genetic materials for their physiological and genetic properties is required. Two distinct progenies derived from Tanzanian origin used for more adaptive to unwatered stress, and Nigerian origin used for more sensitive, were subjected for analysis. Physiological related variables were observed for sap flow, water potential, soil water content, greenhouse temperature and relative humidity, stomatal density, stomatal pore width, and proline content. The Tanzanian origin has more stable in sap flow, longer water potential detected, more adaptive in stomatal closure, and a lower in proline content than Nigerian origins. The genome comparison of both materials was performed by double digest Restriction Associated DNA and captured 299 294 SNPs. It found 9.3 % of those SNPs that were having a different allele with a minor frequency between progenies. And, 0.7 % from filtered SNPs were located and distributed in 167 genes. Two SNP markers were located in aquaporin NIP1-1 gene that related to water translocation between cells. One SNP marker was located in glutamate receptor 2.7-like gene that related to glutamate release and proline biosynthesis. The remaining SNPs will be in further analyzed.

The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target propensity of guide RNAs and thereby allowing the user to select the optimum guides. The approach used by CROP involves generating substitution, deletion and insertion combinations which are then mapped into the reference genome. Based on these mapped variants, scoring and alignment are conducted and then reported as a table comprising the off-target propensity of all guide RNAs from a given gene sequence. The Python script for this program is freely available from: https://github.com/vaprilyanto/crop.

SPolyketide synthase (PKS) is an essential catalyzing enzyme in the polyketide (PK) biosynthesis pathway of bacteria, fungi and plants which have diverse beneficial functions such as antibiotic and antiparasitic. This study was aimed to identify specific plant type III PKSs in the African oil palm, Elaeis guineensis, and predict its biosynthesized metabolites as plant defense compounds against the most threatening fungal pathogen, Ganoderma boninense that causing the basal stem rot disease. We used the oil palm protein database to detect the presence of type III PKS domains using the HMMER version V3.1b2. An artificial inoculation was made on oil palm root tissues and RNA sequencing was performed to obtain the transcriptome profile after 7 days exposure to G. boninense. Among 40,421 proteins, we identified 38 of which containing type III PKS domains. Signal peptide signature motifs were absence in all PKSs suggesting their intracellular functions during the polyketide biosynthesis. A molecular phylogeny analysis reflected the relationships among these PKSs that clustered into PKS-A, -B and -C clades. Most of the PKS-A members were up-regulated after G. boninense infection, indicating their essential role in the biosynthesis of PK products which might needed for defense.