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.
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.
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.
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