The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

Overgrowth of Agrobacterium tumefaciens has frequently been found in Agrobacterium-mediated plant transformation. This overgrowth can reduce transformation efficiency and even lead to explant death. Therefore, this research investigates an alternative way to mitigate or eliminate Agrobacterium after transformation using a bacteriophage. To develop this alternative method, we conducted effectiveness studies of two lytic bacteriophages (ΦK2 and ΦK4) and performed an application test to control Agrobacterium growth after transformation. According to plaque morphological characterization and molecular analysis, the two bacteriophages used in this experiment were distinct. Moreover, some stability physicochemical and growth kinetics, such as adsorption time and susceptibility test, also showed that both bacteriophages differed. On the other hand, the optimum temperature and pH of both phages were the same at 28–30 °C and pH 7. Further investigation showed that both ΦK2 and ΦK4 were able to reduce the overgrowth of A. tumefaciens post transformation. Moreover, applying the cocktail (mixture of ΦK2 and ΦK4) with antibiotic application eradicated A. tumefaciens (0% overgrowth percentage). This result indicates that the application of bacteriophage could be used as an alternative way to eradicate the overgrowth of A. tumefaciens subsequent to transformation.

The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm ( Elaeis guineensis ) is one of the most important palms. However, the genome sequences of palms available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm Dura . The genome of 1.7 Gb was assembled by integrating long reads with ∼ 150 × genome coverage. The assembled genome covered 94.5% of the estimated genome size, within which 91.6% were assigned into 16 pseudochromosomes and 73.7% were repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons (LTRs) retrotransposons, following the last whole-genome duplication (WGD), likely explains genome size variation across palms. Convergent evolution of fruit colors tends to eliminate the roles of the virescens gene in controlling accumulation of anthocyanins in exocarp of ripe fruit of palms. Recent duplications of high tandemly repeated pathogenesis-related proteins (PRs) from the same tandem arrays played an important role in defense responses to Ganoderma . Whole genome re-sequencing of both ancestral African and introduced oil palms in Southeast Asia revealed that genes under putative selection were notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

Oil palm clonal propagation seeds (ramets) often give rise to somaclonal variation, which is a cause of hypomethylation in the Karma sequence as a part of the Eg DEF1 gene that can lead to abnormalities in flowers and “mantled” fruits, causing a decrease in oil production. The loss of beneficial endophytic bacteria due to aseptic conditions in tissue culture is one of the causes of hypomethylation. This study analyzed the effect of inoculating beneficial endophyte bacteria in hypomethylated oil palm ramets and their impact on plant growth through measurement of the methylation level in the Karma sequence using methylation-specific restriction enzymes and quantitative PCR analysis. Our findings via inoculation of endophyte bacteria indicated that the most significant alteration in methylation occurred in ramets treated with the mixed isolates (3AK, PsJN, R6, GS 4.4) (62.5%), and the 3AK isolate showed a 44.4% increase in hypomethylation to normal methylation. In addition, all inoculation treatments showed more significant growth of oil palm ramets than the control group. These results demonstrate that inoculating appropriate beneficial microbes could significantly enhance the hypomethylated Karma sequence, leading to normal methylated oil palm ramets and promoting their growth.