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Freshwater bacteria’s vulnerability to climate change due to limited adaptability

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Studies Study First Submitted Date 2019-03-27 Study First Posted Date 2019-03-29 Last Update Posted Date 2023-04-19 Start Month Year April...

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A study on the whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, using a combination of short- and long-read sequencing techniques

Basal stem rot disease, caused by the fungus Ganoderma boninense, is a major threat to the oil palm industry worldwide. This devastating disease can lead to significant yield losses and even the death of infected palm trees. In order to better understand the genetic makeup of this pathogen and develop effective control strategies, researchers have conducted a study on the whole-genome sequencing of Ganoderma boninense using a combination of short- and long-read sequencing techniques.

Short-read sequencing techniques, such as Illumina sequencing, are commonly used for genome sequencing due to their high accuracy and cost-effectiveness. However, these techniques are limited in their ability to accurately assemble repetitive regions of the genome, which can be common in fungal genomes. Long-read sequencing techniques, such as PacBio and Oxford Nanopore sequencing, are able to generate much longer reads, making them ideal for resolving complex genomic regions.

In the study, researchers first used Illumina sequencing to generate short reads of the Ganoderma boninense genome. These short reads were then assembled into contigs using bioinformatics tools. However, due to the repetitive nature of the fungal genome, the assembly was fragmented and incomplete. To overcome this limitation, researchers turned to long-read sequencing techniques.

Using PacBio and Oxford Nanopore sequencing, researchers were able to generate long reads that spanned repetitive regions of the Ganoderma boninense genome. These long reads were then used to scaffold the short-read assembly, resulting in a more complete and accurate genome assembly. By combining short- and long-read sequencing techniques, researchers were able to overcome the limitations of each method and obtain a high-quality genome assembly of Ganoderma boninense.

Analysis of the assembled genome revealed several interesting findings. Researchers identified genes involved in pathogenicity, such as those encoding enzymes that degrade plant cell walls. They also found genes associated with stress response and virulence, which may play a role in the ability of Ganoderma boninense to infect oil palm trees. Additionally, researchers identified potential targets for fungicide development that could help control basal stem rot disease in oil palm plantations.

Overall, this study highlights the power of combining short- and long-read sequencing techniques for whole-genome sequencing of complex fungal pathogens like Ganoderma boninense. By obtaining a high-quality genome assembly, researchers can gain valuable insights into the genetic basis of pathogenicity and develop targeted strategies for disease control. This research represents an important step towards protecting the oil palm industry from the devastating effects of basal stem rot disease.