NGS Expert Blog

To conduct genome sequencing and analysis of Ash (Fraxinus excelsior), researchers in the UK received £2.4 million ($3.6 million / €2.8 million). The major aim of this project is to increase the understanding of the wide spreading fungal tree disease, which is widespread in northern Europe and has already been found at more than 300 sites across the UK (see http://www.forestry.gov.uk/chalara). Those fungi attack ash tress but some tress resists those attacks.

For this reason a lot of samples of the ash dieback fungus will be sequenced and – funded by an urgency grant from the Natural Environment Research Council – the complete genome sequence of Ash is aimed to be available by August.

Sequencing of the approximately 900 Mb plant genome will be performed applying the latest hybrid de novo sequencing strategy, recently proven to deliver excellent scaffolding and assembly results. This new golden standard in de novo sequencing employs a combination of Roche/454 FLX++ long read technology (software version 2.8 with read lengths up to 1,100 bp) and Illumina HiSeq 2000/2500 high throughput sequencing with several ultra-accurate long jumping distance libraries (LJD of 3kb, 8kb, 20kb and 40kb), supplemented by sequencing of Illumina shotgun libraries with different fragment sizes.

With the sequenced ash tree genome the researchers hope to hold clues to how some of the trees (2% are able to defend the disease) are able to resist attack, and knowledge about the genetic differences between resistant and non-resistant trees. This knowledge could be used to develop trees that can’t be infected.

Project leader, Dr. Richard Buggs from Queen Mary’s School of Biological and Chemical Sciences: “Sequencing the ash genome is a foundational step towards discovering the genetic basis of resistance to ash dieback – the future of ash trees in Britain may depend on this”.

Read more about that exciting project at GenomeWeb about the general project and at Eurofins MWG Operon about the genome sequencing.

Recently, I just discovered a study from Harvard Researchers that uses genome sequencing to investigate the genetic basis for antibiotic resistance in E. coli.

The authors used continuous culture systems that are slowly increasing the concentrations of three different antibiotics, separately. They observed that the resistance increased significantly over a period of approx. 20 days. And by sequencing the genomes of the resistant populations on GAIIx, they found in total 47 SNPs contributing to the resistances.

In trimethoprim-resistant bacteria most of the mutations occurred in the E. coli gene encoding the target enzyme that is normally inhibited by the antibiotic compound. In bacterial populations resistant to the antibiotics chloramphenicol and doxycycline, in contrast, the mutations accumulate in a broad spectrum of genes involved in translation, transcription and protein transport. This is consistent with chloramphenicol and doxycycline being inhibitors of protein synthesis.

This is of high importance since the prevalence of resistant bacteria is continuously increasing. As a result, in more and more cases, the standard antibiotics are no longer effective to treat seriously ill patients. New findings in antibacterial research are crucial to stop this progression as soon as possible.