- CLC bio and UK Scientists Assemble Ash Tree Genome
Product News: CLC bio and UK Scientists Assemble Ash Tree GenomeThis week, collaborating researchers at CLC bio and Queen Mary University of London have released a genome assembly of the European ash tree, Fraxinus excelsior, as part of the British Ash Tree Genome project.
The release comes as populations of ash trees across Europe have been devastated by the ash dieback fungus, which spread to Denmark and to the UK in 2003 and 2012, respectively. Fortunately, a small number of ash trees appear to have low susceptibility to the disease. It is hoped that by releasing the genome sequence publicly, scientists around the world can use it to determine the genetic or epigenetic causes of the variation in susceptibility.
Senior Lecturer at QMUL, Dr. Richard Buggs, states, "We were very fortunate to sequence a tree that was the progeny of a self-pollination, produced ten years ago by David Boshier from the University of Oxford. The tree is now an invaluable resource, because its low heterozygosity enables a higher quality genome assembly than would have been possible in a more heterozygous tree."
PhD student at CLC bio, Lizzy Sollars, continues, "Using CLC bio's de novo assembler, along with the open-source scaffolding tool SSPACE, we produced our best de novo assembly so far. The current version consists of 142,000 scaffolds, with an N50 of almost 69,000, and hits 97% of 248 conserved eukaryotic genes. Although several plant species have now been sequenced, there is still no closely related reference sequence for the ash. We hope that the new reference genome can lay the foundations of research into the ash dieback disease, as well as enable other forestry researchers to use genomic approaches in their studies."
The British Ash Tree Genome project, funded by an urgency grant from NERC, started in January 2013. Samples were taken from the selfed tree, owned by The Earth Trust, Oxfordshire, UK, and DNA was extracted from the sample by QMUL PhD student Jasmin Zohren. Samples were then sent to Eurofins, Germany, for sequencing on Illumina and Roche 454 platforms, and the resulting data was assembled into contigs using the CLC bio de novo assembler and open-source software.