Wednesday, May 23, 2012

Rutgers Scientists Sequence
the EFB Genome

EFB presents as cankers on hazelnut branches.
Severe cankering is followed by branch dieback
and death of most European (Corylus avellana)
hazelnut plants.
One of the major accomplishments of the Hybrid Hazelnut Consortium’s work to date is sequencing the genome of Anisogramma anomala, the filamentous fungus that causes eastern filbert blight (EFB). EFB is one of the key factors limiting commercial hazelnut production.

Understanding the genetic sequence of A. anomala will allow us to determine which plants contain useful genetic resistance, whether various fungal strains affect plants differently and whether environment plays a part in resistance and/or disease progression. This will help us determine which parent plants to breed, how likely EFB is to change over time and how that would affect host resistance.

Dr. Brad Hillman and Dr. Guohong Cai from Rutgers successfully sequenced the genome after isolating the fungus DNA from a two-month-old sample, and analyzed it using an Illumina sequencer. A. anomala is particularly difficult to work with because it doesn’t grow well outside of infected plants.

The massive amount of sequence data was assembled using a short-read method called SOAPdenovo, and the assembled sequence was analyzed to develop simple sequence repeat (SSR, also called microsatellite) gene markers for the fungus. The A. anomala genome was found to be surprisingly large, and 85% of it was “repetitive” DNA typical of transposable genetic elements.

Next steps in the research are to sequence the genome in greater depth to obtain a better genome assembly as a platform for future work. We also will complete “draft” sequences of additional strains of A. anomala from different populations around the U.S. and will combine this information with experimental screening of microsatellite loci.

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