Oat genome browser

SNIC 2018/6-59


SNAC Small Compute

Principal Investigator:

Nick Sirijovski


Lunds universitet

Start Date:


End Date:


Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)



Relative to other cereals such as rice, barley and wheat, very little is know about the genetics of oat. Cultivated oat (Avena sativa) is a hexaploid comprised of three diploid genomes (AACCDD). It has a 1C genome of 21 chromosomes with a total size estimated to 13Gb. The large genome size and polyploidy has meant that deciphering the genetics of cultivated oat has lagged behind other cereals. Recently, oat has received much attention due to well documented health benefits of consuming this ‘super food’, which in turn has lead to increased production of oat-based novel foods and ingredients e.g. dairy alternatives, beta-glucan extracts, and even meat substitutes. With the fast paced development of next generation sequencing technologies, it has now become possible and affordable to undertake genome sequencing of hexaploid oat using short read technology. As a part of the newly inaugurated ScanOats research center in Lund, we have sequenced the hexaploid oat genome to 260X redundancy, and the raw data will be assembled into mega-scaffolds and then psuedochromosomes. The assembled genome needs to be visualised in a user friendly manner, which will make complex characterisation/annotations more easily visualisable and subsequent human-curation possible. We have now recruited a bioinformatician that will work on developing a genome browser.