Re-sequencing and hybrid assembly strategy of two nematode resistant Beta vulgaris translocation lines

Sugar beet (Beta vulgaris L.) is a host of the beet cyst nematode (BCN) Heterodera schachtii Schmidt, which causes high yield losses. BCN resistance genes had been identified in the wild relative Patellifolia procumbens. We are cloning a new resistance gene Hs2 which is located on a wild beet translocation attached at the end of chromosome 9 of sugar beet. Two resistant translocation lines were sequenced by using whole genome shotgun sequencing on an Illumina HiSeq 2000 with ≥ 110 –fold coverage. Their translocations are expected to be ≥ 1.5 MB in size (0.2 % of the beet genome) with a ~ 700 kb region they share in common. A hybrid assembly, combining the two resistant translocation lines short reads, BAC sequences of a physical map of the translocation line, and draft reference sequences of a sugar beet and a wild beet genome, is presented to identify the wild beet translocation and candidate resistance genes located thereon.