In collaboration with Dr. Tim Langdon at Aberystwyth University we are sequencing the A. atlantica AA-genome and the A. eriantha CC-genome diploids using Pacific Biosciences sequencing. This is in addition to the pop-seq based work done at Aberystwyth University. These data will aid in the anchoring of the hexaploid (AADDCC) A. sativa genome.
We will generate optical maps for six hexaploid Avena genomes, as well as two AA-diploid genomes, two CC-diploid genomes, and a putative DD-diploid genome using BioNano Genomics technology. These high-density physical maps aid in the assembly of the Avena diploid C-genomes as well as the hexaploid Avena genome.
We are using a Pacific Biosciences approach to achieve a nearly 40x sequencing depth in hexaploid oats with funding from both NSF and PepsiCo. This is in addition to 70x Illumina sequence with varying library sizes. The assembled genome will be anchored by a high density linkage map in collaboration with KeyGene. Diploid resources from the AA-genome and CC-genome will be combined with the PacBio assembly to aid in ordering and orienting contigs.