Recipe for a Successful Shotgun Assembly in Wheat

For many years, a wheat genome assembly using only short reads produced from a whole genome sample was considered impossible due to the genome size, polyploidity and a high level of repetitive DNA. The successful shotgun assembly of the tetraploid wild emmer wheat using the DeNovoMAGIC software has proven differently, gaining a N50 of 7 Million bp, N90 of 1.1 M, and unfilled gaps of 1.6%. Since then, 6 more diploid, tetraploid and hexaploid wheat/wheat relative genomes have been fully assembled with similar results -- including the Chinese-spring variety. However, the use of different Illumina chemistry, machines and diverged coverage of sequencing in the 7 projects allowed for optimization of the software parameters used in each case. We will present the results and comparisons, towards the most recommended protocol for sequencing and assembly of a wheat genome.

Collaborators: Omer Barad, Kobi Baruch, Gil Ben-Zvi, Guy Kol (NRGene Ltd, Ness Ziona, Israel)