de novo Construction of a "Gene Space" for a Diploid Plant Genome Rich in Repetitive Sequences

An iterative protocol of de novo assembly has been developed to rebuild targeted genome portions with limited computing resources. The assembly is guided by a partial reference sequence which will be completed in an iterative way by the addition of NGS data. Then the complexity of the large genomes and the repeated sequences (which are actually very demanding upon computing resources) can be solved. This protocol has been tested on Pea (Pisum sativum) and the final assembled gene sequences were validated by the genotyping results on the first pea Illumina Infinium 15K SNP BeadChip.