Towards A First Draft Of The Octoploid Strawberry Genome Sequence

Assembly of sequences from genomes of polyploid species is challenging due to the abundant presence of highly homologous regions and their intrinsic complexity. Strawberry is an octoploid fruit of economical importance. It has been estimated to have a genome size of 600 Mb, though its sequence remains to be determined yet. Generation of a consensus sequence of the genome is capital for the development of new markers and their association to relevant qualitative trait loci (QTL). The goal of this study was to generate a consensus sequence of the octoploid strawberry (Fragaria x ananassa) genome. A highly homozygous individual from an F2 population was selected and two pair-end libraries with insert sizes of 490 and 520 nucleotides were constructed and sequenced in 8 lanes of an Illumina GenomeAnalyzer II. Several trials were conducted to determine the best combination of assembly software and kmer size. The assemblers tested include Abyss_v1.2.7, Abyss_v1.3.0, Velvet_v1.0.18, SOAPdenovo_v1.05. After trimming reads with a quality score below 30, approximately 557 million reads with an average length of 129 nucleotides (71.8 Gb of raw sequences) were used to assemble.  To test the goodness of the assemblies, 49,132 ESTs of all the Fragaria genus and 13,289 ESTs specific for F. x ananassa were blasted against each assembly, obtaining a high rate (>93%) of positive hits. Homology studies with F. vesca, one of the diploid ancestors, are being conducted. We are currently developing a first draft of F. x ananassa genome sequence.