Progress towards a reference genome for sunflower
Résumé
The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower (Helianthus annuus), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5-6 kb across the genome. Thus far, our physical map covers similar to 85% of the sunflower genome, and we have generated similar to 80x genome coverage with Solexa reads and 15.5x with 454 reads. Preliminary analyses indicated that similar to 78% of the sunflower genome consists of repetitive sequences. Nonetheless, similar to 76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.