Reference Genome of Sunflower, line HA412: Version 0.9

Here we present a reference genome of the domestic sunflower, Helianthus annuus. The sunflower genome contains ~3.6 billion base pairs. Retrotransposons make up ~80% of the genome, most of which derive from a recent expansion of the Ty3/Gypsytype. Pervasive high-copy repeats make genome reconstruction difficult, as they form tight knots in an assembly graph constructed from short NGS reads. Additionally, several paleopolyploidy events in the sunflower’s lineage have contributed to redundancy of the gene space. Despite challenges posed by the sunflower’s genome biology, we now present the first linearized golden path of the sunflower’s seventeen chromosomes. These include reference sequence assembled from Illumina and 454 data that has been ordered and oriented using three high quality maps: (1) an ultra-high density sequence-based genetic map, (2) an FPC physical map, and (3) a 10,000-locus genetic map based on multiple crosses. The sunflower’s NORs and telomeric repeats have been anchored to the path. A high quality reference sequence for sunflower is expected to facilitate ecological and evolutionary genomic studies in sunflower, as well as sunflower breeding and improvement.