The Reference Genome of the Common Sunflower Helianthus annuus Sequenced by Single Molecule, Real-Time Sequencing

The genome of Helianthus annuus has proven very challenging to assemble due to its very large size (a diploid genome of 3.6Gb spanning 17 linkage groups) and complexity (over 81% of transposable elements). Here we report the first high-quality reference for the sunflower genome, assembled with single-molecule-real-time sequencing technology, together with extensive transcriptomic data from vegetative and floral organs. Genome analyses enabled reconstruction of the evolutionary history of the Asterids. An integrative approach combining information from the reference sequence with quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism. We investigated whether there is a link between the genomic architecture of flowering time and the latest whole genome duplication. We identified organ-specific transcription factors and long non-coding RNAs, and compared their distributions across organs. We also analyzed the repertoire of conserved and novel miRNA and their targets to find evidence of functional diversification. This genome represents a cornerstone of future research programs exploiting genetic diversity to improve biotic and abiotic stress resistance and oil production while considering agricultural constraints and human nutrition needs.