The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 . Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences 5 and required single-molecule realtime sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade 6 and a sunflowerspecific whole-genome duplication around 29 million years ago 7 . An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs 8,9 .As the only major crop domesticated in North America, with its sunlike inflorescence that inspired artists, the sunflower is both a social icon and a major research focus for scientists. In evolutionary biology, the Helianthus genus is a long-time model for hybrid speciation and adaptive introgression 10 . In plant science, the sunflower is a model for understanding solar tracking 11 and inflorescence development 12 .Despite this large interest, assembling its genome has been extremely difficult as it mainly consists of long and highly similar repeats. This complexity has challenged leading-edge assembly protocols for close to a decade 13 .To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 singlemolecule real-time (SMRT) cells on the PacBio RS II platform. Production of 32 million very long reads allowed us to generate a genome assembly that captures 3 gigabases (Gb) (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content (Fig.

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• Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses.• Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family.• Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

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SUMMARYAside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size ($3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.