Pacific Biosciences of California Inc (PACB)

[Paulieme]

Published online 22 May 2017 The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution 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 drought1. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives2, 3, including numerous extremophile species4. 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 sequences5 and required single-molecule real-time 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 clade6 and a sunflower-specific whole-genome duplication around 29 million years ago7. 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 needs8, 9. As the only major crop domesticated in North America, with its sun-like 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 introgression10. In plant science, the sunflower is a model for understanding solar tracking11 and inflorescence development12. 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 decade13.

To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 single-molecule 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. 1 and Supplementary Note 1.1–1.6). This compares favourably to an assembly of another sunflower genotype (HA412-HO; Supplementary Note 1.7), based on second-generation sequencing data, in which 2 Gb of sequence are placed in 816,854 contigs and 31,392 scaffolds. The sunflower genome encodes 52,232 inferred protein-coding genes and 5,803 spliced long non-coding RNAs (lncRNAs, Supplementary Note 2.1). To build the first small-RNA-mediated regulatory network for the sunflower, we identified 123 microRNA (miRNA) genes that we classified into 43 families (Supplementary Data 1), including 16 novel families. Sixty-three lncRNAs and 1,020 mRNAs are predicted to be miRNA targets, including 71 loci that probably produce secondary phased short-interfering RNAs (siRNAs, Supplementary Note 2.2). (More @ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22380.html